From neena.susaneappen at mail.utoronto.ca Wed Apr 1 02:05:57 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Wed, 01 Apr 2020 00:05:57 -0000 Subject: [gmx-users] Effect of atomic charge on bonding parameters Message-ID: Hello gromacs users, Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? ; name bond_type mass charge ptype sigma epsilon opls_237 N 7 14.00670 -0.760 A 3.25000e-01 7.11280e-01 opls_238 N 7 14.00670 -0.500 A 3.25000e-01 7.11280e-01 (Taken from ffnonbonded.itp file) Thank you, Neena From jalemkul at vt.edu Wed Apr 1 02:30:32 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 00:30:32 -0000 Subject: [gmx-users] How to reduce the penalty of small molecule from CGenFF In-Reply-To: References: <00a401d602c5$c6ff6ed0$54fe4c70$@gmail.com> Message-ID: <60ecd8a6-73bf-d1a6-0238-ad172dbc48a9@vt.edu> On 3/29/20 1:29 AM, Rolly Ng wrote: > Hello Justin, > Thank you and yes. I went to the paper and it shows the steps for > optimization. > However, I have the following problems as I tried to follow the tutorial on > CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor > > (1) what are these parameters in water_constr.inp? what values should I use > in my case? > if @stage eq 4 echo ######## USING MP2 GEOMETRY!!! ######## > echo QM dipole (Debye) > echo mp2/6-31g*: X= -3.1938 Y= 1.2595 Z= 0.0011 Tot= > 3.4332 > echo hf/6-31g*: X= -3.4411 Y= 1.3570 Z= 0.0012 Tot= > 3.6990 > > (2) How can I get the correct value for the IC table for surface of > interest? I suppose H2O molecules are placed one at a time to the C and N > atoms of my molecule but where to place the dummy? > generate dum first none last none setup warn noangle nodihedral > join @residue dum renumber > !preparation of IC table for surface of interest > ic edit > dihe 1 N2 1 C1 1 H1 3 dum 0.0 > dihe 1 C1 1 H1 3 dum 4 dum 0.0 > dihe 4 dum 3 dum 1 H1 2 oh2 180.0 > end > ic fill preserve > ic edit > dihe 3 dum 1 H1 2 oh2 2 h1 90.0 > dihe 3 dum 1 H1 2 oh2 2 h2 -90.0 > bond 1 H1 3 dum 1. > bond 3 dum 4 dum 1. > bond 1 H1 2 oh2 @d !varied > bond 2 oh2 2 h1 0.9572 > bond 2 oh2 2 h2 0.9572 > angl 1 C1 1 H1 3 dum 90.0 > angl 1 H1 3 dum 4 dum 90.0 > angl 3 dum 1 H1 2 oh2 90.0 > angl 1 H1 2 oh2 2 h1 127.74 > angl 1 H1 2 oh2 2 h2 127.74 > end > > How can I know the bond, angle and dihedral without a GUI show these > parameters? > > Thanks for your patient. If you have questions about CHARMM, you should use the CHARMM forum. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 1 02:30:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 00:30:47 -0000 Subject: [gmx-users] Different force constants for different umbrella windows? In-Reply-To: <4cf4aa27-fd9b-dc12-d56f-9e8de0b1d236@tu-braunschweig.de> References: <4cf4aa27-fd9b-dc12-d56f-9e8de0b1d236@tu-braunschweig.de> Message-ID: On 3/31/20 2:07 AM, Andreas Mecklenfeld wrote: > Dear GROMACS users, > > I've a question regarding umbrella sampling and its evaluation with > gmx wham. Is it possible to use different force constants for > different umbrella windows? > Yes. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 1 02:32:31 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 00:32:31 -0000 Subject: [gmx-users] 1-4 LJ interactions In-Reply-To: References: Message-ID: <87945787-f94f-9f54-d96e-81652557dc41@vt.edu> On 3/31/20 12:59 PM, Andrey Gurtovenko wrote: > Dear All, > > Recently I realized that I don't fully understand what should be done > in Gromacs to account for 1-4 LJ interactions. > > According to the manual: > > "gen-pairs is for pair generation. The default is ?no?, i.e. get 1-4 > parameters from the pairtypes list. When parameters are not present in > the list, stop with a fatal error. Setting ?yes? generates 1-4 > parameters that are not present in the pair list from normal > Lennard-Jones parameters using fudgeLJ." > > http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html > > Therefore, I had an impression that to account for 1-4 interactions in > some generic force-field, it is enough to > set gen-pairs=yes. > > However, it turns out that this is not the case: > in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the > [pairs] section of the topology file of a system. > Otherwise 1-4 interactions are NOT accounted for. > > Can someone comment on this? > If I am right, maybe it is worth to clarify this point in the manual? The language in the manual is correct, either pair *parameters* are generated, or they are not. The topology is different from the parameters; if *interactions* are not there, then nothing is done. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 1 02:33:13 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 00:33:13 -0000 Subject: [gmx-users] Effect of atomic charge on bonding parameters In-Reply-To: References: Message-ID: On 3/31/20 8:05 PM, Neena Susan Eappen wrote: > Hello gromacs users, > > Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? > > ; name bond_type mass charge ptype sigma epsilon > opls_237 N 7 14.00670 -0.760 A 3.25000e-01 7.11280e-01 > opls_238 N 7 14.00670 -0.500 A 3.25000e-01 7.11280e-01 > > (Taken from ffnonbonded.itp file) Charges in ffnonbonded.itp are never used for anything and have no meaning. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From 272699575 at qq.com Wed Apr 1 03:10:38 2020 From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=) Date: Wed, 01 Apr 2020 01:10:38 -0000 Subject: [gmx-users] PCA analysis with different atoms in -s and -f Message-ID: I am trying to compare trajectories from different MD simulations, including different pH and different mutants. The initial PDB (i.e. 0.pdb) is the same, but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to protonation states and mutations. Those different PDBs were used individually for the MD. To obtain the eigen vectors, should I use the 0.pdb as the reference structure? # gmx covar -s 0.pdb -f 1.xtc -v 1.trr (use 0.pdb as reference, and calculate the eigen vectors from trajectories of 1.pdb) The first is to choose the least squares fit. Though the atoms in "Protein", "Protein-H" are different between 0.pdb and 1.xtc, they are same in "C-alpha", "Backbone" and "MainChain". However, when I choose "C-alpha" for the "least squares fit", I still got the warning: # WARNING: number of atoms in tpx (442) and trajectory (6622) do not match The calculation can still be done. So must I provide "1.pdb" as reference for "1.xtc", or is it still okay to use "-s 0.pdb"? Afterwards, I want to run # gmx anaeig -s 0.pdb -over overlap_1_2.xvg -v2 1.trr -v 2.trr to compare the similarity between Condition 1 and Condition 2. Is this correct? From weitali.md at gmail.com Wed Apr 1 05:29:30 2020 From: weitali.md at gmail.com (Wei-Ta Li) Date: Wed, 01 Apr 2020 03:29:30 -0000 Subject: [gmx-users] gmx rms divergence from the starting structure Message-ID: Hello everyone, I am trying to evaluate the convergence of protein structure during simulation to equilibrium state with "gmx rms", however I see strange (to me) results when RMSD goes from high in the beginning of simulation to low in the end of simulation - I would expect the trend to be opposite. System: Small 37 aa protein interacting with infinite slab of polymer surface. RMSD calculation: echo 4 4 | gmx rms -f trjconv_processed_results.trr -s beginning-structure-nowater.gro -o rms-backbone-start.xvg where: "trjconv_processed_results.trr" = post-simulation .trr with water removed and system made "whole" by successive trjconv runs with -pbc flags: -pbc whole --> -pbc nojump --> -pbc mol "beginning-structure-nowater.gro " = .gro without water used to setup .tpr of the simulation analyzed Problem: The RMSD trend goes from high to low, which is different to what I would expect - shouldn't it go from 0, up to some point and then hopefully equilibrate? The visual inspection of output simulation .pdb files shows very clear deviation from the shape of original structure as protein binds to the polymer surface. The RMSD calculations of 5 independent simulations of the same system (staring with different velocities/configurations) can be seen at the link below: https://www.dropbox.com/s/gmo61ah6txu6pty/Untitled1.png?dl=0 Question: Am I doing something wrong with "gmx rms" command? Or such output is expected and my expectations are wrong? Thanks in advance! Wei-Ta Li From weitali.md at gmail.com Wed Apr 1 06:03:46 2020 From: weitali.md at gmail.com (Wei-Ta Li) Date: Wed, 01 Apr 2020 04:03:46 -0000 Subject: [gmx-users] distance from geometrical center of protein to the surface Message-ID: Hello everyone, I have run simulation of protein interacting with the infinite slab of polymer surface and now I'm trying to calculate the distance between protein geometrical center and the closest atom of the surface. I have read through the manual but still don't understand how to measure such distance with gmx tools. I have come up with the command below: gmx distance -f protein-surface.trr -s protein-surface.tpr -n protein-surface.ndx -oav protein-surface_dist_oav.xvg -select 'cog of group "Protein" plus cog of group "Surface"' However, as far as I understand it calculates distance between geometric centers of protein and polymer slab, which is not what I am looking for. Is there a way to select "surface" NOT "cog" for the distance measurement between groups? Thanks in advance! Wei-Ta Li From sekekeretsu at gmail.com Wed Apr 1 06:05:10 2020 From: sekekeretsu at gmail.com (Seketoulie Keretsu) Date: Wed, 01 Apr 2020 04:05:10 -0000 Subject: [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out Message-ID: Dear Gromacs Community, I have come across this problem during NVT equilibration of an all atom protein-ligand MD simulation. Fatal error: 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. I basically used the nvt and npt equilibration approach given in tutorial by Justin. I have tried changing the equilibration process by gradually increasing temperature to 100K. However it still shows the same error. I have tried with other conformation of ligand as initial structure also but no improvement. Could you advise how to go about this? Thank you all. Sincerely, Seke From robert.cordina at strath.ac.uk Wed Apr 1 10:03:36 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Wed, 01 Apr 2020 08:03:36 -0000 Subject: [gmx-users] Optimising mdrun Message-ID: Hi, I'm trying to use GROMACS 2019.3 on two different machines, simulating the same system. The system is made up of 100 identical molecules, consisting of 61 united atoms each, in a non-aqueous system. I am however getting vastly different performance on the two machines, and I don't really understand why. The two machines' specs are as follows: Machine 1 (stand-alone machine) * 40-core CPU (Intel Xeon Gold 6148 2.4GHz, 3.7GHz, 20C, 10.4GT/s 2UPI, 27M Cache, HT (150W) DDR4-2666) - so 20 hyper-threaded cores to give a total of 40, although in my case only 20 cores are being used given the size of the system (see below) * 1 GPU (Nvidia Quadro RTX5000, 16GB, 4DP, VirtualLink (XX20T)) * Memory (512GB (8x64GB) 2666MHz DDR4 LRDIMM ECC) - although in reality only about 10 GB are used during my simulation * CUDA 10.10 When I simulate my system, I've found that the optimal mdrun settings are extremely simple mdrun -pin on This setting uses 1 MPI thread and 20 OpenMP threads, while the PP and PME tasks are carried out automatically on the GPU. With this I'm getting about 800 ns/day. Machine 2 (part of a HPC cluster - of which I can only use 1 node at a time - the below details are for a GPU node) * 16 core CPU (Intel Xeon E5-2600, 2.2 GHz) * 1 GPU (NVIDIA Tesla V100-PCIE-32GB) * Memory (64GB RAM) * CUDA 10.0 I've tried reading the GROMACS documentation, repeatedly, but I really can't understand much about how to go about choosing the right mdrun settings for this machine. I've tried several, and the best performance I could get is with mpirun -np 16 gmx_mpi mdrun -ntomp 1 Even then, I get a performance of about 45-50 ns/day, which is way lower than the 800 ns/day I get with the stand-alone machine. This setting is using 16 MPI process and using 2 OpenMP thrads per MPI process. Also, only PP tasks are being carried out on the GPU. The log states "Will do PME sum in reciprocal space for electrostatic interactions". Also I get a Warning "On rank 0: oversubscribing the available 16 logical CPU cores per node with 32 threads. This will cause considerable performance loss", with Note "Oversubscribing the CPU, will not pin threads". Does anyone have any guidance as to what I should try to get good performance on the GPU node of the cluster please? Any help will be really appreciated. Thanks, Robert From paul.bauer.q at gmail.com Wed Apr 1 14:06:31 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Wed, 01 Apr 2020 12:06:31 -0000 Subject: [gmx-users] GROMACS mailing-list will move to a forum Message-ID: <95f28686-d98a-fa05-e414-399a46fcc4a3@gmail.com> Hello gmx-users! We have been working behind the scenes the last few months on some changes to the organization of the GROMACS project, one of them is switching our gmx-users mailing list to a forum We are continuously re-thinking about how we can best engage with you and how people can get the best help when it comes to questions about using GROMACS for different scientific problems. While the user list has worked well for this in the past, it has also shown some deficiencies, mostly in finding already existing questions and the correct answers for them. To hopefully change this in the future we are now in the process of moving the existing list to use a Discourse forum instead that will be made public in the beginning of May. At the switching point, the current list will be read only (and the archive will be kept alive) so people will still be able to search it in the future for existing answers, but won't be able to post any new questions. The forum will still support the pure email based conversation if you prefer this kind of interaction, but it will also allow ranking of responses and make it easier to see which answers are coming from whom. You will have the opportunity to sign up for the forum when it goes live and I'll send a reminder for it when the time comes. Cheers Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From a.gurtovenko at googlemail.com Wed Apr 1 14:57:58 2020 From: a.gurtovenko at googlemail.com (Andrey Gurtovenko) Date: Wed, 01 Apr 2020 12:57:58 -0000 Subject: [gmx-users] 1-4 LJ interactions In-Reply-To: <87945787-f94f-9f54-d96e-81652557dc41@vt.edu> References: <87945787-f94f-9f54-d96e-81652557dc41@vt.edu> Message-ID: Dear Justin, thank you for the clarification. I think my confusion is in part due to the urea topology file used in the manual as an example, which does not contain the [pairs] section. with kind regards, Andrey On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul wrote: > > > > On 3/31/20 12:59 PM, Andrey Gurtovenko wrote: > > Dear All, > > > > Recently I realized that I don't fully understand what should be done > > in Gromacs to account for 1-4 LJ interactions. > > > > According to the manual: > > > > "gen-pairs is for pair generation. The default is ?no?, i.e. get 1-4 > > parameters from the pairtypes list. When parameters are not present in > > the list, stop with a fatal error. Setting ?yes? generates 1-4 > > parameters that are not present in the pair list from normal > > Lennard-Jones parameters using fudgeLJ." > > > > http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html > > > > Therefore, I had an impression that to account for 1-4 interactions in > > some generic force-field, it is enough to > > set gen-pairs=yes. > > > > However, it turns out that this is not the case: > > in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the > > [pairs] section of the topology file of a system. > > Otherwise 1-4 interactions are NOT accounted for. > > > > Can someone comment on this? > > If I am right, maybe it is worth to clarify this point in the manual? > > The language in the manual is correct, either pair *parameters* are > generated, or they are not. The topology is different from the > parameters; if *interactions* are not there, then nothing is done. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Wed Apr 1 15:00:25 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 13:00:25 -0000 Subject: [gmx-users] 1-4 LJ interactions In-Reply-To: References: <87945787-f94f-9f54-d96e-81652557dc41@vt.edu> Message-ID: <63ef7b23-ea68-1b24-6f43-ada752b35d34@vt.edu> On 4/1/20 8:57 AM, Andrey Gurtovenko wrote: > Dear Justin, > > thank you for the clarification. > > I think my confusion is in part due to the urea topology file > used in the manual as an example, which does not contain > the [pairs] section. Urea is probably a poor example because it actually doesn't have 1-4 interactions since the H atoms have no LJ. So any [pairs] that are defined will have all zero parameters. -Justin > with kind regards, > > Andrey > > On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul wrote: >> >> >> On 3/31/20 12:59 PM, Andrey Gurtovenko wrote: >>> Dear All, >>> >>> Recently I realized that I don't fully understand what should be done >>> in Gromacs to account for 1-4 LJ interactions. >>> >>> According to the manual: >>> >>> "gen-pairs is for pair generation. The default is ?no?, i.e. get 1-4 >>> parameters from the pairtypes list. When parameters are not present in >>> the list, stop with a fatal error. Setting ?yes? generates 1-4 >>> parameters that are not present in the pair list from normal >>> Lennard-Jones parameters using fudgeLJ." >>> >>> http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html >>> >>> Therefore, I had an impression that to account for 1-4 interactions in >>> some generic force-field, it is enough to >>> set gen-pairs=yes. >>> >>> However, it turns out that this is not the case: >>> in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the >>> [pairs] section of the topology file of a system. >>> Otherwise 1-4 interactions are NOT accounted for. >>> >>> Can someone comment on this? >>> If I am right, maybe it is worth to clarify this point in the manual? >> The language in the manual is correct, either pair *parameters* are >> generated, or they are not. The topology is different from the >> parameters; if *interactions* are not there, then nothing is done. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 1 15:01:33 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 01 Apr 2020 13:01:33 -0000 Subject: [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out In-Reply-To: References: Message-ID: <28279d3c-2e59-f7f3-898f-482a2b097c7a@vt.edu> On 4/1/20 12:04 AM, Seketoulie Keretsu wrote: > Dear Gromacs Community, > > I have come across this problem during NVT equilibration of an all atom > protein-ligand MD simulation. > > Fatal error: > 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off > out > of the domain decomposition cell of their charge group in dimension x. > This usually means that your system is not well equilibrated. > > I basically used the nvt and npt equilibration approach given in tutorial > by Justin. I have tried changing the equilibration process by gradually > increasing temperature to 100K. However it still shows the same error. I > have tried with other conformation of ligand as initial structure also but > no improvement. Could you advise how to go about this? http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system Protein-ligand complexes are addressed specifically there. Make sure your ligand topology is sufficiently accurate. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From benjamin.joseph at rwth-aachen.de Wed Apr 1 18:24:51 2020 From: benjamin.joseph at rwth-aachen.de (Joseph, Benjamin Philipp) Date: Wed, 01 Apr 2020 16:24:51 -0000 Subject: [gmx-users] Problem with REST2 Message-ID: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de> Dear members of the gromacs mailing list, I have problems setting up REST2 (replica exchange with solute tempering) calculations. The version of PLUMED with GROMACS I use is GROMACS/2018.3-plumed and the forcefield I am using is amber14sb_parmbsc1.ff. The error occurs when I try to set up the different topol.top files for the different replicas after having performed the minimisation, simulated annealing, NVT, NPT and 100 ns production MD. I get the following error message: ???????????????????? GROMACS: gmx grompp, version 2018.3 Executable: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi Data prefix: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu Command line: gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p topol1.top Ignoring obsolete mdp entry 'title' Setting the LD random seed to -1452668066 WARNING 1 [file topol1.top, line 95]: Too few parameters on line (source file /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, line 345) WARNING 2 [file topol1.top, line 97]: Too few parameters on line (source file /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, line 345) Generated 14878 of the 14878 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 14878 of the 14878 1-4 parameter combinations ERROR 1 [file topol1.top, line 1813]: Atomtype 3C_ not found _ ???????????????????? The script I use to generate the topol and tpr files is the following: ???????????????????? #!/bin/bash #16 replicas nrep=16 # "effective" temperature range tmin=287 tmax=400 # build geometric progression list=$( awk -v n=$nrep \ -v tmin=$tmin \ -v tmax=$tmax \ 'BEGIN{for(i=0;i topol$i.top # prepare tpr file # -maxwarn is often needed because box could be charged gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p topol$i.top done ???????????????????? I think that the problem might be that PLUMED does not support the force field I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have these issues (using the same script). Do you have any suggestions what could be the problem here? Thanks a lot! Best, Benjamin Joseph From gmxquestions at gmail.com Wed Apr 1 18:52:58 2020 From: gmxquestions at gmail.com (Gmx QA) Date: Wed, 01 Apr 2020 16:52:58 -0000 Subject: [gmx-users] Free energy of protonation Message-ID: Dear list, I am trying to calculate the free energy for protonating a single monomer of oleic acid with the martini forcefield. This in preparation for other work, and I wanted to start by reproducing what is already done. To do this, I have defined the following in my topology to describe the change in protonation state going from A (protonated) to state B (charged). The martini bead type needs to change as well in this process. [ atoms ] ; id typeA resnr residu atom cgnr chargeA massA typeB chargeB massB 1 P4 1 OAN COO 1 0 Qa -1 I also have this very simple mdp file for doing the transformation free_energy = yes init_lambda-state = 1 fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 And I am using fep-lambdas to describe the entire process. With this, I can run through grompp and mdrun with different values of init-lambda-state, but the output I get in each case is the same for each different simulation. I check this by gmx analyze -f md.xvg -ee And I always get the same value for the average. Is there something I am missing or not specifying properly? Thanks /PK From dburns at iastate.edu Wed Apr 1 19:09:41 2020 From: dburns at iastate.edu (Daniel Burns) Date: Wed, 01 Apr 2020 17:09:41 -0000 Subject: [gmx-users] Problem with REST2 In-Reply-To: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de> References: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de> Message-ID: I haven't had an error from the underscore myself but I haven't been using the Amber force field. Maybe you could try deleting the underscores on the input .top files since the plumed script has already scaled them. The atomtype might be recognized then. On Wed, Apr 1, 2020 at 11:25 AM Joseph, Benjamin Philipp < benjamin.joseph at rwth-aachen.de> wrote: > Dear members of the gromacs mailing list, > > I have problems setting up REST2 (replica exchange with solute tempering) > calculations. The version of PLUMED with GROMACS I use is > GROMACS/2018.3-plumed and the forcefield I am using is > amber14sb_parmbsc1.ff. The error occurs when I try to set up the different > topol.top files for the different replicas after having performed the > minimisation, simulated annealing, NVT, NPT and 100 ns production MD. I get > the following error message: > > ???????????????????? > GROMACS: gmx grompp, version 2018.3 > Executable: > /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi > Data prefix: > /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed > Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu > Command line: > gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p topol1.top > > Ignoring obsolete mdp entry 'title' > Setting the LD random seed to -1452668066 > > WARNING 1 [file topol1.top, line 95]: > Too few parameters on line (source file > > /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, > line 345) > > > WARNING 2 [file topol1.top, line 97]: > Too few parameters on line (source file > > /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, > line 345) > > Generated 14878 of the 14878 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 14878 of the 14878 1-4 parameter combinations > > ERROR 1 [file topol1.top, line 1813]: > Atomtype 3C_ not found > _ > ???????????????????? > The script I use to generate the topol and tpr files is the following: > ???????????????????? > #!/bin/bash > #16 replicas > nrep=16 > # "effective" temperature range > tmin=287 > tmax=400 > > # build geometric progression > list=$( > awk -v n=$nrep \ > -v tmin=$tmin \ > -v tmax=$tmax \ > 'BEGIN{for(i=0;i t=tmin*exp(i*log(tmax/tmin)/(n-1)); > printf(t); if(i } > }' > ) > > # clean directory > rm -fr \#* > rm -fr topol* > > for((i=0;i do > > # choose lambda as T[0]/T[i] > # remember that high temperature is equivalent to low lambda > lambda=$(echo $list | awk 'BEGIN{FS=",";}{print $1/$'$((i+1))';}') > # process topology > # (if you are curious, try "diff topol0.top topol1.top" to see the changes) > plumed partial_tempering $lambda < processed.top > topol$i.top > # prepare tpr file > # -maxwarn is often needed because box could be charged > gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p topol$i.top > done > ???????????????????? > I think that the problem might be that PLUMED does not support the force > field I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have > these issues (using the same script). Do you have any suggestions what > could be the problem here? Thanks a lot! > > Best, > Benjamin Joseph > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From benjamin.joseph at rwth-aachen.de Wed Apr 1 19:40:11 2020 From: benjamin.joseph at rwth-aachen.de (Joseph, Benjamin Philipp) Date: Wed, 01 Apr 2020 17:40:11 -0000 Subject: [gmx-users] Problem with REST2 In-Reply-To: References: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de>, Message-ID: <09B71752-5F5C-4146-AB9B-82466B714F18@rwth-aachen.de> Dear Daniel, I thought the underscores in the processed.gro file are necessary in order to mark the hot atoms and am not sure if all atoms are recognised as cold atoms when deleting the underscores. Best, Benjamin > Am 01.04.2020 um 19:10 schrieb Daniel Burns : > > ?I haven't had an error from the underscore myself but I haven't been using > the Amber force field. Maybe you could try deleting the underscores on the > input .top files since the plumed script has already scaled them. The > atomtype might be recognized then. > >> On Wed, Apr 1, 2020 at 11:25 AM Joseph, Benjamin Philipp < >> benjamin.joseph at rwth-aachen.de> wrote: >> >> Dear members of the gromacs mailing list, >> >> I have problems setting up REST2 (replica exchange with solute tempering) >> calculations. The version of PLUMED with GROMACS I use is >> GROMACS/2018.3-plumed and the forcefield I am using is >> amber14sb_parmbsc1.ff. The error occurs when I try to set up the different >> topol.top files for the different replicas after having performed the >> minimisation, simulated annealing, NVT, NPT and 100 ns production MD. I get >> the following error message: >> >> ???????????????????? >> GROMACS: gmx grompp, version 2018.3 >> Executable: >> /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi >> Data prefix: >> /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed >> Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu >> Command line: >> gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p topol1.top >> >> Ignoring obsolete mdp entry 'title' >> Setting the LD random seed to -1452668066 >> >> WARNING 1 [file topol1.top, line 95]: >> Too few parameters on line (source file >> >> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, >> line 345) >> >> >> WARNING 2 [file topol1.top, line 97]: >> Too few parameters on line (source file >> >> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b-plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, >> line 345) >> >> Generated 14878 of the 14878 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 0.5 >> Generated 14878 of the 14878 1-4 parameter combinations >> >> ERROR 1 [file topol1.top, line 1813]: >> Atomtype 3C_ not found >> _ >> ???????????????????? >> The script I use to generate the topol and tpr files is the following: >> ???????????????????? >> #!/bin/bash >> #16 replicas >> nrep=16 >> # "effective" temperature range >> tmin=287 >> tmax=400 >> >> # build geometric progression >> list=$( >> awk -v n=$nrep \ >> -v tmin=$tmin \ >> -v tmax=$tmax \ >> 'BEGIN{for(i=0;i> t=tmin*exp(i*log(tmax/tmin)/(n-1)); >> printf(t); if(i> } >> }' >> ) >> >> # clean directory >> rm -fr \#* >> rm -fr topol* >> >> for((i=0;i> do >> >> # choose lambda as T[0]/T[i] >> # remember that high temperature is equivalent to low lambda >> lambda=$(echo $list | awk 'BEGIN{FS=",";}{print $1/$'$((i+1))';}') >> # process topology >> # (if you are curious, try "diff topol0.top topol1.top" to see the changes) >> plumed partial_tempering $lambda < processed.top > topol$i.top >> # prepare tpr file >> # -maxwarn is often needed because box could be charged >> gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p topol$i.top >> done >> ???????????????????? >> I think that the problem might be that PLUMED does not support the force >> field I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have >> these issues (using the same script). Do you have any suggestions what >> could be the problem here? Thanks a lot! >> >> Best, >> Benjamin Joseph >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From dburns at iastate.edu Wed Apr 1 20:20:21 2020 From: dburns at iastate.edu (Daniel Burns) Date: Wed, 01 Apr 2020 18:20:21 -0000 Subject: [gmx-users] Problem with REST2 In-Reply-To: <09B71752-5F5C-4146-AB9B-82466B714F18@rwth-aachen.de> References: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de> <09B71752-5F5C-4146-AB9B-82466B714F18@rwth-aachen.de> Message-ID: Once you run your processed.top with selected hot atoms (via underscore) through the plumed script, the new .top files (denoted with numbers) should have scaled values replaced in the appropriate places. Compare the charges for instance on the selected atoms in your original processed.top and the plumed script output .top files. If they have been scaled appropriately, removing the underscore shouldn?t matter. Disclaimer - I?m new at this too! On Wednesday, April 1, 2020, Joseph, Benjamin Philipp < benjamin.joseph at rwth-aachen.de> wrote: > Dear Daniel, > > I thought the underscores in the processed.gro file are necessary in order > to mark the hot atoms and am not sure if all atoms are recognised as cold > atoms when deleting the underscores. > > Best, > > Benjamin > > > Am 01.04.2020 um 19:10 schrieb Daniel Burns : > > > > ?I haven't had an error from the underscore myself but I haven't been > using > > the Amber force field. Maybe you could try deleting the underscores on > the > > input .top files since the plumed script has already scaled them. The > > atomtype might be recognized then. > > > >> On Wed, Apr 1, 2020 at 11:25 AM Joseph, Benjamin Philipp < > >> benjamin.joseph at rwth-aachen.de> wrote: > >> > >> Dear members of the gromacs mailing list, > >> > >> I have problems setting up REST2 (replica exchange with solute > tempering) > >> calculations. The version of PLUMED with GROMACS I use is > >> GROMACS/2018.3-plumed and the forcefield I am using is > >> amber14sb_parmbsc1.ff. The error occurs when I try to set up the > different > >> topol.top files for the different replicas after having performed the > >> minimisation, simulated annealing, NVT, NPT and 100 ns production MD. I > get > >> the following error message: > >> > >> ???????????????????? > >> GROMACS: gmx grompp, version 2018.3 > >> Executable: > >> /usr/local/software/jureca/Stages/Devel-2018b/software/ > GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi > >> Data prefix: > >> /usr/local/software/jureca/Stages/Devel-2018b/software/ > GROMACS/2018.3-intel-para-2018b-plumed > >> Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu > >> Command line: > >> gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p > topol1.top > >> > >> Ignoring obsolete mdp entry 'title' > >> Setting the LD random seed to -1452668066 > >> > >> WARNING 1 [file topol1.top, line 95]: > >> Too few parameters on line (source file > >> > >> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b- > plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, > >> line 345) > >> > >> > >> WARNING 2 [file topol1.top, line 97]: > >> Too few parameters on line (source file > >> > >> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b- > plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, > >> line 345) > >> > >> Generated 14878 of the 14878 non-bonded parameter combinations > >> Generating 1-4 interactions: fudge = 0.5 > >> Generated 14878 of the 14878 1-4 parameter combinations > >> > >> ERROR 1 [file topol1.top, line 1813]: > >> Atomtype 3C_ not found > >> _ > >> ???????????????????? > >> The script I use to generate the topol and tpr files is the following: > >> ???????????????????? > >> #!/bin/bash > >> #16 replicas > >> nrep=16 > >> # "effective" temperature range > >> tmin=287 > >> tmax=400 > >> > >> # build geometric progression > >> list=$( > >> awk -v n=$nrep \ > >> -v tmin=$tmin \ > >> -v tmax=$tmax \ > >> 'BEGIN{for(i=0;i >> t=tmin*exp(i*log(tmax/tmin)/(n-1)); > >> printf(t); if(i >> } > >> }' > >> ) > >> > >> # clean directory > >> rm -fr \#* > >> rm -fr topol* > >> > >> for((i=0;i >> do > >> > >> # choose lambda as T[0]/T[i] > >> # remember that high temperature is equivalent to low lambda > >> lambda=$(echo $list | awk 'BEGIN{FS=",";}{print $1/$'$((i+1))';}') > >> # process topology > >> # (if you are curious, try "diff topol0.top topol1.top" to see the > changes) > >> plumed partial_tempering $lambda < processed.top > topol$i.top > >> # prepare tpr file > >> # -maxwarn is often needed because box could be charged > >> gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p > topol$i.top > >> done > >> ???????????????????? > >> I think that the problem might be that PLUMED does not support the force > >> field I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have > >> these issues (using the same script). Do you have any suggestions what > >> could be the problem here? Thanks a lot! > >> > >> Best, > >> Benjamin Joseph > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From benjamin.joseph at rwth-aachen.de Wed Apr 1 20:22:43 2020 From: benjamin.joseph at rwth-aachen.de (Joseph, Benjamin Philipp) Date: Wed, 01 Apr 2020 18:22:43 -0000 Subject: [gmx-users] Problem with REST2 In-Reply-To: References: <79ea230f81ac41e6a09359cf728e1d0e@rwth-aachen.de> <09B71752-5F5C-4146-AB9B-82466B714F18@rwth-aachen.de>, Message-ID: <4905342C-E8A5-4C09-86A5-5535DCCF89EB@rwth-aachen.de> Okay, now I understand what you mean. Then I should try deleting the underscores in the created top files. This really startled me though, because I never had this problem in the past. Thanks for your help! Best, Benjamin > Am 01.04.2020 um 20:20 schrieb Daniel Burns : > > ?Once you run your processed.top with selected hot atoms (via underscore) > through the plumed script, the new .top files (denoted with numbers) should > have scaled values replaced in the appropriate places. Compare the charges > for instance on the selected atoms in your original processed.top and the > plumed script output .top files. If they have been scaled appropriately, > removing the underscore shouldn?t matter. Disclaimer - I?m new at this too! > >> On Wednesday, April 1, 2020, Joseph, Benjamin Philipp < >> benjamin.joseph at rwth-aachen.de> wrote: >> >> Dear Daniel, >> >> I thought the underscores in the processed.gro file are necessary in order >> to mark the hot atoms and am not sure if all atoms are recognised as cold >> atoms when deleting the underscores. >> >> Best, >> >> Benjamin >> >>>> Am 01.04.2020 um 19:10 schrieb Daniel Burns : >>> >>> ?I haven't had an error from the underscore myself but I haven't been >> using >>> the Amber force field. Maybe you could try deleting the underscores on >> the >>> input .top files since the plumed script has already scaled them. The >>> atomtype might be recognized then. >>> >>>> On Wed, Apr 1, 2020 at 11:25 AM Joseph, Benjamin Philipp < >>>> benjamin.joseph at rwth-aachen.de> wrote: >>>> >>>> Dear members of the gromacs mailing list, >>>> >>>> I have problems setting up REST2 (replica exchange with solute >> tempering) >>>> calculations. The version of PLUMED with GROMACS I use is >>>> GROMACS/2018.3-plumed and the forcefield I am using is >>>> amber14sb_parmbsc1.ff. The error occurs when I try to set up the >> different >>>> topol.top files for the different replicas after having performed the >>>> minimisation, simulated annealing, NVT, NPT and 100 ns production MD. I >> get >>>> the following error message: >>>> >>>> ???????????????????? >>>> GROMACS: gmx grompp, version 2018.3 >>>> Executable: >>>> /usr/local/software/jureca/Stages/Devel-2018b/software/ >> GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi >>>> Data prefix: >>>> /usr/local/software/jureca/Stages/Devel-2018b/software/ >> GROMACS/2018.3-intel-para-2018b-plumed >>>> Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu >>>> Command line: >>>> gmx_mpi grompp -maxwarn 2 -o topol1.tpr -c sa.gro -f md.mdp -p >> topol1.top >>>> >>>> Ignoring obsolete mdp entry 'title' >>>> Setting the LD random seed to -1452668066 >>>> >>>> WARNING 1 [file topol1.top, line 95]: >>>> Too few parameters on line (source file >>>> >>>> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b- >> plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, >>>> line 345) >>>> >>>> >>>> WARNING 2 [file topol1.top, line 97]: >>>> Too few parameters on line (source file >>>> >>>> /dev/shm/swmanage/GROMACS/2018.3/intel-para-2018b- >> plumed/gromacs-2018.3/src/gromacs/gmxpreprocess/toppush.cpp, >>>> line 345) >>>> >>>> Generated 14878 of the 14878 non-bonded parameter combinations >>>> Generating 1-4 interactions: fudge = 0.5 >>>> Generated 14878 of the 14878 1-4 parameter combinations >>>> >>>> ERROR 1 [file topol1.top, line 1813]: >>>> Atomtype 3C_ not found >>>> _ >>>> ???????????????????? >>>> The script I use to generate the topol and tpr files is the following: >>>> ???????????????????? >>>> #!/bin/bash >>>> #16 replicas >>>> nrep=16 >>>> # "effective" temperature range >>>> tmin=287 >>>> tmax=400 >>>> >>>> # build geometric progression >>>> list=$( >>>> awk -v n=$nrep \ >>>> -v tmin=$tmin \ >>>> -v tmax=$tmax \ >>>> 'BEGIN{for(i=0;i>>> t=tmin*exp(i*log(tmax/tmin)/(n-1)); >>>> printf(t); if(i>>> } >>>> }' >>>> ) >>>> >>>> # clean directory >>>> rm -fr \#* >>>> rm -fr topol* >>>> >>>> for((i=0;i>>> do >>>> >>>> # choose lambda as T[0]/T[i] >>>> # remember that high temperature is equivalent to low lambda >>>> lambda=$(echo $list | awk 'BEGIN{FS=",";}{print $1/$'$((i+1))';}') >>>> # process topology >>>> # (if you are curious, try "diff topol0.top topol1.top" to see the >> changes) >>>> plumed partial_tempering $lambda < processed.top > topol$i.top >>>> # prepare tpr file >>>> # -maxwarn is often needed because box could be charged >>>> gmx_mpi grompp -maxwarn 2 -o topol$i.tpr -c md.gro -f md.mdp -p >> topol$i.top >>>> done >>>> ???????????????????? >>>> I think that the problem might be that PLUMED does not support the force >>>> field I am using. Using AMBER99SB-ILDN, nucleic AMBER 94 I did not have >>>> these issues (using the same script). Do you have any suggestions what >>>> could be the problem here? Thanks a lot! >>>> >>>> Best, >>>> Benjamin Joseph >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From neelam.wafa at gmail.com Wed Apr 1 20:56:22 2020 From: neelam.wafa at gmail.com (neelam wafa) Date: Wed, 01 Apr 2020 18:56:22 -0000 Subject: [gmx-users] Reviewing docking resluts Message-ID: Hi everyone This may be irrelevant to the list but i have a big problem. I have designed some inhibitors using molecular docking and then performed 10 nsmd simulations. I have to submit the article for publication. But the journal is asking for the names of persons to review the article. Can you please suggest me some reviewers who are willing to review the article for the journal?. Any suggestions will be highly appreciated Regards From sinaomrani96 at gmail.com Wed Apr 1 23:05:32 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Wed, 01 Apr 2020 21:05:32 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> Message-ID: Dear Mr Spoel, I have found out that I couldn't attach an image and I am sorry about that. here is a link to the picture. https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png On Tue, 31 Mar 2020 at 09:59, David van der Spoel wrote: > Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > > Hi dear Gromacs users, > > Sorry to ask again but I really appreciate the help on this subject. > > > > thanks. > > > > On Fri, 27 Mar 2020 at 02:23, Sina Omrani > wrote: > > > >> Hi, I would like to calculate the Onsager coefficient but after > months of > >> study, I'm not able to do that. if anybody can help me I would really > >> appreciate it. I don't know if there is a specific command to do it or > it > >> needs a series of analyses. > >> > >> P.S. I attached a picture of a formula that calculates the Onsager > >> coefficient from MD. > >> > >> sincerely, > >> Sina Omrani > >> > I see no attachment and google does not help either. What is an Onsager > coefficient? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From ha.rahmaani at gmail.com Thu Apr 2 00:12:37 2020 From: ha.rahmaani at gmail.com (Hadi Rahmaninejad) Date: Wed, 01 Apr 2020 22:12:37 -0000 Subject: [gmx-users] converting gromacs topology file to namd topology file Message-ID: Hello Dear Gromacs users, I hope this email finds you well. I am sending this email to ask is there any way I can convert gromacs topology file (.itp) to namd (top) file? I appreciate any help, Best regards, Hadi From h.jardon at correo.ler.uam.mx Thu Apr 2 03:08:03 2020 From: h.jardon at correo.ler.uam.mx (=?UTF-8?Q?Eduardo_Jard=C3=B3n?=) Date: Thu, 02 Apr 2020 01:08:03 -0000 Subject: [gmx-users] PCA analysis with different atoms in -s and -f In-Reply-To: References: Message-ID: Dear Zhang Chen, In order to calculate the covariance matrix, you have to decide what will be the reference frame. I suggest play around with option "-ref no/yes". The reference can be the average coordinates of the C-alpha atoms of the protein of trajectory 0.pdb. Now, if you changed only the protonation of a residue in trajectory 1.pdb, the reference can still be the same as trajectory 0.pdb, but the average of C alpha atoms would not correspond to the average of the trajectory 1.pdb, so the covariance matrix will be different from the other 0.pdb trajectory. Often this analysis is done for a reduced degrees of freedom, like the C alpha, or the dihedral angles, and rarely for the whole protein including the hydrogen atoms. The main point, I think, is to decide at what level would you expect the protonationated residue would have the major impact. Have you considered to perform alternative analysis to see first the local local impact ? >From there you could consider to run secondary structure analysis, side chains H-bonds, radius of gyration, etc. If you still want to run PCA, you have to make sure your trajectory is long enough to have at least two halves of trajectory 0.pdb CA. 100% overlap of covariance matrices, or block analysis to calculate overlap error as a function of time length. best, Eduardo El mar., 31 mar. 2020 a las 19:11, ZHANG Cheng (<272699575 at qq.com>) escribi?: > I am trying to compare trajectories from different MD simulations, > including different pH and different mutants. The initial PDB (i.e. 0.pdb) > is the same, but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to > protonation states and mutations. Those different PDBs were used > individually for the MD. > > > To obtain the eigen vectors, should I use the 0.pdb as the reference > structure? > # gmx covar -s 0.pdb -f 1.xtc -v 1.trr > (use 0.pdb as reference, and calculate the eigen vectors from trajectories > of 1.pdb) > > > The first is to choose the least squares fit. Though the atoms in > "Protein", "Protein-H" are different between 0.pdb and 1.xtc, they are same > in "C-alpha", "Backbone" and "MainChain". However, when I choose "C-alpha" > for the "least squares fit", I still got the warning: > # WARNING: number of atoms in tpx (442) and trajectory (6622) do not match > > > The calculation can still be done. So must I provide "1.pdb" as reference > for "1.xtc", or is it still okay to use "-s 0.pdb"? > > > Afterwards, I want to run > # gmx anaeig -s 0.pdb -over overlap_1_2.xvg -v2 1.trr -v 2.trr > to compare the similarity between Condition 1 and Condition 2. Is this > correct? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From kevin.boyd at uconn.edu Thu Apr 2 05:59:01 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Thu, 02 Apr 2020 03:59:01 -0000 Subject: [gmx-users] Optimising mdrun In-Reply-To: References: Message-ID: Hi - > This setting is using 16 MPI process and using 2 OpenMP thrads per MPI proces With ntomp 1 you should only be getting one OpenMP thread, not sure why that's not working. Can you post a link to a log file? For a small system like that and a powerful GPU, you're likely going to have some inefficiency. Can you run replicates? You'd want to do something like this (though I'm not sure about the mpirun part, I usually do non-MPI gromacs): mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi 1 -pin on -pinoffset 0 -nb gpu -pme gpu mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi 1 -pin on -pinoffset 8 -nb gpu -pme gpu where the first job runs on cores 0-7 and the second job runs on cores 8-15, sharing the same GPU. > The log states "Will do PME sum in reciprocal space for electrostatic interactions" Reciprocal space does not indicate whether PME was run on the CPU or GPU, it's just reporting math. On Wed, Apr 1, 2020 at 1:03 AM Robert Cordina wrote: > *Message sent from a system outside of UConn.* > > > Hi, > > I'm trying to use GROMACS 2019.3 on two different machines, simulating the > same system. The system is made up of 100 identical molecules, consisting > of 61 united atoms each, in a non-aqueous system. I am however getting > vastly different performance on the two machines, and I don't really > understand why. The two machines' specs are as follows: > > Machine 1 (stand-alone machine) > > > * 40-core CPU (Intel Xeon Gold 6148 2.4GHz, 3.7GHz, 20C, 10.4GT/s > 2UPI, 27M Cache, HT (150W) DDR4-2666) - so 20 hyper-threaded cores to give > a total of 40, although in my case only 20 cores are being used given the > size of the system (see below) > * 1 GPU (Nvidia Quadro RTX5000, 16GB, 4DP, VirtualLink (XX20T)) > * Memory (512GB (8x64GB) 2666MHz DDR4 LRDIMM ECC) - although in > reality only about 10 GB are used during my simulation > * CUDA 10.10 > > When I simulate my system, I've found that the optimal mdrun settings are > extremely simple > > mdrun -pin on > > This setting uses 1 MPI thread and 20 OpenMP threads, while the PP and PME > tasks are carried out automatically on the GPU. With this I'm getting > about 800 ns/day. > > > Machine 2 (part of a HPC cluster - of which I can only use 1 node at a > time - the below details are for a GPU node) > > > * 16 core CPU (Intel Xeon E5-2600, 2.2 GHz) > * 1 GPU (NVIDIA Tesla V100-PCIE-32GB) > * Memory (64GB RAM) > * CUDA 10.0 > > I've tried reading the GROMACS documentation, repeatedly, but I really > can't understand much about how to go about choosing the right mdrun > settings for this machine. I've tried several, and the best performance I > could get is with > > mpirun -np 16 gmx_mpi mdrun -ntomp 1 > > Even then, I get a performance of about 45-50 ns/day, which is way lower > than the 800 ns/day I get with the stand-alone machine. This setting is > using 16 MPI process and using 2 OpenMP thrads per MPI process. Also, only > PP tasks are being carried out on the GPU. The log states "Will do PME sum > in reciprocal space for electrostatic interactions". Also I get a Warning > "On rank 0: oversubscribing the available 16 logical CPU cores per node > with 32 threads. This will cause considerable performance loss", with Note > "Oversubscribing the CPU, will not pin threads". > > > Does anyone have any guidance as to what I should try to get good > performance on the GPU node of the cluster please? Any help will be really > appreciated. > > Thanks, > > Robert > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sunaoran16 at mails.ucas.ac.cn Thu Apr 2 09:21:30 2020 From: sunaoran16 at mails.ucas.ac.cn (=?UTF-8?B?5a2Z5YKy54S2?=) Date: Thu, 02 Apr 2020 07:21:30 -0000 Subject: [gmx-users] Missing gromacs.lib when building Grmoacs 2020.1 in vs 2019 Message-ID: <67dc8026.7f41.17139c40b5e.Coremail.sunaoran16@mails.ucas.ac.cn> Greetings! I try to build the newest release (2020.1) using cmake 3.16.4 and vs 2019 in windows 10 Enterprise. I finish the configuring and generating using cmake following the instruction, but when I try to build the sln file with vs 2019, I get about fifty errors "LNK1104 cannot open file?..\..\..\..\lib\Debug\gromacs.lib".I have no idea where exactly the gromacs.lib is supposed to be since vs only tells me ..\ instead of detailed path, and I cannot find such a file named gromacs.lib anywhere on my computer or via the internet. So what exactly is the problem and how can I solve it? Best wishes Aoran Sun From spoel at xray.bmc.uu.se Thu Apr 2 11:25:28 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 02 Apr 2020 09:25:28 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> Message-ID: <105ade9a-2712-5d8c-6b1b-ec641c9b40ca@xray.bmc.uu.se> Den 2020-04-01 kl. 23:05, skrev Sina Omrani: > Dear Mr Spoel, > I have found out that I couldn't attach an image and I am sorry about that. > here is a link to the picture. > https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png Not sure what is meant by r or v with two subscripts. Otherwise it looks a bit like Einsteins formula. > > On Tue, 31 Mar 2020 at 09:59, David van der Spoel > wrote: > >> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: >>> Hi dear Gromacs users, >>> Sorry to ask again but I really appreciate the help on this subject. >>> >>> thanks. >>> >>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani >> wrote: >>> >>>> Hi, I would like to calculate the Onsager coefficient but after >> months of >>>> study, I'm not able to do that. if anybody can help me I would really >>>> appreciate it. I don't know if there is a specific command to do it or >> it >>>> needs a series of analyses. >>>> >>>> P.S. I attached a picture of a formula that calculates the Onsager >>>> coefficient from MD. >>>> >>>> sincerely, >>>> Sina Omrani >>>> >> I see no attachment and google does not help either. What is an Onsager >> coefficient? >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From johnwhittake at zedat.fu-berlin.de Thu Apr 2 15:19:23 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Thu, 02 Apr 2020 13:19:23 -0000 Subject: [gmx-users] converting gromacs topology file to namd topology file In-Reply-To: References: Message-ID: <64688.89.14.193.188.1585833561.webmail@webmail.zedat.fu-berlin.de> Hi, A quick google search led me to this: https://www.ks.uiuc.edu/Research/namd/2.10/ug/node14.html I've never used NAMD before but apparently you can use gromacs topologies directly in NAMD. Note the caveats at the bottom of the page. Would this work or does it not accomplish what you are looking for? - John > Hello Dear Gromacs users, > > I hope this email finds you well. I am sending this email to ask is there > any way I can convert gromacs topology file (.itp) to namd (top) file? I > appreciate any help, > > Best regards, > Hadi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-request at gromacs.org. > From si.papadatos at edu.cut.ac.cy Thu Apr 2 15:40:19 2020 From: si.papadatos at edu.cut.ac.cy (Sotirios Dionysios I. Papadatos) Date: Thu, 02 Apr 2020 13:40:19 -0000 Subject: [gmx-users] Free energy of protonation In-Reply-To: References: Message-ID: My advise is a bit general. Try the same process with a different molecule (one that can support this change), try the same molecule with an AA ff, since it is already done (as you mentioned) do you get similar results? These tests might help you find out if there is something wrong with your mdp. I haven't changed a bead in free energy so I am not 100% sure, but the few mdp options that you provided seem reasonable. ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Gmx QA Sent: Wednesday, April 1, 2020 7:52 PM To: Discussion list for GROMACS users Subject: [gmx-users] Free energy of protonation Dear list, I am trying to calculate the free energy for protonating a single monomer of oleic acid with the martini forcefield. This in preparation for other work, and I wanted to start by reproducing what is already done. To do this, I have defined the following in my topology to describe the change in protonation state going from A (protonated) to state B (charged). The martini bead type needs to change as well in this process. [ atoms ] ; id typeA resnr residu atom cgnr chargeA massA typeB chargeB massB 1 P4 1 OAN COO 1 0 Qa -1 I also have this very simple mdp file for doing the transformation free_energy = yes init_lambda-state = 1 fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 And I am using fep-lambdas to describe the entire process. With this, I can run through grompp and mdrun with different values of init-lambda-state, but the output I get in each case is the same for each different simulation. I check this by gmx analyze -f md.xvg -ee And I always get the same value for the average. Is there something I am missing or not specifying properly? Thanks /PK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From sinaomrani96 at gmail.com Thu Apr 2 17:40:13 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Thu, 02 Apr 2020 15:40:13 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: <105ade9a-2712-5d8c-6b1b-ec641c9b40ca@xray.bmc.uu.se> References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <105ade9a-2712-5d8c-6b1b-ec641c9b40ca@xray.bmc.uu.se> Message-ID: Yes, they are very similar. r with two subscripts means the position of the center of mass of the lth molecules of component i. On Thu, 2 Apr 2020 at 13:55, David van der Spoel wrote: > Den 2020-04-01 kl. 23:05, skrev Sina Omrani: > > Dear Mr Spoel, > > I have found out that I couldn't attach an image and I am sorry about > that. > > here is a link to the picture. > > > https://cdn1.imggmi.com/uploads/2020/4/1/1599cd9ac1102e329ff91759d3314725-full.png > > Not sure what is meant by r or v with two subscripts. Otherwise it looks > a bit like Einsteins formula. > > > > On Tue, 31 Mar 2020 at 09:59, David van der Spoel > > wrote: > > > >> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > >>> Hi dear Gromacs users, > >>> Sorry to ask again but I really appreciate the help on this subject. > >>> > >>> thanks. > >>> > >>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani > >> wrote: > >>> > >>>> Hi, I would like to calculate the Onsager coefficient but after > >> months of > >>>> study, I'm not able to do that. if anybody can help me I would really > >>>> appreciate it. I don't know if there is a specific command to do it or > >> it > >>>> needs a series of analyses. > >>>> > >>>> P.S. I attached a picture of a formula that calculates the Onsager > >>>> coefficient from MD. > >>>> > >>>> sincerely, > >>>> Sina Omrani > >>>> > >> I see no attachment and google does not help either. What is an Onsager > >> coefficient? > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From robert.cordina at strath.ac.uk Thu Apr 2 18:00:02 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Thu, 02 Apr 2020 16:00:02 -0000 Subject: [gmx-users] Optimising mdrun In-Reply-To: References: Message-ID: Hi Kevin, I'm working with the HPC cluster administrator and we manged to get much better performance with mpirun -np 1 gmx_mpi mdrun -ntomp 16 which got it up to 500 ns/day. Will now be trying with -nb gpu -pme gpu and also with -pin on to see if that helps even further. Thanks, Robert -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Kevin Boyd Sent: 02 April 2020 04:59 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Optimising mdrun Hi - > This setting is using 16 MPI process and using 2 OpenMP thrads per MPI proces With ntomp 1 you should only be getting one OpenMP thread, not sure why that's not working. Can you post a link to a log file? For a small system like that and a powerful GPU, you're likely going to have some inefficiency. Can you run replicates? You'd want to do something like this (though I'm not sure about the mpirun part, I usually do non-MPI gromacs): mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi 1 -pin on -pinoffset 0 -nb gpu -pme gpu mpirun -np 8 gmx_mpi mdrun -nt 8 -ntomp 8 -ntmpi 1 -pin on -pinoffset 8 -nb gpu -pme gpu where the first job runs on cores 0-7 and the second job runs on cores 8-15, sharing the same GPU. > The log states "Will do PME sum in reciprocal space for electrostatic interactions" Reciprocal space does not indicate whether PME was run on the CPU or GPU, it's just reporting math. On Wed, Apr 1, 2020 at 1:03 AM Robert Cordina wrote: > *Message sent from a system outside of UConn.* > > > Hi, > > I'm trying to use GROMACS 2019.3 on two different machines, simulating > the same system. The system is made up of 100 identical molecules, > consisting of 61 united atoms each, in a non-aqueous system. I am > however getting vastly different performance on the two machines, and > I don't really understand why. The two machines' specs are as follows: > > Machine 1 (stand-alone machine) > > > * 40-core CPU (Intel Xeon Gold 6148 2.4GHz, 3.7GHz, 20C, 10.4GT/s > 2UPI, 27M Cache, HT (150W) DDR4-2666) - so 20 hyper-threaded cores to > give a total of 40, although in my case only 20 cores are being used > given the size of the system (see below) > * 1 GPU (Nvidia Quadro RTX5000, 16GB, 4DP, VirtualLink (XX20T)) > * Memory (512GB (8x64GB) 2666MHz DDR4 LRDIMM ECC) - although in > reality only about 10 GB are used during my simulation > * CUDA 10.10 > > When I simulate my system, I've found that the optimal mdrun settings > are extremely simple > > mdrun -pin on > > This setting uses 1 MPI thread and 20 OpenMP threads, while the PP and > PME tasks are carried out automatically on the GPU. With this I'm > getting about 800 ns/day. > > > Machine 2 (part of a HPC cluster - of which I can only use 1 node at a > time - the below details are for a GPU node) > > > * 16 core CPU (Intel Xeon E5-2600, 2.2 GHz) > * 1 GPU (NVIDIA Tesla V100-PCIE-32GB) > * Memory (64GB RAM) > * CUDA 10.0 > > I've tried reading the GROMACS documentation, repeatedly, but I really > can't understand much about how to go about choosing the right mdrun > settings for this machine. I've tried several, and the best > performance I could get is with > > mpirun -np 16 gmx_mpi mdrun -ntomp 1 > > Even then, I get a performance of about 45-50 ns/day, which is way > lower than the 800 ns/day I get with the stand-alone machine. This > setting is using 16 MPI process and using 2 OpenMP thrads per MPI > process. Also, only PP tasks are being carried out on the GPU. The > log states "Will do PME sum in reciprocal space for electrostatic > interactions". Also I get a Warning "On rank 0: oversubscribing the > available 16 logical CPU cores per node with 32 threads. This will > cause considerable performance loss", with Note "Oversubscribing the CPU, will not pin threads". > > > Does anyone have any guidance as to what I should try to get good > performance on the GPU node of the cluster please? Any help will be > really appreciated. > > Thanks, > > Robert > -- > Gromacs Users mailing list > > * Please search the archive at > https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g > romacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C315ea393228247714fb608d7d6ba437e%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637213967796410028&sdata=U3Y5vSj5lZXp68PFEerHc0qVtgPDDUuR169ahdbsnag%3D&reserved=0 before posting! > > * Can't post? Read > https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.g > romacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Crobert.cordina > %40strath.ac.uk%7C315ea393228247714fb608d7d6ba437e%7C631e0763153347eba > 5cd0457bee5944e%7C0%7C0%7C637213967796410028&sdata=9NqaDxydhHN7Lsi > AbgRzm4qxq0z28RvD3F0MU2Qmn8M%3D&reserved=0 > > * For (un)subscribe requests visit > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail > list.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C315ea393228247714fb608d7d6ba437e%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637213967796410028&sdata=IQTo3qrzS4u6RKkGe6%2B94zHz2xSCkV4VndupszFntTg%3D&reserved=0 or send a mail to gmx-users-request at gromacs.org. > -- Gromacs Users mailing list * Please search the archive at https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C315ea393228247714fb608d7d6ba437e%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637213967796410028&sdata=U3Y5vSj5lZXp68PFEerHc0qVtgPDDUuR169ahdbsnag%3D&reserved=0 before posting! * Can't post? 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From alexanderwien2k at gmail.com Thu Apr 2 18:54:20 2020 From: alexanderwien2k at gmail.com (Alex) Date: Thu, 02 Apr 2020 16:54:20 -0000 Subject: [gmx-users] Issue with PMF Message-ID: Dear all, By using the below setting I am getting a very nice umbrella histogram and iact also shows a very good integrated Autocorrelation time. However, the PMF profile is unexpected. Below I have also provided a gmx wham command I am using, part of the pullx.xvg of one of the windows and also corresponding part in log file. Would you please help me find out what the problem might be? One more question: does it make sense to manually shift the plateau of the PMF plot to zero (when we plot it), instead of using using the -zprof0 flag? %-------------------------------- pull = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Mol_A pull-group2-name = Thin_film pull-coord1-groups = 1 2 pull-coord1-type = umbrella pull-coord1-dim = N N Y pull-coord1-start = no ;--> manually we define the distance for all windows pull-coord1-rate = 0.0 ;--> We don't want the roups to move pull-coord1-geometry = distance pull-coord1-k = 10000 ;;kJ/(mol nm^2) pull-print-components = Yes pull-nstxout = 2000 pull-nstfout = 2000 pull-print-com1 = yes pull-coord1-init = 1.650000 %------------------------------------ #Part of the one of the pullx.xvg file @ legend length 2 @ s0 legend "1" @ s1 legend "1 dZ" @ s2 legend "1 g 1 Z" @ s3 legend "1 g 2 Z" 0.0000 0.0155171 0.0155171 9.89805 9.91357 2.0000 0.0103956 0.0103956 9.90227 9.91266 4.0000 0.0146962 0.0146962 9.89733 9.91202 6.0000 0.00656533 0.00656533 9.90404 9.91061 8.0000 0.00228074 0.00228074 9.90945 9.91174 10.0000 0.00967605 0.00967605 9.90514 9.91482 .... %-------------------------------------------- gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o profile.xvg -b 3000 -unit kCal -v %------------------------------------------------ #Similar massage as below I have for all windows (tpr files). Reading file prd.1.tpr, VERSION 2018.7 (single precision) File prd.1.tpr, 1 coordinates, with these options: Geometry distance k = 10000 position = 0 dimensions [N N Y] (1 dimensions). Used: Yes Pull group coordinates of 2 groups expected in pullx files. Reference value of the coordinate not expected in pullx files. Reading pull force file prd_pullf.1.xvg, expecting 2 columns: Columns for pull coordinate 1 reaction coordinate: 1 center-of-mass of groups: 0 reference position column: No Found 2501 times in prd_pullf.1.xvg %---------------------------------------------------------- Thank you, Alex From neena.susaneappen at mail.utoronto.ca Thu Apr 2 20:45:22 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Thu, 02 Apr 2020 18:45:22 -0000 Subject: [gmx-users] Effect of atomic charge on bonding parameters In-Reply-To: References: Message-ID: Hi Justin, What is the criteria for opls bond types? Thank you, Neena ________________________________ From: Neena Susan Eappen Sent: Wednesday, April 1, 2020 12:05 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] Effect of atomic charge on bonding parameters Hello gromacs users, Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? ; name bond_type mass charge ptype sigma epsilon opls_237 N 7 14.00670 -0.760 A 3.25000e-01 7.11280e-01 opls_238 N 7 14.00670 -0.500 A 3.25000e-01 7.11280e-01 (Taken from ffnonbonded.itp file) Thank you, Neena From youli97 at hotmail.com Thu Apr 2 21:05:14 2020 From: youli97 at hotmail.com (Feriel Terbeche) Date: Thu, 02 Apr 2020 19:05:14 -0000 Subject: [gmx-users] (no subject) Message-ID: Hello! My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im preparing my last study's project (master degrees), wich is about hemophila A and factor VIII where I have to use gromacs, but, I don't know how to use it even I have it on my computer and unfortunately no one here can help me because no one used it before. I really need help but I don't know from where I'll get it, so can I have some advices. Thank you From dburns at iastate.edu Thu Apr 2 21:10:32 2020 From: dburns at iastate.edu (Daniel Burns) Date: Thu, 02 Apr 2020 19:10:32 -0000 Subject: [gmx-users] (no subject) In-Reply-To: References: Message-ID: Start here: http://www.mdtutorials.com/gmx/. An introduction to linux book might be helpful as well if you are not already familiar with it. Good luck! On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche wrote: > Hello! > My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im > preparing my last study's project (master degrees), wich is about > hemophila A and factor VIII where I have to use gromacs, but, I don't know > how to use it even I have it on my computer and unfortunately no one here > can help me because no one used it before. I really need help but I don't > know from where I'll get it, so can I have some advices. Thank you > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From suryasanjay720 at gmail.com Thu Apr 2 21:19:18 2020 From: suryasanjay720 at gmail.com (Surya Sanjay) Date: Thu, 02 Apr 2020 19:19:18 -0000 Subject: [gmx-users] Simulation of Protein-Protein Complex Message-ID: Hello all, I am a beginner Gromacs user and I have been using the Gromacs tutorials on mdtutorials.com/gmx/. I would like to simulate the binding of the infectious and normally-folded prion variants, and I want to know if the protein-protein complex procedure is different from that of protein-ligand systems. Thanks, Surya From jalemkul at vt.edu Thu Apr 2 21:21:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 19:21:05 -0000 Subject: [gmx-users] Issue with PMF In-Reply-To: References: Message-ID: On 4/2/20 12:53 PM, Alex wrote: > Dear all, > By using the below setting I am getting a very nice umbrella histogram and > iact also shows a very good integrated Autocorrelation time. However, the > PMF profile is unexpected. Below I have also provided a gmx wham command I > am using, part of the pullx.xvg of one of the windows and also > corresponding part in log file. > Would you please help me find out what the problem might be? What is the problem? > One more question: does it make sense to manually shift the plateau of the > PMF plot to zero (when we plot it), instead of using using the -zprof0 flag? There is no difference. The -zprof0 just adds a constant so the PMF is zero at the specified point on the reaction coordinate. > %-------------------------------- > pull = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Mol_A > pull-group2-name = Thin_film > > pull-coord1-groups = 1 2 > pull-coord1-type = umbrella > pull-coord1-dim = N N Y > pull-coord1-start = no ;--> manually we define the distance for > all windows > pull-coord1-rate = 0.0 ;--> We don't want the roups to move > pull-coord1-geometry = distance > pull-coord1-k = 10000 ;;kJ/(mol nm^2) > pull-print-components = Yes > pull-nstxout = 2000 > pull-nstfout = 2000 > pull-print-com1 = yes > pull-coord1-init = 1.650000 > %------------------------------------ > #Part of the one of the pullx.xvg file > @ legend length 2 > @ s0 legend "1" > @ s1 legend "1 dZ" > @ s2 legend "1 g 1 Z" > @ s3 legend "1 g 2 Z" > 0.0000 0.0155171 0.0155171 9.89805 9.91357 > 2.0000 0.0103956 0.0103956 9.90227 9.91266 > 4.0000 0.0146962 0.0146962 9.89733 9.91202 > 6.0000 0.00656533 0.00656533 9.90404 9.91061 > 8.0000 0.00228074 0.00228074 9.90945 9.91174 > 10.0000 0.00967605 0.00967605 9.90514 9.91482 > .... > %-------------------------------------------- > gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist > -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o > profile.xvg -b 3000 -unit kCal -v > > %------------------------------------------------ > #Similar massage as below I have for all windows (tpr files). > Reading file prd.1.tpr, VERSION 2018.7 (single precision) > > File prd.1.tpr, 1 coordinates, with these options: > Geometry distance k = 10000 position = 0 dimensions > [N N Y] (1 dimensions). Used: Yes > Pull group coordinates of 2 groups expected in pullx files. > Reference value of the coordinate not expected in pullx files. > > Reading pull force file prd_pullf.1.xvg, expecting 2 columns: > Columns for pull coordinate 1 > reaction coordinate: 1 > center-of-mass of groups: 0 > reference position column: No > Found 2501 times in prd_pullf.1.xvg > %---------------------------------------------------------- > > Thank you, > Alex -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Thu Apr 2 21:23:08 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 19:23:08 -0000 Subject: [gmx-users] Effect of atomic charge on bonding parameters In-Reply-To: References: Message-ID: <34d222ca-72b3-7c98-b024-385ae6e2ca18@vt.edu> On 4/2/20 2:45 PM, Neena Susan Eappen wrote: > Hi Justin, > > What is the criteria for opls bond types? I don't understand the question. Nonbonded and bonded atom types can be separate (this is uncommon, but something that OPLS does) because bonded interactions may be more transferable than nonbonded paramters. I have no idea why OPLS has opls_237 and opls_238 when they have the same bonded type and same LJ parameters. They're effectively identical so this is probably a very poor example when trying to learn how the force field works. If you're trying to generate a topology for some new species, try the LigParGen server rather than going about it manually. -Justin > Thank you, > Neena > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, April 1, 2020 12:05 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] Effect of atomic charge on bonding parameters > > Hello gromacs users, > > Following two atoms (opls_ 237 and 238) have different atomic charges, but same bond type and thereby same parameters in the ffbonded.itp file. Is the effect of charge on bonding ignored? Is that possible? > > ; name bond_type mass charge ptype sigma epsilon > opls_237 N 7 14.00670 -0.760 A 3.25000e-01 7.11280e-01 > opls_238 N 7 14.00670 -0.500 A 3.25000e-01 7.11280e-01 > > (Taken from ffnonbonded.itp file) > > Thank you, > Neena -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From nelgho at gmail.com Thu Apr 2 21:23:51 2020 From: nelgho at gmail.com (Nadia Elghobashi-Meinhardt) Date: Thu, 02 Apr 2020 19:23:51 -0000 Subject: [gmx-users] Fwd: geometry optimization of metalloenzyme In-Reply-To: References: Message-ID: Hello everyone, I am trying to minimize the potential energy of a metalloenzyme containing Ni and Fe atoms. What is the best way to constrain (fix?) the position of the active site atoms during the geometry optimization? I have tried introducing bonds with relatively high force constants and alternatively, tried introducing a [constraints] section, but the atoms are still not staying put. Or should one use extra position restraints? Any tips are welcome! Thank you. From jalemkul at vt.edu Thu Apr 2 21:24:28 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 19:24:28 -0000 Subject: [gmx-users] Simulation of Protein-Protein Complex In-Reply-To: References: Message-ID: <33b57965-0df5-a387-f433-8e67246a8b83@vt.edu> On 4/2/20 3:19 PM, Surya Sanjay wrote: > Hello all, > I am a beginner Gromacs user and I have been using the Gromacs tutorials on > mdtutorials.com/gmx/. I would like to simulate the binding of the > infectious and normally-folded prion variants, and I want to know if the > protein-protein complex procedure is different from that of protein-ligand > systems. A system containing several proteins is functionally no different than simulating one protein. Don't equate protein-protein systems to protein-ligand systems, which often require external ligand parametrization. None of that is necessary when dealing with proteins. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Thu Apr 2 21:26:37 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 19:26:37 -0000 Subject: [gmx-users] Fwd: geometry optimization of metalloenzyme In-Reply-To: References: Message-ID: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: > Hello everyone, > > I am trying to minimize the potential energy of a > metalloenzyme containing Ni and Fe atoms. > What is the best way to constrain (fix?) the position of the active site > atoms > during the geometry optimization? > I have tried introducing bonds with relatively high force constants and > alternatively, tried introducing a [constraints] section, > but the atoms are still not staying put. Bonds or constraints will maintain distances between atoms (relative position) but not absolute position. > Or should one use extra position restraints? If the absolute position matters, yes. I would think the approach of adding restraints or constraints between atoms would be more meaningful given that preserving coordination geometry is often the defect in MM treatment of transition metals. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Thu Apr 2 21:40:19 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 19:40:19 -0000 Subject: [gmx-users] Simulation of Protein-Protein Complex In-Reply-To: References: <33b57965-0df5-a387-f433-8e67246a8b83@vt.edu> Message-ID: <0e064f1f-0c55-f67b-b855-898ae0efe443@vt.edu> Please keep the discussion on the mailing list. On 4/2/20 3:38 PM, Surya Sanjay wrote: > Hello Dr. Lemkul, > You were very helpful (I was pondering this problem for about four > days before you told me this and it all makes sense now). To complete > the solvation step, should I combine the topol.top files of both > protein chains? You should only ever have one topol.top. pdb2gmx will write each protein chain topology to .itp files that are #included within it. -Justin > Thanks, > Surya > > On Thu, Apr 2, 2020 at 3:25 PM Justin Lemkul > wrote: > > > > On 4/2/20 3:19 PM, Surya Sanjay wrote: > > Hello all, > > I am a beginner Gromacs user and I have been using the Gromacs > tutorials on > > mdtutorials.com/gmx/ . I would like > to simulate the binding of the > > infectious and normally-folded prion variants, and I want to > know if the > > protein-protein complex procedure is different from that of > protein-ligand > > systems. > > A system containing several proteins is functionally no different > than > simulating one protein. Don't equate protein-protein systems to > protein-ligand systems, which often require external ligand > parametrization. None of that is necessary when dealing with proteins. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-request at gromacs.org > . > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Thu Apr 2 22:20:22 2020 From: alexanderwien2k at gmail.com (Alex) Date: Thu, 02 Apr 2020 20:20:22 -0000 Subject: [gmx-users] Issue with PMF In-Reply-To: References: Message-ID: Thanks Justin for the response. On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul wrote: > > > On 4/2/20 12:53 PM, Alex wrote: > > Dear all, > > By using the below setting I am getting a very nice umbrella histogram > and > > iact also shows a very good integrated Autocorrelation time. However, the > > PMF profile is unexpected. Below I have also provided a gmx wham command > I > > am using, part of the pullx.xvg of one of the windows and also > > corresponding part in log file. > > Would you please help me find out what the problem might be? > > What is the problem? > Below link shows the histogram and PMF, actually I was expecting that the PMF reach a plateau in the region marked by B in the figure as we are fully inside the bulk area of the thin film. However, there are some region from 15 to 20 kcal/mol different respect to the expected plateau. Here we have 10nm thick thin film. https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz > > One more question: does it make sense to manually shift the plateau of > the > > PMF plot to zero (when we plot it), instead of using using the -zprof0 > flag? > > There is no difference. The -zprof0 just adds a constant so the PMF is > zero at the specified point on the reaction coordinate. > > > %-------------------------------- > > pull = yes > > pull-ngroups = 2 > > pull-ncoords = 1 > > pull-group1-name = Mol_A > > pull-group2-name = Thin_film > > > > pull-coord1-groups = 1 2 > > pull-coord1-type = umbrella > > pull-coord1-dim = N N Y > > pull-coord1-start = no ;--> manually we define the distance for > > all windows > > pull-coord1-rate = 0.0 ;--> We don't want the roups to move > > pull-coord1-geometry = distance > > pull-coord1-k = 10000 ;;kJ/(mol nm^2) > > pull-print-components = Yes > > pull-nstxout = 2000 > > pull-nstfout = 2000 > > pull-print-com1 = yes > > pull-coord1-init = 1.650000 > > %------------------------------------ > > #Part of the one of the pullx.xvg file > > @ legend length 2 > > @ s0 legend "1" > > @ s1 legend "1 dZ" > > @ s2 legend "1 g 1 Z" > > @ s3 legend "1 g 2 Z" > > 0.0000 0.0155171 0.0155171 9.89805 9.91357 > > 2.0000 0.0103956 0.0103956 9.90227 9.91266 > > 4.0000 0.0146962 0.0146962 9.89733 9.91202 > > 6.0000 0.00656533 0.00656533 9.90404 9.91061 > > 8.0000 0.00228074 0.00228074 9.90945 9.91174 > > 10.0000 0.00967605 0.00967605 9.90514 9.91482 > > .... > > %-------------------------------------------- > > gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist > > -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o > > profile.xvg -b 3000 -unit kCal -v > > > > %------------------------------------------------ > > #Similar massage as below I have for all windows (tpr files). > > Reading file prd.1.tpr, VERSION 2018.7 (single precision) > > > > File prd.1.tpr, 1 coordinates, with these options: > > Geometry distance k = 10000 position = 0 > dimensions > > [N N Y] (1 dimensions). Used: Yes > > Pull group coordinates of 2 groups expected in pullx files. > > Reference value of the coordinate not expected in pullx files. > > > > Reading pull force file prd_pullf.1.xvg, expecting 2 columns: > > Columns for pull coordinate 1 > > reaction coordinate: 1 > > center-of-mass of groups: 0 > > reference position column: No > > Found 2501 times in prd_pullf.1.xvg > > %---------------------------------------------------------- > Actually, I was suspicious of these "Reference value of the coordinate not expected in pullx files." and "reference position column: No" which I have in log file of gmx wham for each windows's tpr. Concerning your PMF tutorial, when the distance between chain_A and chain_B is calculated by gmx distance, why the -oall is used to get the absolute distance out of x,y and z, while the -oxyz would be much better as we can take the Z component of the distance similar (corresponding) to the considered reaction coordinate in the tutorial? Regards, Alex > > > > Thank you, > > Alex > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Thu Apr 2 22:28:20 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 02 Apr 2020 20:28:20 -0000 Subject: [gmx-users] Issue with PMF In-Reply-To: References: Message-ID: <3d42d466-afe8-2108-27d0-0c6586f8c752@vt.edu> On 4/2/20 4:19 PM, Alex wrote: > Thanks Justin for the response. > > On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul wrote: > >> >> On 4/2/20 12:53 PM, Alex wrote: >>> Dear all, >>> By using the below setting I am getting a very nice umbrella histogram >> and >>> iact also shows a very good integrated Autocorrelation time. However, the >>> PMF profile is unexpected. Below I have also provided a gmx wham command >> I >>> am using, part of the pullx.xvg of one of the windows and also >>> corresponding part in log file. >>> Would you please help me find out what the problem might be? >> What is the problem? >> > Below link shows the histogram and PMF, actually I was expecting that the > PMF reach a plateau in the region marked by B in the figure as we are fully > inside the bulk area of the thin film. However, there are some region from > 15 to 20 kcal/mol different respect to the expected plateau. Here we have > 10nm thick thin film. > > https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz > Bootstrapping may underestimate the real error. How well converged is the PMF with respect to time, e.g. computing the PMF from the first half and last half of the simulation time? >>> One more question: does it make sense to manually shift the plateau of >> the >>> PMF plot to zero (when we plot it), instead of using using the -zprof0 >> flag? >> >> There is no difference. The -zprof0 just adds a constant so the PMF is >> zero at the specified point on the reaction coordinate. >> >>> %-------------------------------- >>> pull = yes >>> pull-ngroups = 2 >>> pull-ncoords = 1 >>> pull-group1-name = Mol_A >>> pull-group2-name = Thin_film >>> >>> pull-coord1-groups = 1 2 >>> pull-coord1-type = umbrella >>> pull-coord1-dim = N N Y >>> pull-coord1-start = no ;--> manually we define the distance for >>> all windows >>> pull-coord1-rate = 0.0 ;--> We don't want the roups to move >>> pull-coord1-geometry = distance >>> pull-coord1-k = 10000 ;;kJ/(mol nm^2) >>> pull-print-components = Yes >>> pull-nstxout = 2000 >>> pull-nstfout = 2000 >>> pull-print-com1 = yes >>> pull-coord1-init = 1.650000 >>> %------------------------------------ >>> #Part of the one of the pullx.xvg file >>> @ legend length 2 >>> @ s0 legend "1" >>> @ s1 legend "1 dZ" >>> @ s2 legend "1 g 1 Z" >>> @ s3 legend "1 g 2 Z" >>> 0.0000 0.0155171 0.0155171 9.89805 9.91357 >>> 2.0000 0.0103956 0.0103956 9.90227 9.91266 >>> 4.0000 0.0146962 0.0146962 9.89733 9.91202 >>> 6.0000 0.00656533 0.00656533 9.90404 9.91061 >>> 8.0000 0.00228074 0.00228074 9.90945 9.91174 >>> 10.0000 0.00967605 0.00967605 9.90514 9.91482 >>> .... >>> %-------------------------------------------- >>> gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method b-hist >>> -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac -o >>> profile.xvg -b 3000 -unit kCal -v >>> >>> %------------------------------------------------ >>> #Similar massage as below I have for all windows (tpr files). >>> Reading file prd.1.tpr, VERSION 2018.7 (single precision) >>> >>> File prd.1.tpr, 1 coordinates, with these options: >>> Geometry distance k = 10000 position = 0 >> dimensions >>> [N N Y] (1 dimensions). Used: Yes >>> Pull group coordinates of 2 groups expected in pullx files. >>> Reference value of the coordinate not expected in pullx files. >>> >>> Reading pull force file prd_pullf.1.xvg, expecting 2 columns: >>> Columns for pull coordinate 1 >>> reaction coordinate: 1 >>> center-of-mass of groups: 0 >>> reference position column: No >>> Found 2501 times in prd_pullf.1.xvg >>> %---------------------------------------------------------- > Actually, I was suspicious of these "Reference value of the coordinate not > expected in pullx files." and "reference position column: No" which > I have in log file of gmx wham for each windows's tpr. I have no experience with that; the pullx.xvg file format has changed a lot over time. I always use pullf.xvg and it's never an issue. > Concerning your PMF tutorial, when the distance between chain_A and chain_B > is calculated by gmx distance, why the -oall is used to get the absolute > distance out of x,y and z, while the -oxyz would be much better as we can > take the Z component of the distance similar (corresponding) to the > considered reaction coordinate in the tutorial? The two quantities should be essentially equivalent for the purposes of the tutorial. -Justin > Regards, > Alex > >>> Thank you, >>> Alex >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sadafrani6 at gmail.com Fri Apr 3 03:02:41 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Fri, 03 Apr 2020 01:02:41 -0000 Subject: [gmx-users] Fwd: no atom pairs for dispersion correction In-Reply-To: References: Message-ID: Dear Gromacs users I am running an MD simulation of the protein-ligand complex. At the start of the production run, I am getting this warning. What does it mean and how should I fix it? *WARNING: There are no atom pairs for dispersion correction* Thanks in advance. Sadaf From 272699575 at qq.com Fri Apr 3 13:26:50 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Fri, 03 Apr 2020 11:26:50 -0000 Subject: [gmx-users] PCA analysis with different atoms in -s and -f In-Reply-To: References: Message-ID: Dear Eduardo, Many thanks for your detailed explanation. Sorry I am not an expert on the PCA. So I may need more explanations from you if you do not mind. Feel free to correct if I am wrong. I have done the common analysis to the MD run at different conditions, including RMSD, Rg, secondary structure, native contacts, etc. I can find some differences among those conditions. But I feel that there are infinite properties to choose to compare. So I am trying to find a more systematic way to quantify the difference. I found the "gmx anaeig -over" seems to be an ideal option. Can I ask, 1) How the "-ref" is used in the PCA analysis? i.e. How the "deviation" is used in the process of PCA? Do I need to fully understand the mathmatical equations in order to understand it? # -ref no (default) Use the deviation from the structure file (i.e. -s name.pdb) # -ref yes Use the deviation from the average of the trajectories 2) So far, I choose "MainChain" as the least square fit, and "C-alpha" for the PCA. I hope I can see the significant difference between the different conditions at the C-alpha level. But if not, I may choose "Backbone" or "MainChain" for the PCA. 3) Can you explain what is "long enough to have at least two halves of trajectory 0.pdb CA. 100% overlap of covariance matrices", and what is "block analysis to calculate overlap error as a function of time length"? Thank you! Yours sincerely Cheng ------------------ Original ------------------ From: "ZHANG Cheng"<272699575 at qq.com>; Date: Wed, Apr 1, 2020 09:10 AM To: "gromacs.org_gmx-users" Dear All, I need to scale the a and b parameters of a triclinic crystalline unit cell. When I use the editconf command, only the cell parameters are scaled while the coordinates of atoms are not remapped in the new cell. gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 1.9724 -angles 90.00 126.91 90.00 The unit cell consists of 4 polymer chains, each chain having 7 repeating (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. The original cell parameters are: a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, gamma: 90.00 Any suggestions how I can remap the coordinates (keeping the bonds and angles constant) together with scaling the box? Thanks, From qasimpars at gmail.com Fri Apr 3 23:12:34 2020 From: qasimpars at gmail.com (Qasim Pars) Date: Fri, 03 Apr 2020 21:12:34 -0000 Subject: [gmx-users] change the top file of a homodimer protein Message-ID: Dear users, My protein has a homodimer structure. Here is the last part of the topology (.top) file: [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 The topology (.itp) files of both chains are the same. My question is that can I change the last part of the topology file as follows? [ molecules ] ; Compound #mols Protein 2 Thanks in advance, -- Qasim Pars From jalemkul at vt.edu Fri Apr 3 23:14:11 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 03 Apr 2020 21:14:11 -0000 Subject: [gmx-users] change the top file of a homodimer protein In-Reply-To: References: Message-ID: <4b508194-1c6d-913a-6833-d02bc9f5a683@vt.edu> On 4/3/20 5:12 PM, Qasim Pars wrote: > Dear users, > > My protein has a homodimer structure. Here is the last part of the topology > (.top) file: > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_B 1 > > The topology (.itp) files of both chains are the same. My question is that > can I change the last part of the topology file as follows? > [ molecules ] > ; Compound #mols > Protein 2 Not without modifying/removing #include statements and renaming the [moleculetype] in one of those #included .itp files to "Protein" -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From salman.zarrini at gmail.com Fri Apr 3 23:53:46 2020 From: salman.zarrini at gmail.com (Salman Zarrini) Date: Fri, 03 Apr 2020 21:53:46 -0000 Subject: [gmx-users] Scale Triclinic Box In-Reply-To: References: Message-ID: Hi Maryam, The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I am just not sure if it could handle a triclinic cell. Since your unit cell is not that large, you even can use Avogadro or ASE-gui which both are good molecule editors and visualizers. Cheers, Salman On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi wrote: > Dear All, > > I need to scale the a and b parameters of a triclinic crystalline unit > cell. When I use the editconf command, only the cell parameters are scaled > while the coordinates of atoms are not remapped in the new cell. > > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 > 1.9724 -angles 90.00 126.91 90.00 > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, > 340 angles and 376 dihedrals. > > The original cell parameters are: > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > gamma: 90.00 > > Any suggestions how I can remap the coordinates (keeping the bonds and > angles constant) together with scaling the box? > > Thanks, > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From hcgeorg at ufg.br Sat Apr 4 03:13:11 2020 From: hcgeorg at ufg.br (Herbert de Castro Georg) Date: Sat, 04 Apr 2020 01:13:11 -0000 Subject: [gmx-users] How to parametrize a new molecule? Message-ID: Dear users, I want to perform a simulation of a molecule inside DNA. I'm probably going to use CHARMM for DNA. But how do I parametrize the molecule? Thanks in advance. Yours, Herbert Georg From jalemkul at vt.edu Sat Apr 4 03:15:03 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 04 Apr 2020 01:15:03 -0000 Subject: [gmx-users] How to parametrize a new molecule? In-Reply-To: References: Message-ID: On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > Dear users, > > I want to perform a simulation of a molecule inside DNA. I'm probably going > to use CHARMM for DNA. But how do I parametrize the molecule? http://cgenff.umaryland.edu/ -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From hcgeorg at ufg.br Sat Apr 4 03:20:54 2020 From: hcgeorg at ufg.br (Herbert de Castro Georg) Date: Sat, 04 Apr 2020 01:20:54 -0000 Subject: [gmx-users] How to parametrize a new molecule? In-Reply-To: References: Message-ID: Thanks, Justin! Em sex., 3 de abr. de 2020 ?s 22:15, Justin Lemkul escreveu: > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > Dear users, > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > going > > to use CHARMM for DNA. But how do I parametrize the molecule? > > http://cgenff.umaryland.edu/ > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From maryam.sadeghi.90 at gmail.com Sat Apr 4 05:16:39 2020 From: maryam.sadeghi.90 at gmail.com (Maryam Sadeghi) Date: Sat, 04 Apr 2020 03:16:39 -0000 Subject: [gmx-users] Scale Triclinic Box In-Reply-To: References: Message-ID: Hi Salman, Tnx for the info, I actually want to do the cold-compression on my crystalline structure. So basically I need to both compress and expand the a and b parameters of the unit cell (the c parameter is already optimized)... so it's not just building a supercell, but rather scaling only 2 parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this? Best Maryam On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini wrote: > Hi Maryam, > > The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I > am just not sure if it could handle a triclinic cell. > Since your unit cell is not that large, you even can use Avogadro or > ASE-gui which both are good molecule editors and visualizers. > > Cheers, > Salman > > On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi > > wrote: > > > Dear All, > > > > I need to scale the a and b parameters of a triclinic crystalline unit > > cell. When I use the editconf command, only the cell parameters are > scaled > > while the coordinates of atoms are not remapped in the new cell. > > > > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 > 0.5686 > > 1.9724 -angles 90.00 126.91 90.00 > > > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 > bonds, > > 340 angles and 376 dihedrals. > > > > The original cell parameters are: > > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > > gamma: 90.00 > > > > Any suggestions how I can remap the coordinates (keeping the bonds and > > angles constant) together with scaling the box? > > > > Thanks, > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From poojakesari10 at gmail.com Sat Apr 4 09:55:30 2020 From: poojakesari10 at gmail.com (pooja kesari) Date: Sat, 04 Apr 2020 07:55:30 -0000 Subject: [gmx-users] Calculate probability of presence of water around a residues Message-ID: Dear Users, I have two queries 1. I have tried using the select command to Calculate probability of presence of water around a residues by creating an a group in my index analyze.ndx contains a group named ser76 which has the atom position near which i want to find this water (say atom 1313) *gmx select -s md_0_1.tpr -f md_0_1_center.xtc -os no_solv.xvg -select 'name OW and within 0.3 of group ser76' -n analyze.ndx* This command gives an error Error in user input: Selection 'name OW and within 0.3 of group ser76' never matches any atoms. 2. Regarding *MMPBSA calculation* for my protein-ligand simulation. i m using GROMACS 2018 version on the server. What is the procedure for doing the same. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay INDIA From jalemkul at vt.edu Sat Apr 4 13:54:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 04 Apr 2020 11:54:21 -0000 Subject: [gmx-users] Scale Triclinic Box In-Reply-To: References: Message-ID: <417c4691-9844-7d6e-8d64-badaee2ca055@vt.edu> On 4/3/20 11:16 PM, Maryam Sadeghi wrote: > Hi Salman, > > Tnx for the info, I actually want to do the cold-compression on my > crystalline structure. So basically I need to both compress and expand the > a and b parameters of the unit cell (the c parameter is already > optimized)... so it's not just building a supercell, but rather scaling > only 2 parameters of the unit cell simultaneously while remaping the new > coordinates inside the scaled cell... could "gmx genconf -nbox ... ... > ..." handle this? It sounds like you need to actually perform a simulation in which high pressure is applied to compress the box. genconf is for duplicating a box N times in each dimension, and while you can change box vectors and scale coordinates with editconf (-scale option), this is not the same as compressing them and bond lengths, etc. will become distorted. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From scinikhil at gmail.com Sat Apr 4 16:18:59 2020 From: scinikhil at gmail.com (Nikhil Maroli) Date: Sat, 04 Apr 2020 14:18:59 -0000 Subject: [gmx-users] How to use GROMACS license? Message-ID: Dear GMX team, The GROMACS license allows one to use the codes inside a proprietary software? Basically, building a GUI and selling it for a higher price? -- Regards, Nikhil Maroli From spoel at xray.bmc.uu.se Sat Apr 4 17:24:25 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 04 Apr 2020 15:24:25 -0000 Subject: [gmx-users] How to use GROMACS license? In-Reply-To: References: Message-ID: Den 2020-04-04 kl. 16:18, skrev Nikhil Maroli: > Dear GMX team, > > The GROMACS license allows one to use the codes inside a proprietary > software? Basically, building a GUI and selling it for a higher price? > Yes. As long as modifications to gromacs are available under the LGPL license as well. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From mehdi.bpour at gmail.com Sat Apr 4 17:57:23 2020 From: mehdi.bpour at gmail.com (Mahdi Bagherpoor) Date: Sat, 04 Apr 2020 15:57:23 -0000 Subject: [gmx-users] How to parametrize a new molecule? In-Reply-To: References: Message-ID: Hello Herbert, Not related to your question, but be careful if you are going to use CHARMM36 force field for DNA, as a recent study ( https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does not preserve DNA stability at a longer time scale, in case you are going to do so. Best, Mahdi On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg wrote: > Thanks, Justin! > > > > Em sex., 3 de abr. de 2020 ?s 22:15, Justin Lemkul > escreveu: > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > Dear users, > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > going > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > http://cgenff.umaryland.edu/ > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From Weitse.Hsu at colorado.edu Sat Apr 4 22:40:43 2020 From: Weitse.Hsu at colorado.edu (Wei-Tse Hsu) Date: Sat, 04 Apr 2020 20:40:43 -0000 Subject: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0 Message-ID: Dear gmx users, Recently I've been trying to install GROMACS 2020.1. However, I encounter a compilation error while using the make command. The error is as follows: */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* >From the error above, it seemed that GROMACS was unable to find library like libpthread.so.0 and libpthread_nonshared.a. After checking I found that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add the paths of the libraries for GROMACS to search for. Specifically, the command I was using is: *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > gmx_compile.log* However, it turned out that I still got the same error. I'm confused right now since I thought that gromacs should be able to find the files. I'm wondering if I missed something. Could someone please tell me what I can do or share some relevant experience? Any help is much appreciated! Best, Wei-Tse From maryam.sadeghi.90 at gmail.com Sat Apr 4 23:04:56 2020 From: maryam.sadeghi.90 at gmail.com (Maryam Sadeghi) Date: Sat, 04 Apr 2020 21:04:56 -0000 Subject: [gmx-users] Scale Triclinic Box In-Reply-To: <417c4691-9844-7d6e-8d64-badaee2ca055@vt.edu> References: <417c4691-9844-7d6e-8d64-badaee2ca055@vt.edu> Message-ID: Hi Justin, I actually want to scale the box (both moving the chains apart and close to each other by changing the a and b parameters of the cell). I don't want to run any dynamics at this point as I have already done quantum mechanics minimization on this structure. When I use the editconf command the cell parameters change but the coordinates of the atoms remain unchanged, i.e. by compression the polymer chains remain outside of the cell... I was wondering if editconf could scale the coordinates proportionally with the cell parameters without distorting the bonds lengths? gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 1.9724 -angles 90.00 126.91 90.00 The original cell parameters are: a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, gamma: 90.00 The unit cell consists of 4 polymer chains, each chain having 7 repeating (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. Best Maryam On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul wrote: > > > On 4/3/20 11:16 PM, Maryam Sadeghi wrote: > > Hi Salman, > > > > Tnx for the info, I actually want to do the cold-compression on my > > crystalline structure. So basically I need to both compress and expand > the > > a and b parameters of the unit cell (the c parameter is already > > optimized)... so it's not just building a supercell, but rather scaling > > only 2 parameters of the unit cell simultaneously while remaping the new > > coordinates inside the scaled cell... could "gmx genconf -nbox ... ... > > ..." handle this? > > It sounds like you need to actually perform a simulation in which high > pressure is applied to compress the box. genconf is for duplicating a > box N times in each dimension, and while you can change box vectors and > scale coordinates with editconf (-scale option), this is not the same as > compressing them and bond lengths, etc. will become distorted. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > From jalemkul at vt.edu Sat Apr 4 23:08:20 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 04 Apr 2020 21:08:20 -0000 Subject: [gmx-users] Scale Triclinic Box In-Reply-To: References: <417c4691-9844-7d6e-8d64-badaee2ca055@vt.edu> Message-ID: On 4/4/20 5:07 PM, Maryam Sadeghi wrote: > Hi Justin, > I actually want to scale the box (both moving the chains apart and close to > each other by changing the a and b parameters of the cell). I don't want to > run any dynamics at this point as I have already done quantum mechanics > minimization on this structure. When I use the editconf command the cell > parameters change but the coordinates of the atoms remain unchanged, i.e. > by compression the polymer chains remain outside of the cell... I was > wondering if editconf could scale the coordinates proportionally with the > cell parameters without distorting the bonds lengths? You can apply a scaling vector with editconf -scale as I suggested in my last message, but I do not think it will do what you want. That's the only GROMACS tool that has any such capability, so if that doesn't work, GROMACS isn't going to do what you want. -Justin > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 > 1.9724 -angles 90.00 126.91 90.00 > > The original cell parameters are: > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > gamma: 90.00 > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, > 340 angles and 376 dihedrals. > > Best > Maryam > > > > > On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul wrote: > >> >> On 4/3/20 11:16 PM, Maryam Sadeghi wrote: >>> Hi Salman, >>> >>> Tnx for the info, I actually want to do the cold-compression on my >>> crystalline structure. So basically I need to both compress and expand >> the >>> a and b parameters of the unit cell (the c parameter is already >>> optimized)... so it's not just building a supercell, but rather scaling >>> only 2 parameters of the unit cell simultaneously while remaping the new >>> coordinates inside the scaled cell... could "gmx genconf -nbox ... ... >>> ..." handle this? >> It sounds like you need to actually perform a simulation in which high >> pressure is applied to compress the box. genconf is for duplicating a >> box N times in each dimension, and while you can change box vectors and >> scale coordinates with editconf (-scale option), this is not the same as >> compressing them and bond lengths, etc. will become distorted. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From kevin.boyd at uconn.edu Sun Apr 5 00:12:52 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 04 Apr 2020 22:12:52 -0000 Subject: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0 In-Reply-To: References: Message-ID: Hi, I've had problems in the past with syntax requirements for CMAKE_PREFIX_PATH. Try putting the path in quotes and separating with a semicolon instead of a colon. Kevin On Sat, Apr 4, 2020 at 1:40 PM Wei-Tse Hsu wrote: > *Message sent from a system outside of UConn.* > > > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From vuqv.phys at gmail.com Sun Apr 5 13:10:01 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Sun, 05 Apr 2020 11:10:01 -0000 Subject: [gmx-users] Issue with PMF In-Reply-To: <3d42d466-afe8-2108-27d0-0c6586f8c752@vt.edu> References: <3d42d466-afe8-2108-27d0-0c6586f8c752@vt.edu> Message-ID: Dear Justin, In your tutorial, you selected the initial configuration for each umbrella by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)] and in umbrella sampling simulation, your setting is: pull_coord1_dim = N N Y pull_coord1_start = yes so as the draw I attached here you can see that conf1,conf2 and conf3 are satisfied the distance criteria and you used the staring z-separation as reaction coordinates, this mean umbrella 1 and 2 will sample the same region while the region between zeta_1 and zeta_3 is not sampled well if |zeta3-zeta1| is large. https://drive.google.com/open?id=1nUKLmaBhjL29ZadgUcPk6DlG08ZVP_Nx Is it true? Best regards, Quyen On Thu, Apr 2, 2020 at 10:28 PM Justin Lemkul wrote: > > > On 4/2/20 4:19 PM, Alex wrote: > > Thanks Justin for the response. > > > > On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul wrote: > > > >> > >> On 4/2/20 12:53 PM, Alex wrote: > >>> Dear all, > >>> By using the below setting I am getting a very nice umbrella histogram > >> and > >>> iact also shows a very good integrated Autocorrelation time. However, > the > >>> PMF profile is unexpected. Below I have also provided a gmx wham > command > >> I > >>> am using, part of the pullx.xvg of one of the windows and also > >>> corresponding part in log file. > >>> Would you please help me find out what the problem might be? > >> What is the problem? > >> > > Below link shows the histogram and PMF, actually I was expecting that the > > PMF reach a plateau in the region marked by B in the figure as we are > fully > > inside the bulk area of the thin film. However, there are some region > from > > 15 to 20 kcal/mol different respect to the expected plateau. Here we have > > 10nm thick thin film. > > > > https://drive.google.com/open?id=1ve50thHG4wORe0-fKdoIsPncQpEyuwcz > > > > Bootstrapping may underestimate the real error. How well converged is > the PMF with respect to time, e.g. computing the PMF from the first half > and last half of the simulation time? > > >>> One more question: does it make sense to manually shift the plateau of > >> the > >>> PMF plot to zero (when we plot it), instead of using using the -zprof0 > >> flag? > >> > >> There is no difference. The -zprof0 just adds a constant so the PMF is > >> zero at the specified point on the reaction coordinate. > >> > >>> %-------------------------------- > >>> pull = yes > >>> pull-ngroups = 2 > >>> pull-ncoords = 1 > >>> pull-group1-name = Mol_A > >>> pull-group2-name = Thin_film > >>> > >>> pull-coord1-groups = 1 2 > >>> pull-coord1-type = umbrella > >>> pull-coord1-dim = N N Y > >>> pull-coord1-start = no ;--> manually we define the distance > for > >>> all windows > >>> pull-coord1-rate = 0.0 ;--> We don't want the roups to move > >>> pull-coord1-geometry = distance > >>> pull-coord1-k = 10000 ;;kJ/(mol nm^2) > >>> pull-print-components = Yes > >>> pull-nstxout = 2000 > >>> pull-nstfout = 2000 > >>> pull-print-com1 = yes > >>> pull-coord1-init = 1.650000 > >>> %------------------------------------ > >>> #Part of the one of the pullx.xvg file > >>> @ legend length 2 > >>> @ s0 legend "1" > >>> @ s1 legend "1 dZ" > >>> @ s2 legend "1 g 1 Z" > >>> @ s3 legend "1 g 2 Z" > >>> 0.0000 0.0155171 0.0155171 9.89805 9.91357 > >>> 2.0000 0.0103956 0.0103956 9.90227 9.91266 > >>> 4.0000 0.0146962 0.0146962 9.89733 9.91202 > >>> 6.0000 0.00656533 0.00656533 9.90404 9.91061 > >>> 8.0000 0.00228074 0.00228074 9.90945 9.91174 > >>> 10.0000 0.00967605 0.00967605 9.90514 9.91482 > >>> .... > >>> %-------------------------------------------- > >>> gmx_mpi wham -hist Histo.xvg -nBootstrap 200 -bins 200 -bs-method > b-hist > >>> -bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -ac > -o > >>> profile.xvg -b 3000 -unit kCal -v > >>> > >>> %------------------------------------------------ > >>> #Similar massage as below I have for all windows (tpr files). > >>> Reading file prd.1.tpr, VERSION 2018.7 (single precision) > >>> > >>> File prd.1.tpr, 1 coordinates, with these options: > >>> Geometry distance k = 10000 position = 0 > >> dimensions > >>> [N N Y] (1 dimensions). Used: Yes > >>> Pull group coordinates of 2 groups expected in pullx files. > >>> Reference value of the coordinate not expected in pullx > files. > >>> > >>> Reading pull force file prd_pullf.1.xvg, expecting 2 columns: > >>> Columns for pull coordinate 1 > >>> reaction coordinate: 1 > >>> center-of-mass of groups: 0 > >>> reference position column: No > >>> Found 2501 times in prd_pullf.1.xvg > >>> %---------------------------------------------------------- > > Actually, I was suspicious of these "Reference value of the coordinate > not > > expected in pullx files." and "reference position column: No" > which > > I have in log file of gmx wham for each windows's tpr. > > I have no experience with that; the pullx.xvg file format has changed a > lot over time. I always use pullf.xvg and it's never an issue. > > > Concerning your PMF tutorial, when the distance between chain_A and > chain_B > > is calculated by gmx distance, why the -oall is used to get the absolute > > distance out of x,y and z, while the -oxyz would be much better as we can > > take the Z component of the distance similar (corresponding) to the > > considered reaction coordinate in the tutorial? > > The two quantities should be essentially equivalent for the purposes of > the tutorial. > > -Justin > > > Regards, > > Alex > > > >>> Thank you, > >>> Alex > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Sun Apr 5 14:29:48 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 05 Apr 2020 12:29:48 -0000 Subject: [gmx-users] Issue with PMF In-Reply-To: References: <3d42d466-afe8-2108-27d0-0c6586f8c752@vt.edu> Message-ID: <2887db96-3c4b-6979-3c54-24afb7e7cd84@vt.edu> On 4/5/20 7:13 AM, Quyen V. Vu wrote: > Dear Justin, > In your tutorial, you selected the initial configuration for each umbrella > by the radial distance between chain A and B [ r = sqrt(x^2+y^2+z^2)] > and in umbrella sampling simulation, your setting is: > pull_coord1_dim = N N Y > > pull_coord1_start = yes > > so as the draw I attached here you can see that conf1,conf2 and conf3 > are satisfied the distance criteria and you used the staring > z-separation as reaction coordinates, this mean umbrella 1 and 2 will > sample the same region while the region between zeta_1 and zeta_3 is > not sampled well if |zeta3-zeta1| is large. > > https://drive.google.com/open?id=1nUKLmaBhjL29ZadgUcPk6DlG08ZVP_Nx > > Is it true? Of course it is possible to draw infinitely many configurations that satisfy one dimension but not the total distance. The tutorial uses COM distance primarily for generating reasonable starting configurations, and over the time scale used, the z-distance and COM distance should not differ much (I proved this to my self 10 years ago when I first wrote the tutorial and did the underlying study). The restraint is applied along z only during the umbrella sampling and that is the reaction coordinate for which the free energy change is computed. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From Weitse.Hsu at colorado.edu Sun Apr 5 21:23:28 2020 From: Weitse.Hsu at colorado.edu (Wei-Tse Hsu) Date: Sun, 05 Apr 2020 19:23:28 -0000 Subject: [gmx-users] GROMACS 2020.1 failed to pass make check Message-ID: Dear gmx users, Recently I've been trying to install GROMACS 20201. After successfully compilng GROMACS 2020.1, when executing make check command, I encountered the following error. Specifically, one out of 56 tests failed, which was related to Mdrun Test.WritesHelp. Looking at the error message, I'm still not sure what it means and how I should solve this problem. I wonder if anyone had this before that could give me some insights about how I could solve the problem. Any help would be appreciated! Here is the error message in the middle. *[----------] 1 test from MdrunTest[ RUN ] MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867: Failure In item: /Help string Actual: 'SYNOPSIS* And here is the error message in the end. *The following tests FAILED: 43 - MdrunTests (Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target 'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all' failedCMakeFiles/Makefile2:445: recipe for target 'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check' failed* And here is the whole STDOUT message of the command printed by make *check > make_check.log*. https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing Best, Wei-Tse From marko at kth.se Sun Apr 5 23:05:43 2020 From: marko at kth.se (Marko Petrovic) Date: Sun, 05 Apr 2020 21:05:43 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling Message-ID: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> Hello. I've been trying to do coordinate pulling of dihedral angles of an alanine dipeptide in vacuum and used the umbrella sampling tutorial as a starting point. I'm trying to generate initial configurations for later runs, but the mdrun ends in a segmentation fault with error messages like: Step 15707, time 31.414 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025328, max 0.098100 (between atoms 11 and 13) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 90.4 0.1006 0.1054 0.0997 11 13 90.2 0.1110 0.1220 0.1111 Step 15708, time 31.416 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 52572448.000000, max 238546496.000000 (between atoms 7 and 8) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 109.3 0.1054 23783084.0000 0.0997 9 11 119.5 0.1543 1995948.6250 0.1538 11 12 162.6 0.1127 1995948.6250 0.1111 11 13 115.6 0.1220 1995948.5000 0.1111 11 14 112.7 0.1124 1995948.6250 0.1111 Wrote pdb files with previous and current coordinates Segmentation fault: 11 Perhaps the seg fault is not related to the warnings at all but as I am not certain what they mean and do think they are enough to cause some problems anyway I would like to understand them in general and also know what columns previous and current are saying. As the original tutorial was done for a water solution and mine is conducted in vacuum I am guessing my modifications to the .mdp files are not completely updated so any tips on that woul also be helpful. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalemkul at vt.edu Sun Apr 5 23:10:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 05 Apr 2020 21:10:05 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling In-Reply-To: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> References: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> Message-ID: <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> On 4/5/20 5:05 PM, Marko Petrovic wrote: > Hello. > > I've been trying to do coordinate pulling of dihedral angles of an alanine dipeptide in vacuum and used the umbrella sampling tutorial as a starting point. I'm trying to generate initial configurations for later runs, but the mdrun ends in a segmentation fault with error messages like: > > Step 15707, time 31.414 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.025328, max 0.098100 (between atoms 11 and 13) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 7 8 90.4 0.1006 0.1054 0.0997 > 11 13 90.2 0.1110 0.1220 0.1111 > > Step 15708, time 31.416 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 52572448.000000, max 238546496.000000 (between atoms 7 and 8) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 7 8 109.3 0.1054 23783084.0000 0.0997 > 9 11 119.5 0.1543 1995948.6250 0.1538 > 11 12 162.6 0.1127 1995948.6250 0.1111 > 11 13 115.6 0.1220 1995948.5000 0.1111 > 11 14 112.7 0.1124 1995948.6250 0.1111 > Wrote pdb files with previous and current coordinates > Segmentation fault: 11 > > Perhaps the seg fault is not related to the warnings at all but as I am not certain what they mean and do think they are enough to cause some problems anyway I would like to understand them in general and also know what columns previous and current are saying. They refer to bond lengths, what the length was at the previous step and what it is now, compared to what the reference value should be. Your values indicate catastrophic distortion of the structure. > As the original tutorial was done for a water solution and mine is conducted in vacuum I am guessing my modifications to the .mdp files are not completely updated so any tips on that woul also be helpful. There's no way to provide any useful advice without you posting your .mdp file. Note that the umbrella sampling tutorial has basically no relevance to anything you're doing because enforced dihedral rotation didn't exist when I wrote it :) -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From marko at kth.se Mon Apr 6 08:33:50 2020 From: marko at kth.se (Marko Petrovic) Date: Mon, 06 Apr 2020 06:33:50 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling In-Reply-To: <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> References: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> Message-ID: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 5 Apr 2020, at 23:09, Justin Lemkul > wrote: On 4/5/20 5:05 PM, Marko Petrovic wrote: Hello. I've been trying to do coordinate pulling of dihedral angles of an alanine dipeptide in vacuum and used the umbrella sampling tutorial as a starting point. I'm trying to generate initial configurations for later runs, but the mdrun ends in a segmentation fault with error messages like: Step 15707, time 31.414 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025328, max 0.098100 (between atoms 11 and 13) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 90.4 0.1006 0.1054 0.0997 11 13 90.2 0.1110 0.1220 0.1111 Step 15708, time 31.416 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 52572448.000000, max 238546496.000000 (between atoms 7 and 8) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 109.3 0.1054 23783084.0000 0.0997 9 11 119.5 0.1543 1995948.6250 0.1538 11 12 162.6 0.1127 1995948.6250 0.1111 11 13 115.6 0.1220 1995948.5000 0.1111 11 14 112.7 0.1124 1995948.6250 0.1111 Wrote pdb files with previous and current coordinates Segmentation fault: 11 Perhaps the seg fault is not related to the warnings at all but as I am not certain what they mean and do think they are enough to cause some problems anyway I would like to understand them in general and also know what columns previous and current are saying. They refer to bond lengths, what the length was at the previous step and what it is now, compared to what the reference value should be. Your values indicate catastrophic distortion of the structure. As the original tutorial was done for a water solution and mine is conducted in vacuum I am guessing my modifications to the .mdp files are not completely updated so any tips on that woul also be helpful. There's no way to provide any useful advice without you posting your .mdp file. Note that the umbrella sampling tutorial has basically no relevance to anything you're doing because enforced dihedral rotation didn't exist when I wrote it :) -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From paul.bauer.q at gmail.com Mon Apr 6 09:23:23 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 06 Apr 2020 07:23:23 -0000 Subject: [gmx-users] GROMACS 2020.1 failed to pass make check In-Reply-To: References: Message-ID: Hello, you are using a plumed modified version that adds extra options to mdrun. Our unit tests check that the output from mdrun -h stays invariant, and this is no longer the case once you modify the code for plumed. You can ignore this failure in this case, but please mention in the future if you are using modified versions of the code. Cheers Paul On 05/04/2020 21:23, Wei-Tse Hsu wrote: > Dear gmx users, > Recently I've been trying to install GROMACS 20201. After successfully > compilng GROMACS 2020.1, when executing make check command, I > encountered the following error. Specifically, one out of 56 tests failed, > which was related to Mdrun Test.WritesHelp. Looking at the error message, > I'm still not sure what it means and how I should solve this problem. I > wonder if anyone had this before that could give me some insights about how > I could solve the problem. Any help would be appreciated! > > Here is the error message in the middle. > > > > > > *[----------] 1 test from MdrunTest[ RUN ] > MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867: > Failure In item: /Help string Actual: 'SYNOPSIS* > And here is the error message in the end. > > > > > > *The following tests FAILED: 43 - MdrunTests > (Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target > 'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for > target 'CMakeFiles/run-ctest-nophys.dir/all' > failedCMakeFiles/Makefile2:445: recipe for target > 'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check' > failed* > > And here is the whole STDOUT message of the command printed by make *check >> make_check.log*. > https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing > > Best, > Wei-Tse -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From sinaomrani96 at gmail.com Mon Apr 6 13:24:31 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Mon, 06 Apr 2020 11:24:31 -0000 Subject: [gmx-users] Bonds definition in itp files Message-ID: Hi, I wanted to know how we specify a bond order in our simulation? For example, if we have a triple bond in our structure between atoms 1 and 2, is it by length and force constants or we define 1 and 2 bonds three times in the bond section of itp file? What if we use a constraint on this bond? because I get better results when I define the bond three times but haven't seen this method. is it wrong? Thank you. Sina Omrani. From jluquedisalvo at gmail.com Mon Apr 6 14:10:17 2020 From: jluquedisalvo at gmail.com (Javier Luque Di Salvo) Date: Mon, 06 Apr 2020 12:10:17 -0000 Subject: [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx Message-ID: Dear Gromacs users, I'm aware that there might be plenty of discussions on this matter, anyway I would like to get your advice. Which is the proper way to know the protonation state that is generated with pdb2gmx? I have downloaded a pdb file from the Protein Data Bank. The structure has no hydrogens, these are added by pdb2mx. Is this information usually available on the original pdb (like residue names) or in the generated topology? I would like to know where to search. Javier -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universit? Degli Studi di Palerm*o* From jluquedisalvo at gmail.com Mon Apr 6 14:14:53 2020 From: jluquedisalvo at gmail.com (Javier Luque Di Salvo) Date: Mon, 06 Apr 2020 12:14:53 -0000 Subject: [gmx-users] NAG N-Acetylglucosamine force field parameters Message-ID: Dear Gromacs users, Do you know where can I search for force field parameters of N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force fields, my Gromacs version is 2018.3 Thanks in advance, Javier -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universit? Degli Studi di Palerm*o* From tommaso.casalini at chem.ethz.ch Mon Apr 6 14:23:00 2020 From: tommaso.casalini at chem.ethz.ch (Casalini Tommaso) Date: Mon, 06 Apr 2020 12:23:00 -0000 Subject: [gmx-users] NAG N-Acetylglucosamine force field parameters In-Reply-To: References: Message-ID: Dear Javier, NAG is surely available in the GLYCAM library, an AMBER-based force field. Pay attention to the scaling factors when you use GLYCAM force field, especially if you use it with other AMBER-based FF (which are mutually compatible) in GROMACS. Best, Tommaso ________________________________ Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se per conto di Javier Luque Di Salvo Inviato: luned? 6 aprile 2020 14:14:39 A: gromacs.org_gmx-users at maillist.sys.kth.se Oggetto: [gmx-users] NAG N-Acetylglucosamine force field parameters Dear Gromacs users, Do you know where can I search for force field parameters of N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force fields, my Gromacs version is 2018.3 Thanks in advance, Javier -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universit? Degli Studi di Palerm*o* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From tommaso.casalini at chem.ethz.ch Mon Apr 6 14:23:01 2020 From: tommaso.casalini at chem.ethz.ch (Casalini Tommaso) Date: Mon, 06 Apr 2020 12:23:01 -0000 Subject: [gmx-users] NAG N-Acetylglucosamine force field parameters In-Reply-To: References: Message-ID: Dear Javier, NAG is surely available in the GLYCAM library, an AMBER-based force field. Pay attention to the scaling factors when you use GLYCAM force field, especially if you use it with other AMBER-based FF (which are mutually compatible) in GROMACS. Best, Tommaso ________________________________ Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se per conto di Javier Luque Di Salvo Inviato: luned? 6 aprile 2020 14:14:39 A: gromacs.org_gmx-users at maillist.sys.kth.se Oggetto: [gmx-users] NAG N-Acetylglucosamine force field parameters Dear Gromacs users, Do you know where can I search for force field parameters of N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force fields, my Gromacs version is 2018.3 Thanks in advance, Javier -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universit? Degli Studi di Palerm*o* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Mon Apr 6 14:41:00 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 12:41:00 -0000 Subject: [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx In-Reply-To: References: Message-ID: <12baec17-4ce5-c707-c30f-96d3d6591871@vt.edu> On 4/6/20 8:10 AM, Javier Luque Di Salvo wrote: > Dear Gromacs users, > > I'm aware that there might be plenty of discussions on this matter, anyway > I would like to get your advice. Which is the proper way to know the > protonation state that is generated with pdb2gmx? I have downloaded a pdb > file from the Protein Data Bank. The structure has no hydrogens, these are > added by pdb2mx. > > Is this information usually available on the original pdb (like residue > names) or in the generated topology? I would like to know where to search. pdb2gmx assigns protonation states at neutral pH assuming canonical pKa values for all residues. That assumption is usually good, but obviously is not always correct, in which case you need to manually assign the protonation states using command-line options. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Mon Apr 6 14:42:11 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 12:42:11 -0000 Subject: [gmx-users] Bonds definition in itp files In-Reply-To: References: Message-ID: <544c8c52-b75e-8a25-b9c2-199425e86264@vt.edu> On 4/6/20 7:24 AM, Sina Omrani wrote: > Hi, > I wanted to know how we specify a bond order in our simulation? For > example, if we have a triple bond in our structure between atoms 1 and 2, > is it by length and force constants or we define 1 and 2 bonds three times > in the bond section of itp file? > What if we use a constraint on this bond? because I get better results when > I define the bond three times but haven't seen this method. is it wrong? All interactions should be defined only once, and the parameters used should produce correct behavior. MM force fields have no concept of double or triple bonds; they only know the stiffness of the spring connecting the atoms. My guess is that if you had to add the bond three times, the force field parameters are adding together, indicating that the force constant is unsuitable for what you're trying to and needs to be refined. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Mon Apr 6 14:44:33 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 12:44:33 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling In-Reply-To: References: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> Message-ID: <321a4fe9-60c5-fd66-4e70-41d9de94ffb1@vt.edu> On 4/6/20 2:33 AM, Marko Petrovic wrote: > I figure it might be helpful to see my other files so I include a link: > https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin > Your dihedral definitions are simply incorrect. pull_coord1_groups = 1 2 2 3 3 4 pull_coord2_groups = 2 3 3 4 4 5 should be pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From goossens_kenny at hotmail.com Mon Apr 6 14:44:49 2020 From: goossens_kenny at hotmail.com (Kenny Goossens) Date: Mon, 06 Apr 2020 12:44:49 -0000 Subject: [gmx-users] NAG N-Acetylglucosamine force field parameters In-Reply-To: References: Message-ID: Dear Javier, The way GROMOS force fields are parameterized allows building blocks to be linked together and still provide a good model. You can find parameters for glucose in the force field (in the aminoacids.rtp file) and from there on, you only need to find adequate parameters for the N-acetyl group. You can try using the ATB web server but keep in mind to also validate the parameters that are generated in that case. For CHARMM, you can try using the glycan reader & modeler tool in the CHARMM-GUI web server, which should also provide adequate parameters. With kind regards, ______________________________ Kenneth Goossens, PhD student Laboratory of Medicinal Chemistry (Building A - Room 2.13) University of Antwerp - Campus Drie Eiken Universiteitsplein 1 B-2610 Wilrijk Belgium ________________________________ Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se namens Javier Luque Di Salvo Verzonden: maandag 6 april 2020 14:14 Aan: gromacs.org_gmx-users at maillist.sys.kth.se Onderwerp: [gmx-users] NAG N-Acetylglucosamine force field parameters Dear Gromacs users, Do you know where can I search for force field parameters of N-Acetylglucosamine (NAG)? I'm interested in AMBER, CHARMM and GROMOS force fields, my Gromacs version is 2018.3 Thanks in advance, Javier -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universit? Degli Studi di Palerm*o* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From pall.szilard at gmail.com Mon Apr 6 15:15:24 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 06 Apr 2020 13:15:24 -0000 Subject: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0 In-Reply-To: References: Message-ID: On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu wrote: > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > As Kevin noted, the separator in the prefix path should be ";". However, it seem unnecessary to pass system libraries as custom paths to cmake. Try first without those. -- Szil?rd > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pall.szilard at gmail.com Mon Apr 6 15:15:24 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 06 Apr 2020 13:15:24 -0000 Subject: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0 In-Reply-To: References: Message-ID: On Sat, Apr 4, 2020 at 10:41 PM Wei-Tse Hsu wrote: > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > As Kevin noted, the separator in the prefix path should be ";". However, it seem unnecessary to pass system libraries as custom paths to cmake. Try first without those. -- Szil?rd > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pall.szilard at gmail.com Mon Apr 6 15:25:23 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 06 Apr 2020 13:25:23 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" In-Reply-To: References: Message-ID: On Fri, Mar 27, 2020 at 8:30 PM Leandro Bortot wrote: > Dear users, > > I'm trying to optimize the execution of a system composed by 10 > million atoms on a multi-GPU machine with GROMACS 2020.1. > I've followed the instructions given at > > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ > . However, when I run my simulation, mdrun tells me this: > > " > > *Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU > environment variable, but the following condition(s) were not > satisfied:Domain decomposition without GPU halo exchange is not supported.* > " > > My understanding was that exporting *GMX_GPU_DD_COMMS=true* would > enable such halo communications. > My simulation runs, however the performance is not scaling well with > the number of GPUs. > > I've done the following: > " > > *export GMX_GPU_DD_COMMS=trueexport GMX_GPU_PME_PP_COMMS=trueexport > GMX_FORCE_UPDATE_DEFAULT_GPU=true*" > You are getting the error below because you did not export all three variables there. Those exports are separate commands and need to be issued with some separator, e.g. semicolon or newline. > And my execution line is: > "*mpirun -np 4 gmx_mpi mdrun -s eq.1.tpr -v -deffnm eq.1 -pin on -ntomp 6 > -npme 1 -nb gpu -bonded gpu -pme gpu -nstlist 400*" > Beware that this command line is specific for one use-case presented in your source (i.e. that very hardware and input system) and may not be fully transferable (e.g. "-ntomp 6" or "-nstlist 400"). Cheers, -- Szil?rd > > If I add "-update gpu" to this same line I have the following error: > " > > > > > *Inconsistency in user input:Update task on the GPU was required,but the > following condition(s) were not satisfied:Domain decomposition without GPU > halo exchange is not supported. With separate PME rank(s), PME must use > direct communication.*" > > Also, I'm using constraints = h-bonds in my .mdp file. > > Am I doing something wrong? > > Thank you for your attention, > Leandro > ------- > Leandro Oliveira Bortot > Postdoctoral Fellow > https://www.linkedin.com/in/leandro-obt/ > Laboratory of Computational Biology > Brazilian Biosciences National Laboratory (LNBio) > Brazilian Center for Research in Energy and Materials (CNPEM) > Zip Code 13083-970, Campinas, S?o Paulo, Brazil. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From sinaomrani96 at gmail.com Mon Apr 6 15:55:10 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Mon, 06 Apr 2020 13:55:10 -0000 Subject: [gmx-users] Bonds definition in itp files In-Reply-To: <544c8c52-b75e-8a25-b9c2-199425e86264@vt.edu> References: <544c8c52-b75e-8a25-b9c2-199425e86264@vt.edu> Message-ID: Thanks, dear Justin. if I define a constraint on a bond then force constant isn't useless? On Mon, 6 Apr 2020 at 17:12, Justin Lemkul wrote: > > > On 4/6/20 7:24 AM, Sina Omrani wrote: > > Hi, > > I wanted to know how we specify a bond order in our simulation? For > > example, if we have a triple bond in our structure between atoms 1 and 2, > > is it by length and force constants or we define 1 and 2 bonds three > times > > in the bond section of itp file? > > What if we use a constraint on this bond? because I get better results > when > > I define the bond three times but haven't seen this method. is it wrong? > > All interactions should be defined only once, and the parameters used > should produce correct behavior. MM force fields have no concept of > double or triple bonds; they only know the stiffness of the spring > connecting the atoms. My guess is that if you had to add the bond three > times, the force field parameters are adding together, indicating that > the force constant is unsuitable for what you're trying to and needs to > be refined. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Mon Apr 6 16:04:38 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 14:04:38 -0000 Subject: [gmx-users] Bonds definition in itp files In-Reply-To: References: <544c8c52-b75e-8a25-b9c2-199425e86264@vt.edu> Message-ID: On 4/6/20 9:55 AM, Sina Omrani wrote: > Thanks, dear Justin. if I define a constraint on a bond then force constant > isn't useless? Yes, because you no longer have a harmonic interaction. It is a fixed length. Whether or not the bond should be constrained is dictated by whether or not the force field applies constraints to all bonds or only bonds to H. If the latter, you shouldn't apply ad hoc constraints. -Justin > On Mon, 6 Apr 2020 at 17:12, Justin Lemkul wrote: > >> >> On 4/6/20 7:24 AM, Sina Omrani wrote: >>> Hi, >>> I wanted to know how we specify a bond order in our simulation? For >>> example, if we have a triple bond in our structure between atoms 1 and 2, >>> is it by length and force constants or we define 1 and 2 bonds three >> times >>> in the bond section of itp file? >>> What if we use a constraint on this bond? because I get better results >> when >>> I define the bond three times but haven't seen this method. is it wrong? >> All interactions should be defined only once, and the parameters used >> should produce correct behavior. MM force fields have no concept of >> double or triple bonds; they only know the stiffness of the spring >> connecting the atoms. My guess is that if you had to add the bond three >> times, the force field parameters are adding together, indicating that >> the force constant is unsuitable for what you're trying to and needs to >> be refined. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jkozuch at zedat.fu-berlin.de Mon Apr 6 16:28:35 2020 From: jkozuch at zedat.fu-berlin.de (Jacek Artur Kozuch) Date: Mon, 06 Apr 2020 14:28:35 -0000 Subject: [gmx-users] Anharmonic/Morse flexible water Message-ID: <64603.79.226.117.53.1586183312.webmail@webmail.zedat.fu-berlin.de> Hi all, I am currently trying out various water models for some solute/solvent systems and I was wondering if there are any (reliable) anharmonic/Morse flexbile water models that can be used in Gromacs? I've seen that can set [ Morse ] for bonds, but don't want to start doing random changes to available models. Thanks in advance and stay healthy! Best, Jacek From marko at kth.se Mon Apr 6 16:53:55 2020 From: marko at kth.se (Marko Petrovic) Date: Mon, 06 Apr 2020 14:53:55 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling In-Reply-To: <321a4fe9-60c5-fd66-4e70-41d9de94ffb1@vt.edu> References: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> <321a4fe9-60c5-fd66-4e70-41d9de94ffb1@vt.edu> Message-ID: Thank you. I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences I can not understand and then just ask about those. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 6 Apr 2020, at 14:44, Justin Lemkul > wrote: On 4/6/20 2:33 AM, Marko Petrovic wrote: I figure it might be helpful to see my other files so I include a link: https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin Your dihedral definitions are simply incorrect. pull_coord1_groups = 1 2 2 3 3 4 pull_coord2_groups = 2 3 3 4 4 5 should be pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Mon Apr 6 16:57:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 14:57:35 -0000 Subject: [gmx-users] Fumbling in the dark with dihedral pulling In-Reply-To: References: <4DD79900-A76D-4E2E-890B-EACFC9793236@kth.se> <048b2b98-efde-ee4e-7e35-4d50cf1a9fab@vt.edu> <321a4fe9-60c5-fd66-4e70-41d9de94ffb1@vt.edu> Message-ID: <813b335e-7bc9-964c-457c-7865609badef@vt.edu> On 4/6/20 10:53 AM, Marko Petrovic wrote: > Thank you. > > I updated the mdp file. (Is the dihedral defined as a pair of planes rather than a triplet of vectors?) Perhaps my interpretation of the documentation was incorrect; I thought the planes were supposed to be defined, but I suppose it's defined by vectors instead. http://manual.gromacs.org/current/user-guide/mdp-options.html#com-pulling > Unfortunately I still get the segmentation fault and similar warnings. I will try to compile the differences between the sample mdp and the one I used, then see which differences I can not understand and then just ask about those. Does your simulation run without pulling options? A sanity check is wise. Then test with only one dihedral restrained. It's possible something is buggy; I don't know how widely used the dihedral pulling is used, and I have not used it personally. -Justin > With Regards > Marko Petrovic > Educator > Computational Science and Technology > School of Electrical Engineering and Computer Science > KTH Royal Institute of Technology > > On 6 Apr 2020, at 14:44, Justin Lemkul > wrote: > > > > On 4/6/20 2:33 AM, Marko Petrovic wrote: > I figure it might be helpful to see my other files so I include a link: > https://github.com/SpaceDucK77/StringMethodMaster/tree/master/Prototypes/P3_Pull_coordinates/manual_test_justin > > > Your dihedral definitions are simply incorrect. > > pull_coord1_groups = 1 2 2 3 3 4 > pull_coord2_groups = 2 3 3 4 4 5 should be > pull_coord1_groups = 1 2 3 2 3 4 pull_coord2_groups = 2 3 4 3 4 5 -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sadafrani6 at gmail.com Mon Apr 6 18:06:42 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 06 Apr 2020 16:06:42 -0000 Subject: [gmx-users] restarting a simulation Message-ID: Dear Gromacs users I am restarting a simulation with the following command:- mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append However, I am getting following error message. All the below-named files are there in my directory but it still complains the same. Inconsistency in user input: Some output files listed in the checkpoint file md10_prev.cpt are not present or not named as the output files by the current program:)Expected output files that are present: Expected output files that are not present or named differently: md10.log md10.xtc md10.trr md10.edr md10.xvg To keep your simulation files safe, this simulation will not restart. Either name your output files exactly the same as the previous simulation part (e.g. with -deffnm), or make sure all the output files are present (e.g. run from the same directory as the previous simulation part), or instruct mdrun to write new output files with mdrun -noappend. In the last case, you will not be able to use appending in future for this simulation. I also tried without -append option. Please correct me if I am wrong somewhere. Thanks. Sadaf From m.b.abdelaal at gmail.com Mon Apr 6 18:17:09 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Mon, 06 Apr 2020 16:17:09 -0000 Subject: [gmx-users] Velocities from the .gro file Message-ID: Hello everybody :) Can I use the gmx insert-molecules to insert molecules in my box with velocities by adding the velocities in the .gro file and insert the molecules from this .gro file ? Thanks Mohamed From jalemkul at vt.edu Mon Apr 6 18:19:15 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 06 Apr 2020 16:19:15 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: Message-ID: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > Hello everybody :) > > Can I use the gmx insert-molecules to insert molecules in my box with > velocities by adding the velocities in the .gro file and insert the > molecules from this .gro file ? Have you tried it? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From hcgeorg at ufg.br Mon Apr 6 18:20:57 2020 From: hcgeorg at ufg.br (Herbert de Castro Georg) Date: Mon, 06 Apr 2020 16:20:57 -0000 Subject: [gmx-users] How to parametrize a new molecule? In-Reply-To: References: Message-ID: Thanks, Mahdi. I'm aware of that study. Actually it's because of it that I have chosen the latest CHARMM27 for the simulations. Best, Herbert Em s?b., 4 de abr. de 2020 ?s 12:57, Mahdi Bagherpoor escreveu: > Hello Herbert, > > Not related to your question, but be careful if you are going to use > CHARMM36 force field for DNA, as a recent study ( > https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does > not preserve DNA stability at a longer time scale, in case you are going to > do so. > > Best, > Mahdi > > On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg > wrote: > > > Thanks, Justin! > > > > > > > > Em sex., 3 de abr. de 2020 ?s 22:15, Justin Lemkul > > escreveu: > > > > > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > > Dear users, > > > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > > going > > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > > > http://cgenff.umaryland.edu/ > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Office: 301 Fralin Hall > > > Lab: 303 Engel Hall > > > > > > Virginia Tech Department of Biochemistry > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > jalemkul at vt.edu | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > ================================================== > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From Weitse.Hsu at colorado.edu Mon Apr 6 19:05:37 2020 From: Weitse.Hsu at colorado.edu (Wei-Tse Hsu) Date: Mon, 06 Apr 2020 17:05:37 -0000 Subject: [gmx-users] GROMACS 2020.1 failed to pass make check In-Reply-To: References: Message-ID: Hi Paul, Thank you so much for your reply! That is very helpful. Best, Wei-Tse On Mon, Apr 6, 2020 at 1:23 AM Paul bauer wrote: > Hello, > > you are using a plumed modified version that adds extra options to mdrun. > Our unit tests check that the output from mdrun -h stays invariant, and > this is no longer the case once you modify the code for plumed. > > You can ignore this failure in this case, but please mention in the > future if you are using modified versions of the code. > > Cheers > > Paul > > On 05/04/2020 21:23, Wei-Tse Hsu wrote: > > Dear gmx users, > > Recently I've been trying to install GROMACS 20201. After successfully > > compilng GROMACS 2020.1, when executing make check command, I > > encountered the following error. Specifically, one out of 56 tests > failed, > > which was related to Mdrun Test.WritesHelp. Looking at the error message, > > I'm still not sure what it means and how I should solve this problem. I > > wonder if anyone had this before that could give me some insights about > how > > I could solve the problem. Any help would be appreciated! > > > > Here is the error message in the middle. > > > > > > > > > > > > *[----------] 1 test from MdrunTest[ RUN ] > > > MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867: > > Failure In item: /Help string Actual: 'SYNOPSIS* > > And here is the error message in the end. > > > > > > > > > > > > *The following tests FAILED: 43 - MdrunTests > > (Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target > > 'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for > > target 'CMakeFiles/run-ctest-nophys.dir/all' > > failedCMakeFiles/Makefile2:445: recipe for target > > 'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check' > > failed* > > > > And here is the whole STDOUT message of the command printed by make > *check > >> make_check.log*. > > > https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing > > > > Best, > > Wei-Tse > > > -- > Paul Bauer, PhD > GROMACS Development Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From vuqv.phys at gmail.com Tue Apr 7 11:24:07 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Tue, 07 Apr 2020 09:24:07 -0000 Subject: [gmx-users] restarting a simulation In-Reply-To: References: Message-ID: Hi, Have you read and try what mdrun tells you, like -deffnm option? in recent version of gromacs, if you do not want to append the output to old output files, use option -noappend. On Mon, Apr 6, 2020 at 6:06 PM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From vuqv.phys at gmail.com Tue Apr 7 11:24:08 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Tue, 07 Apr 2020 09:24:08 -0000 Subject: [gmx-users] restarting a simulation In-Reply-To: References: Message-ID: Hi, Have you read and try what mdrun tells you, like -deffnm option? in recent version of gromacs, if you do not want to append the output to old output files, use option -noappend. On Mon, Apr 6, 2020 at 6:06 PM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From 272699575 at qq.com Tue Apr 7 15:41:55 2020 From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=) Date: Tue, 07 Apr 2020 13:41:55 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units Message-ID: It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed. Can I ask 1) Is this a sensible idea to proceed? 2) To fix the neighbours, should I use "constraints" or "restraints"? 3) At which step should I start to introduce the fixation? 4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng From moura at ufscar.br Tue Apr 7 15:50:47 2020 From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=) Date: Tue, 07 Apr 2020 13:50:47 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units In-Reply-To: References: Message-ID: Dear Cheng, Either fixing or constraining the other units will not decrease the computational cost of the simulation since you will still be computing the interactions between the unit that can move and all the other fixed/constrained units. Andre On Tue, Apr 7, 2020 at 10:41 AM ZHANG Cheng <272699575 at qq.com> wrote: > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 From 272699575 at qq.com Tue Apr 7 16:18:55 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Tue, 07 Apr 2020 14:18:55 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units In-Reply-To: References: Message-ID: Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. ------------------ Original ------------------ From: "ZHANG Cheng"<272699575 at qq.com>; Date: Tue, Apr 7, 2020 09:41 PM To: "gromacs.org_gmx-users" References: Message-ID: <616b8a15-ce13-d503-4e0b-570d4f147805@vt.edu> On 4/7/20 10:10 AM, ZHANG Cheng wrote: > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? I would not use "fix" and "restrain" interchangeably. Fixing a quantity means it cannot vary. With a restraint, movement is disfavored but not prevented. Freezing is totally artificial and requires you to ignore nonbonded interactions between the frozen groups. > > 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. > Your approach assumes that the conformations of the proteins are not dependent on their neighbors. I do not think that is a justifiable assumption. If you simulate one protein freely and restrain its neighbors, you're doing a glorified simulation of a crystal, which is not reflective of biological reality for a virus capsid. -Justin > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Tue, Apr 7, 2020 09:41 PM > To: "gromacs.org_gmx-users" Cc: "ZHANG Cheng"<272699575 at qq.com>; > Subject: Simulate only one unit of the virus capsid while fixing its surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From moura at ufscar.br Tue Apr 7 16:50:25 2020 From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=) Date: Tue, 07 Apr 2020 14:50:25 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units In-Reply-To: <616b8a15-ce13-d503-4e0b-570d4f147805@vt.edu> References: <616b8a15-ce13-d503-4e0b-570d4f147805@vt.edu> Message-ID: Dear Cheng, I also think that freezing introduces more artifacts than benefits, since you are probably beginning your simulation from a crystallographic structure and fixing most of the molecules will provide a crystal-like structure, not a relaxed structure closer to the typical physiological conditions. Andre On Tue, Apr 7, 2020 at 11:29 AM Justin Lemkul wrote: > > > On 4/7/20 10:10 AM, ZHANG Cheng wrote: > > Dear Andre, Thank you for the advice. Can I ask, > > > > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > I would not use "fix" and "restrain" interchangeably. Fixing a quantity > means it cannot vary. With a restraint, movement is disfavored but not > prevented. Freezing is totally artificial and requires you to ignore > nonbonded interactions between the frozen groups. > > > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > Your approach assumes that the conformations of the proteins are not > dependent on their neighbors. I do not think that is a justifiable > assumption. If you simulate one protein freely and restrain its > neighbors, you're doing a glorified simulation of a crystal, which is > not reflective of biological reality for a virus capsid. > > -Justin > > > > > > > > > ------------------ Original ------------------ > > From: "ZHANG Cheng"<272699575 at qq.com>; > > Date: Tue, Apr 7, 2020 09:41 PM > > To: "gromacs.org_gmx-users"< > gromacs.org_gmx-users at maillist.sys.kth.se>; > > Cc: "ZHANG Cheng"<272699575 at qq.com>; > > Subject: Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > > > > Can I ask > > > > > > 1) Is this a sensible idea to proceed? > > > > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > > > > 3) At which step should I start to introduce the fixation? > > > > > > 4) If possible, is there a tutorial for this? I feel the information > here is still not straightforward to follow > > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > > > > Thank you! > > > > > > Yours sincerely > > Cheng > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 From dburns at iastate.edu Tue Apr 7 17:47:15 2020 From: dburns at iastate.edu (Daniel Burns) Date: Tue, 07 Apr 2020 15:47:15 -0000 Subject: [gmx-users] restarting a simulation In-Reply-To: References: Message-ID: You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Tue Apr 7 17:50:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 07 Apr 2020 15:50:47 -0000 Subject: [gmx-users] restarting a simulation In-Reply-To: References: Message-ID: <0d99b4c4-c528-6f28-d937-201dfe12f3e5@vt.edu> On 4/7/20 11:47 AM, Daniel Burns wrote: > You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If > so, replace it in your command with just the md10.cpt file. If you don't > have it, try renaming your "_prev.cpt" file to just "md10.cpt". The issue is not with the naming of the checkpoint file but with the output files specified within the checkpoint. The simplest workaround here is simply to use -noappend and concatenate output later. If one moves files around, sometimes the appending mechanism can break for reasons that are still unclear to me. -Justin > Dan > > > On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: > >> Dear Gromacs users >> I am restarting a simulation with the following command:- >> mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append >> >> However, I am getting following error message. All the below-named files >> are there in my directory but it still complains the same. >> >> Inconsistency in user input: >> Some output files listed in the checkpoint file md10_prev.cpt are not >> present >> or not named as the output files by the current program:)Expected output >> files >> that are present: >> >> Expected output files that are not present or named differently: >> md10.log >> md10.xtc >> md10.trr >> md10.edr >> md10.xvg >> To keep your simulation files safe, this simulation will not restart. >> Either >> name your >> output files exactly the same as the previous simulation part (e.g. with >> -deffnm), or >> make sure all the output files are present (e.g. run from the same >> directory >> as the >> previous simulation part), or instruct mdrun to write new output files with >> mdrun -noappend. >> In the last case, you will not be able to use appending in future for this >> simulation. >> >> I also tried without -append option. >> Please correct me if I am wrong somewhere. >> Thanks. >> >> Sadaf >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Tue Apr 7 23:01:27 2020 From: alexanderwien2k at gmail.com (Alex) Date: Tue, 07 Apr 2020 21:01:27 -0000 Subject: [gmx-users] dt in mdp Message-ID: Dear all, After minimization and equalizations using nvt (v-rescale) and npt (both berendsen and ;Parrinello-Rahman), a simulation of mine could run well for 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002 with the particles communication fatal error. Fatal error: 2 particles communicated to PME rank 12 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. So, if the system would not be well equlibrated, then I would expect that with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect that it also crashes for example around 6 ns as the with the dt = 0.002 the simulation last only 3 ns. Any comment that helps to understand the problem would be highly appreciated. Regards, Alex From jalemkul at vt.edu Tue Apr 7 23:06:08 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 07 Apr 2020 21:06:08 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: References: Message-ID: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> On 4/7/20 5:00 PM, Alex wrote: > Dear all, > After minimization and equalizations using nvt (v-rescale) and npt (both > berendsen and ;Parrinello-Rahman), a simulation of mine could run well for > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002 > with the particles communication fatal error. > > Fatal error: > 2 particles communicated to PME rank 12 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension y. > This usually means that your system is not well equilibrated. > > So, if the system would not be well equlibrated, then I would expect that > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect > that it also crashes for example around 6 ns as the with the dt = 0.002 the > simulation last only 3 ns. > > Any comment that helps to understand the problem would be highly > appreciated. Please provide a description of what your system is and a full .mdp file. While most of the time these crashes come from poor equilibration, an inadequately parametrized topology or bad combination/misuse of algorithms can also cause crashes. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Tue Apr 7 23:39:11 2020 From: alexanderwien2k at gmail.com (Alex) Date: Tue, 07 Apr 2020 21:39:11 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> Message-ID: Thanks Justin for the response. Please find below the mdp file. The system is a thin film made out of a epoxy molecule, picture in be below link, with water on top and bottom of the film. I even sometimes have the same issue when I simulate the bulk of this system, I mean a cubic box filled by this molecule and no water. I got the force fields from the latest version of ATB repository by which I have previously done some other simulation for the same molecule. https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb %--------mdp------- title = Thin-Film integrator = md dt = 0.002 ; 2 fs ;0.001 1 fs nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns xtc-precision = 500 ; 1000 ;nstlist = 40 %----------------- ;;in .trr file nstxout = 3000 ; 6000 nstvout = 0 nstfout = 0 ;;in energy file.log nstlog = 2000 ; 4000 nstcalcenergy = 2000 ;4000 nstenergy = 2000 ;4000 ;;in xtc file nstxout-compressed = 0 ;compressed-x-grps = non-Water %----------------- continuation = yes gen-vel = no constraint-algorithm = lincs constraints = h-bonds cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.4 vdwtype = Cut-off rvdw = 1.4 DispCorr = EnerPres tcoupl = v-rescale tc-grps = system tau-t = 1.5 nhchainlength = 10 ref-t = 298.15 pbc = xyz pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 2.5 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling = com energygrps = thin_film SOL comm-mode = Linear nstcomm = 100 comm-grps = Thin_fiml SOL %------------------------- Thank you Alex On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > > > On 4/7/20 5:00 PM, Alex wrote: > > Dear all, > > After minimization and equalizations using nvt (v-rescale) and npt (both > > berendsen and ;Parrinello-Rahman), a simulation of mine could run well > for > > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = > 0.002 > > with the particles communication fatal error. > > > > Fatal error: > > 2 particles communicated to PME rank 12 are more than 2/3 times the > cut-off > > out of the domain decomposition cell of their charge group in dimension > y. > > This usually means that your system is not well equilibrated. > > > > So, if the system would not be well equlibrated, then I would expect that > > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect > > that it also crashes for example around 6 ns as the with the dt = 0.002 > the > > simulation last only 3 ns. > > > > Any comment that helps to understand the problem would be highly > > appreciated. > > Please provide a description of what your system is and a full .mdp > file. While most of the time these crashes come from poor equilibration, > an inadequately parametrized topology or bad combination/misuse of > algorithms can also cause crashes. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From m.b.abdelaal at gmail.com Wed Apr 8 00:38:08 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 07 Apr 2020 22:38:08 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: No, I use the generate velocity option in the .mdp files. However I want now to assign different velocities in the x,y,z directions. Which I thought it could only be done through the .gro file, but I don't know If I did that, should I change the value of the generate velocity to be = NO in the .mdp files ? (otherwise I would have generated the velocities twice). Moreover, if I added the velocities in the .gro file how can I generate the velocities in the .gro file from a distribution (Maxwell) with a specific mean and standard deviation ? I have tried to search in different sources (the user list, manual, user guide, research gate and other platforms) how to solve this velocity problem but I didn't find a clear way to insert different velocities in the x,y,z directions using distribution rater than constant velocities. Please guide me how to do it as I am a little bit confused in the velocity generation mechanisms. Many thanks, Mohamed On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > Hello everybody :) > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > velocities by adding the velocities in the .gro file and insert the > > molecules from this .gro file ? > > Have you tried it? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From 272699575 at qq.com Wed Apr 8 05:02:59 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Wed, 08 Apr 2020 03:02:59 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units In-Reply-To: References: Message-ID: Dear Justin and Andre, Thank you for the advice. So can I ask how commonly the very large virus capsid is simulated? A recent paper "Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations" is using 3880 GPU accelerated Cray-XK nodes, which is impossible for our university to provide. ------------------ Original ------------------ From: "ZHANG Cheng"<272699575 at qq.com>; Date: Tue, Apr 7, 2020 10:10 PM To: "ZHANG Cheng"<272699575 at qq.com>;"gromacs.org_gmx-users" References: Message-ID: Dear Cheng, maybe you should step back and begin the planification of your research project considering how much computer power you have available. If you cannot handle the whole capsid then you have to simplify the model either using some coarse grained force field (MARTINI, for instance) or studying a smaller part of the capsid. but these choices are up to you, they depend on what questions you are trying to answer. Andre On Wed, Apr 8, 2020 at 12:02 AM ZHANG Cheng <272699575 at qq.com> wrote: > Dear Justin and Andre, > > > Thank you for the advice. So can I ask how commonly the very large virus > capsid is simulated? A recent paper "Physical properties of the HIV-1 > capsid from all-atom molecular dynamics simulations" is using 3880 GPU > accelerated Cray-XK nodes, which is impossible for our university to > provide. > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Tue, Apr 7, 2020 10:10 PM > To: "ZHANG Cheng"<272699575 at qq.com>;"gromacs.org_gmx-users"< > gromacs.org_gmx-users at maillist.sys.kth.se>; > > Subject: Re:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Tue, Apr 7, 2020 09:41 PM > To: "gromacs.org_gmx-users" >; > Cc: "ZHANG Cheng"<272699575 at qq.com>; > Subject: Simulate only one unit of the virus capsid while fixing its > surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 From ericsmoll at gmail.com Wed Apr 8 05:48:40 2020 From: ericsmoll at gmail.com (Eric Smoll) Date: Wed, 08 Apr 2020 03:48:40 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal wrote: > No, I use the generate velocity option in the .mdp files. > > However I want now to assign different velocities in the x,y,z directions. > Which I thought it could only be done through the .gro file, but I don't > know If I did that, should I change the value of the generate velocity to > be = NO in the .mdp files ? (otherwise I would have generated the > velocities twice). > That sounds logical. Set it to no if you provide your own initial velocities. > > Moreover, if I added the velocities in the .gro file how can I generate the > velocities in the .gro file from a distribution (Maxwell) with a specific > mean and standard deviation ? > > I have tried to search in different sources (the user list, manual, user > guide, research gate and other platforms) how to solve this velocity > problem but I didn't find a clear way to insert different velocities in the > x,y,z directions using distribution rater than constant velocities. > > There is a good section on this in the manual. For example, section 3.4.1 in the Gromacs 5.1.2 manual. Also, you know that the generate velocities option assigns velocities to atoms from an approximate MB distribution at whatever temperature you specify in the MDP file, right? If I understand you correctly, the generate velocities options should do exactly what you want. With no extra work. > Please guide me how to do it as I am a little bit confused in the velocity > generation mechanisms. > > Many thanks, > Mohamed > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > > Hello everybody :) > > > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > > velocities by adding the velocities in the .gro file and insert the > > > molecules from this .gro file ? > > > > Have you tried it? > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From 272699575 at qq.com Wed Apr 8 06:17:48 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Wed, 08 Apr 2020 04:17:48 -0000 Subject: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units In-Reply-To: References: Message-ID: Dear Andre, Thank you. We are trying to use an adenovirus as a vaccine. As it is not stable, we want to simulate it to identify the unstable regions (e.g. flexible), so as to either engineering (e.g. mutation) it, or adding excipients.  Simulating only one protein of the capsid is of course doable. But do you think simulating one protein without its neighbours could reflect its dynamics? Would its boundary residues behave very differently compared to with neighbours? ------------------ Original ------------------ From: "ZHANG Cheng"<272699575 at qq.com>; Date: Wed, Apr 8, 2020 11:02 AM To: "gromacs.org_gmx-users" References: Message-ID: Dear Cheng, The paper you mentioned (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524983/) uses NAMD (http://www.ks.uiuc.edu/Research/namd/) has somewhat different scalability properties than GROMACS. Regards, Benson On Wed, Apr 8, 2020, at 7:14 AM, ZHANG Cheng wrote: > Dear Andre, > > > Thank you. We are trying to use an adenovirus as a vaccine. As it is > not stable, we want to simulate it to identify the unstable regions > (e.g. flexible), so as to either engineering (e.g. mutation) it, or > adding excipients.  > > > Simulating only one protein of the capsid is of course doable. But do > you think simulating one protein without its neighbours could reflect > its dynamics? Would its boundary residues behave very differently > compared to with neighbours? > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Wed, Apr 8, 2020 11:02 AM > To: "gromacs.org_gmx-users" > Subject: Re:Simulate only one unit of the virus capsid while > fixing its surrounding units > > > > Dear Justin and Andre, > > > Thank you for the advice. So can I ask how commonly the very large > virus capsid is simulated? A recent paper "Physical properties of the > HIV-1 capsid from all-atom molecular dynamics simulations" is using > 3880 GPU accelerated Cray-XK nodes, which is impossible for our > university to provide. > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Tue, Apr 7, 2020 10:10 PM > To: "ZHANG > Cheng"<272699575 at qq.com>;"gromacs.org_gmx-users" > Subject: Re:Simulate only one unit of the virus capsid while > fixing its surrounding units > > > > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another > term? How about "freezegrps"? > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So > fixing the neighbours and only focusing on the protein in the centre > could be the solution. > > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Tue, Apr 7, 2020 09:41 PM > To: "gromacs.org_gmx-users" Cc: "ZHANG Cheng"<272699575 at qq.com>; > Subject: Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I > do not have such computational resources. So I was thinking to only > simulate one coat protein and its surrounding neighbours, but keep the > neighbours relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information > here is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jkozuch at zedat.fu-berlin.de Wed Apr 8 15:52:36 2020 From: jkozuch at zedat.fu-berlin.de (Jacek Artur Kozuch) Date: Wed, 08 Apr 2020 13:52:36 -0000 Subject: [gmx-users] Double-well potential for bonded interaction Message-ID: <63896.79.226.117.53.1586353953.webmail@webmail.zedat.fu-berlin.de> Hi, Does anybody know how to define for a specific bond a double-well potential? I've looking into the definitions in the gromacs manual (manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html and manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html), but for now I can only imagine using bond restraints in a similar manner shown here for position restraints: manual.gromacs.org/current/reference-manual/functions/restraints.html It feels like there should be a more elegant way of doing that. Thanks for your suggestions in advance! Best, Jacek ________________________________________________ Dr. Jacek Kozuch Freie Universit?t Berlin Fachbereich Physik Arnimallee 14 Raum 1.1.35 14 195 Berlin ________________________________________________ From johnwhittake at zedat.fu-berlin.de Wed Apr 8 16:35:24 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 08 Apr 2020 14:35:24 -0000 Subject: [gmx-users] Double-well potential for bonded interaction In-Reply-To: <63896.79.226.117.53.1586353953.webmail@webmail.zedat.fu-berlin.de> References: <63896.79.226.117.53.1586353953.webmail@webmail.zedat.fu-berlin.de> Message-ID: <55158.89.14.137.226.1586356521.webmail@webmail.zedat.fu-berlin.de> Hi Jacek, Gromacs allows for the implementation of any kind of bonded interaction through user-defined tabulated functions. You'll have to build a table for it, but it's definitely more straightforward than messing around with restraints. Check out section 4.2.14 of the manual: "Tabulated bonded interaction functions". Best, John > Hi, > > Does anybody know how to define for a specific bond a double-well > potential? > > I've looking into the definitions in the gromacs manual > (manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html > and > manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html), > but for now I can only imagine using bond restraints in a similar manner > shown here for position restraints: > manual.gromacs.org/current/reference-manual/functions/restraints.html > > It feels like there should be a more elegant way of doing that. > > Thanks for your suggestions in advance! > > Best, > Jacek > > ________________________________________________ > Dr. Jacek Kozuch > > Freie Universit?t Berlin > Fachbereich Physik > Arnimallee 14 > Raum 1.1.35 > 14 195 Berlin > ________________________________________________ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-request at gromacs.org. ---------------------------------------- John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universit?t Berlin +49 0160 936 04221 From fernando at hypernetlabs.io Wed Apr 8 20:05:29 2020 From: fernando at hypernetlabs.io (fernando fuentes de la parra) Date: Wed, 08 Apr 2020 18:05:29 -0000 Subject: [gmx-users] Dockerfile to use gromacs/gromacs in DockerHub? Message-ID: Hi all! My name is Fernando Fuentes and I am working on a project to try to run this simple gmx example in a container in a remote computer using galileoapp.io . In the folder attached a Dockerfile I produced to try to have it be compatible with the image at https://hub.docker.com/r/gromacs/gromacs. I failed, so I was wondering if anyone had a Dockerfile that works with that simulator image or could provide some guidance. Or could point me to someone who knows about this. I'm a rookie but a fast learner = ) I *thank you so much* for your help. Fernando +18147778447 From m.b.abdelaal at gmail.com Thu Apr 9 01:40:45 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 08 Apr 2020 23:40:45 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: Many thanks for your reply ? The limitation in the generate velocity using the .mdp file, is that while I can generate the velocity from Maxwell distribution, I will have the same velocities in the x, y and z directions. On the other hand, generating the velocity from the .gro file will let me specify different velocities in the x,y and z directions but they will be the same velocities for all the atoms (will not be taken from a maxwell distribution with variation in the atoms velocities). Is it possible to generate different velocities in the x,y and z directions from a maxwell distribution ? (for example the velocities to be taken from a maxwell distribution with a mean of 0.1 in the x direction and with a mean of 0.2 in the y direction and with mean of 0.3 in the z direction?) Thanks for your help :) Mohamed On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal > wrote: > > > No, I use the generate velocity option in the .mdp files. > > > > However I want now to assign different velocities in the x,y,z > directions. > > Which I thought it could only be done through the .gro file, but I don't > > know If I did that, should I change the value of the generate velocity to > > be = NO in the .mdp files ? (otherwise I would have generated the > > velocities twice). > > > > That sounds logical. Set it to no if you provide your own initial > velocities. > > > > > Moreover, if I added the velocities in the .gro file how can I generate > the > > velocities in the .gro file from a distribution (Maxwell) with a specific > > mean and standard deviation ? > > > > I have tried to search in different sources (the user list, manual, user > > guide, research gate and other platforms) how to solve this velocity > > problem but I didn't find a clear way to insert different velocities in > the > > x,y,z directions using distribution rater than constant velocities. > > > > There is a good section on this in the manual. For example, section > 3.4.1 > in the Gromacs 5.1.2 manual. > > Also, you know that the generate velocities option assigns velocities to > atoms from an approximate MB distribution at whatever temperature you > specify in the MDP file, right? If I understand you correctly, the > generate velocities options should do exactly what you want. With no extra > work. > > > > Please guide me how to do it as I am a little bit confused in the > velocity > > generation mechanisms. > > > > Many thanks, > > Mohamed > > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > > > > > > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > > > Hello everybody :) > > > > > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > > > velocities by adding the velocities in the .gro file and insert the > > > > molecules from this .gro file ? > > > > > > Have you tried it? > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Office: 301 Fralin Hall > > > Lab: 303 Engel Hall > > > > > > Virginia Tech Department of Biochemistry > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > jalemkul at vt.edu | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > ================================================== > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From ericsmoll at gmail.com Thu Apr 9 04:32:46 2020 From: ericsmoll at gmail.com (Eric Smoll) Date: Thu, 09 Apr 2020 02:32:46 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal wrote: > Many thanks for your reply ? > > The limitation in the generate velocity using the .mdp file, is that while > I can generate the velocity from Maxwell distribution, I will have the > same velocities in the x, y and z directions. > I think you mean "same velocity *distributions* in the x, y, and z directions." The distributions will be approximately the same but each atom will have a different velocity. > > On the other hand, generating the velocity from the .gro file will let me > specify different velocities in the x,y and z directions but they will be > the same velocities for all the atoms (will not be taken from a maxwell > distribution with variation in the atoms velocities). > I think you mean "specify different velocity *distributions* in the x, y, and z directions" > > Is it possible to generate different velocities in the x,y and z directions > I think you mean "generate different velocity *distributions* in the x, y, and z directions." If so, the answer is obviously yes. Because you can type in each individual vxi, vyi, and vzi for every atom i, you can generate different velocity distributions in the x, y, and z directions. > from a maxwell distribution ? I am not sure what this part of the sentence means. If you do what you are suggesting, you will not be working with a maxwell distribution because all three directions should have identical distributions. See comment below. If there is another misunderstanding, you need to spend more time crafting precise sentences to communicate what you are after. > (for example the velocities to be taken from > a maxwell distribution with a mean of 0.1 in the x direction and with a > mean of 0.2 in the y direction and with mean of 0.3 in the z direction?) > In my last email I suggested reading section 3.4.1 of the manual version 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity distribution corresponds to three identical gaussian speed distributions in vx, vy, and vz centered at zero (mean should be zero for vx, vy, vz). Just change the standard deviation of the velocity distribution sqrt(kT/m) for each velocity component if you want them to be different. If you don't want the mean to be zero for whatever reason, add a constant. However, a non-zero mean for any of the velocity components will generate center of mass motion. If you want center of mass motion, turn off center of mass motion removal in the mdp file. > Thanks for your help :) > Mohamed > > On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: > > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal > > wrote: > > > > > No, I use the generate velocity option in the .mdp files. > > > > > > However I want now to assign different velocities in the x,y,z > > directions. > > > Which I thought it could only be done through the .gro file, but I > don't > > > know If I did that, should I change the value of the generate velocity > to > > > be = NO in the .mdp files ? (otherwise I would have generated the > > > velocities twice). > > > > > > > That sounds logical. Set it to no if you provide your own initial > > velocities. > > > > > > > > Moreover, if I added the velocities in the .gro file how can I generate > > the > > > velocities in the .gro file from a distribution (Maxwell) with a > specific > > > mean and standard deviation ? > > > > > > I have tried to search in different sources (the user list, manual, > user > > > guide, research gate and other platforms) how to solve this velocity > > > problem but I didn't find a clear way to insert different velocities in > > the > > > x,y,z directions using distribution rater than constant velocities. > > > > > > There is a good section on this in the manual. For example, section > > 3.4.1 > > in the Gromacs 5.1.2 manual. > > > > Also, you know that the generate velocities option assigns velocities to > > atoms from an approximate MB distribution at whatever temperature you > > specify in the MDP file, right? If I understand you correctly, the > > generate velocities options should do exactly what you want. With no > extra > > work. > > > > > > > Please guide me how to do it as I am a little bit confused in the > > velocity > > > generation mechanisms. > > > > > > Many thanks, > > > Mohamed > > > > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > > > > > > > > > > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > > > > Hello everybody :) > > > > > > > > > > Can I use the gmx insert-molecules to insert molecules in my box > with > > > > > velocities by adding the velocities in the .gro file and insert the > > > > > molecules from this .gro file ? > > > > > > > > Have you tried it? > > > > > > > > -Justin > > > > > > > > -- > > > > ================================================== > > > > > > > > Justin A. Lemkul, Ph.D. > > > > Assistant Professor > > > > Office: 301 Fralin Hall > > > > Lab: 303 Engel Hall > > > > > > > > Virginia Tech Department of Biochemistry > > > > 340 West Campus Dr. > > > > Blacksburg, VA 24061 > > > > > > > > jalemkul at vt.edu | (540) 231-3129 > > > > http://www.thelemkullab.com > > > > > > > > ================================================== > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From m.b.abdelaal at gmail.com Thu Apr 9 05:02:00 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Thu, 09 Apr 2020 03:02:00 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: Many thanks for your reply :) All your language assumptions are true and that is exactly what I wanted to communicate, next time I will try to be more precise and sorry for the confusion ? I will read section 3.4.1 again carefully. Thanks again and sorry for the inconvenience. Mohamed On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: > On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal > wrote: > > > Many thanks for your reply ? > > > > The limitation in the generate velocity using the .mdp file, is that > while > > I can generate the velocity from Maxwell distribution, I will have the > > same velocities in the x, y and z directions. > > > > I think you mean "same velocity *distributions* in the x, y, and z > directions." The distributions will be approximately the same but each > atom will have a different velocity. > > > > > On the other hand, generating the velocity from the .gro file will let me > > specify different velocities in the x,y and z directions but they will be > > the same velocities for all the atoms (will not be taken from a maxwell > > distribution with variation in the atoms velocities). > > > > I think you mean "specify different velocity *distributions* in the x, y, > and z directions" > > > > > Is it possible to generate different velocities in the x,y and z > directions > > > > I think you mean "generate different velocity *distributions* in the x, y, > and z directions." If so, the answer is obviously yes. Because you can > type in each individual vxi, vyi, and vzi for every atom i, you can > generate different velocity distributions in the x, y, and z directions. > > > > from a maxwell distribution ? > > > I am not sure what this part of the sentence means. If you do what you are > suggesting, you will not be working with a maxwell distribution because all > three directions should have identical distributions. See comment below. > If there is another misunderstanding, you need to spend more time crafting > precise sentences to communicate what you are after. > > > > (for example the velocities to be taken from > > a maxwell distribution with a mean of 0.1 in the x direction and with a > > mean of 0.2 in the y direction and with mean of 0.3 in the z direction?) > > > > In my last email I suggested reading section 3.4.1 of the manual version > 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity distribution > corresponds to three identical gaussian speed distributions in vx, vy, and > vz centered at zero (mean should be zero for vx, vy, vz). Just change the > standard deviation of the velocity distribution sqrt(kT/m) for each > velocity component if you want them to be different. If you don't want the > mean to be zero for whatever reason, add a constant. However, a non-zero > mean for any of the velocity components will generate center of mass > motion. If you want center of mass motion, turn off center of mass motion > removal in the mdp file. > > > > Thanks for your help :) > > Mohamed > > > > On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: > > > > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < > m.b.abdelaal at gmail.com> > > > wrote: > > > > > > > No, I use the generate velocity option in the .mdp files. > > > > > > > > However I want now to assign different velocities in the x,y,z > > > directions. > > > > Which I thought it could only be done through the .gro file, but I > > don't > > > > know If I did that, should I change the value of the generate > velocity > > to > > > > be = NO in the .mdp files ? (otherwise I would have generated the > > > > velocities twice). > > > > > > > > > > That sounds logical. Set it to no if you provide your own initial > > > velocities. > > > > > > > > > > > Moreover, if I added the velocities in the .gro file how can I > generate > > > the > > > > velocities in the .gro file from a distribution (Maxwell) with a > > specific > > > > mean and standard deviation ? > > > > > > > > I have tried to search in different sources (the user list, manual, > > user > > > > guide, research gate and other platforms) how to solve this velocity > > > > problem but I didn't find a clear way to insert different velocities > in > > > the > > > > x,y,z directions using distribution rater than constant velocities. > > > > > > > > There is a good section on this in the manual. For example, section > > > 3.4.1 > > > in the Gromacs 5.1.2 manual. > > > > > > Also, you know that the generate velocities option assigns velocities > to > > > atoms from an approximate MB distribution at whatever temperature you > > > specify in the MDP file, right? If I understand you correctly, the > > > generate velocities options should do exactly what you want. With no > > extra > > > work. > > > > > > > > > > Please guide me how to do it as I am a little bit confused in the > > > velocity > > > > generation mechanisms. > > > > > > > > Many thanks, > > > > Mohamed > > > > > > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul > wrote: > > > > > > > > > > > > > > > > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > > > > > Hello everybody :) > > > > > > > > > > > > Can I use the gmx insert-molecules to insert molecules in my box > > with > > > > > > velocities by adding the velocities in t > he > .gro file and insert the > > > > > > molecules from this .gro file ? > > > > > > > > > > Have you tried it? > > > > > > > > > > -Justin > > > > > > > > > > -- > > > > > ================================================== > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > > > Assistant Professor > > > > > Office: 301 Fralin Hall > > > > > Lab: 303 Engel Hall > > > > > > > > > > Virginia Tech Department of Biochemistry > > > > > 340 West Campus Dr. > > > > > Blacksburg, VA 24061 > > > > > > > > > > jalemkul at vt.edu | (540) 231-3129 > > > > > http://www.thelemkullab.com > > > > > > > > > > ================================================== > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From benjamin.joseph at rwth-aachen.de Thu Apr 9 11:23:47 2020 From: benjamin.joseph at rwth-aachen.de (Joseph, Benjamin Philipp) Date: Thu, 09 Apr 2020 09:23:47 -0000 Subject: [gmx-users] Restarting a REST2 simulation Message-ID: <58791f35784b44edbafcbabae128b7a9@rwth-aachen.de> Dear members of the mailing list, I restarted my replica exchange with solute tempering (REST2) simulation (16 replicas on 20 = 480 cores) with the following command: srun gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append and am running into problems as the simulation does not run many steps after the restart. I get the following error message: GROMACS: gmx mdrun, version 2018.3 Executable: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi Data prefix: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu/topos Command line: gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append simulation part is not equal for all subsystems subsystem 0: 4 subsystem 1: 4 subsystem 2: 4 subsystem 3: 4 subsystem 4: 4 subsystem 5: 4 subsystem 6: 4 subsystem 7: 4 subsystem 8: 4 subsystem 9: 3 subsystem 10: 3 subsystem 11: 4 subsystem 12: 3 subsystem 13: 4 subsystem 14: 4 subsystem 15: 4 ------------------------------------------------------- Program: gmx mdrun, version 2018.3 Source file: src/gromacs/mdlib/main.cpp (line 115) MPI rank: 0 (out of 480) ------------------------------------------------------- Program: gmx mdrun, version 2018.3 Source file: src/gromacs/mdlib/main.cpp (line 115) MPI rank: 90 (out of 480) Fatal error: ------------------------------------------------------- ... ------------------------------------------------------- Program: gmx mdrun, version 2018.3 Source file: src/gromacs/mdlib/main.cpp (line 115) MPI rank: 300 (out of 480) Fatal error: The 16 subsystems are not compatible When I look at every md.log file they all stopped at the same simulation step and so I do not understand why they all are not at the same simulation part. Thanks a lot in advance for your help! Best regards, Benjamin From scorpio.liao at gmail.com Thu Apr 9 11:28:48 2020 From: scorpio.liao at gmail.com (Qinghua Liao) Date: Thu, 09 Apr 2020 09:28:48 -0000 Subject: [gmx-users] Restarting a REST2 simulation In-Reply-To: <58791f35784b44edbafcbabae128b7a9@rwth-aachen.de> References: <58791f35784b44edbafcbabae128b7a9@rwth-aachen.de> Message-ID: Hello Joseph, You can have a check all the cpt files, to see whether they were all saved at the same simulation time. Sometimes, some of the cpt files can be incomplete when saved at the last second. All the best, Qinghua On 4/9/20 11:23 AM, Joseph, Benjamin Philipp wrote: > Dear members of the mailing list, > > > I restarted my replica exchange with solute tempering (REST2) simulation (16 replicas on 20 = 480 cores) with the following command: > > srun gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append > > > and am running into problems as the simulation does not run many steps after the restart. I get the following error message: > > > GROMACS: gmx mdrun, version 2018.3 > > Executable: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi > > Data prefix: /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed > > Working dir: /p/scratch/cias-5/joseph1/new/S_1/sys1/neu/topos > > Command line: > > gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append > > > > simulation part is not equal for all subsystems > > subsystem 0: 4 > > subsystem 1: 4 > > subsystem 2: 4 > > subsystem 3: 4 > > subsystem 4: 4 > > subsystem 5: 4 > > subsystem 6: 4 > > subsystem 7: 4 > > subsystem 8: 4 > > subsystem 9: 3 > > subsystem 10: 3 > > subsystem 11: 4 > > subsystem 12: 3 > > subsystem 13: 4 > > subsystem 14: 4 > > subsystem 15: 4 > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2018.3 > > Source file: src/gromacs/mdlib/main.cpp (line 115) > > MPI rank: 0 (out of 480) > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2018.3 > > Source file: src/gromacs/mdlib/main.cpp (line 115) > > MPI rank: 90 (out of 480) > > > Fatal error: > > > ------------------------------------------------------- > > > ... > > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2018.3 > > Source file: src/gromacs/mdlib/main.cpp (line 115) > > MPI rank: 300 (out of 480) > > > Fatal error: > > The 16 subsystems are not compatible > > > When I look at every md.log file they all stopped at the same simulation step and so I do not understand why they all are not at the same simulation part. Thanks a lot in advance for your help! > > > Best regards, > > > Benjamin > From akash.pandya.15 at ucl.ac.uk Thu Apr 9 13:26:07 2020 From: akash.pandya.15 at ucl.ac.uk (Pandya, Akash) Date: Thu, 09 Apr 2020 11:26:07 -0000 Subject: [gmx-users] Concatenating trajectories Message-ID: Hi, I have four trajectories of the same condition (protein only) that I want to concatenate. I used the command below to do this: gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc -cat So this command gives me a file with all four trajectories, pasted together. The combined trajectory has now got four sets of the same time stamps. My question is how can I change the time stamps so that they appear in chronological order, instead of repeated time stamps?. So I would have a combined trajectory e.g. 20 to 200 ns. I hope I'm being clear about what I want to do and someone can guide me on achieving this. Best wishes, Akash From scorpio.liao at gmail.com Thu Apr 9 14:17:43 2020 From: scorpio.liao at gmail.com (Qinghua Liao) Date: Thu, 09 Apr 2020 12:17:43 -0000 Subject: [gmx-users] Concatenating trajectories In-Reply-To: References: Message-ID: Hello, There is an option of -settime for gmx trjcat, with which you can set different starting simulation time for each trajectory. All the best, Qinghua On 4/9/20 1:26 PM, Pandya, Akash wrote: > Hi, > > I have four trajectories of the same condition (protein only) that I want to concatenate. I used the command below to do this: > > gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc -cat > > So this command gives me a file with all four trajectories, pasted together. The combined trajectory has now got four sets of the same time stamps. My question is how can I change the time stamps so that they appear in chronological order, instead of repeated time stamps?. So I would have a combined trajectory e.g. 20 to 200 ns. > > I hope I'm being clear about what I want to do and someone can guide me on achieving this. > > Best wishes, > > Akash > > > > From mariemghoula at gmail.com Thu Apr 9 17:24:44 2020 From: mariemghoula at gmail.com (Mariem Ghoula) Date: Thu, 09 Apr 2020 15:24:44 -0000 Subject: [gmx-users] Converting a tpr file to an older version of gromacs Message-ID: Hi, I would like to use g_mmpbsa on my protein-protein complex simulation. However, after a few errors with the module due to tpr files version mismatch and after reading some posts with the same issue, I came to the conclusion that I need to convert my tpr file to an older version. Can you please help me with this? After installing the old version of gromacs that is compatible with the g_mmpbsa program, how can I convert my tpr file issued from an 2019.5 version to an older one (5.0.7)? Thanks a lot. - Mariem From mark.j.abraham at gmail.com Thu Apr 9 17:47:47 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 09 Apr 2020 15:47:47 -0000 Subject: [gmx-users] Concatenating trajectories In-Reply-To: References: Message-ID: ... and next time you might be better served by using gmx mdrun -cpi and gmx trjconv -extend so that you have your contiguous trajectory by construction! Mark On Thu., 9 Apr. 2020, 14:17 Qinghua Liao, wrote: > Hello, > > There is an option of -settime for gmx trjcat, with which you can set > different starting simulation time > for each trajectory. > > > All the best, > Qinghua > > On 4/9/20 1:26 PM, Pandya, Akash wrote: > > Hi, > > > > I have four trajectories of the same condition (protein only) that I > want to concatenate. I used the command below to do this: > > > > gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc > -cat > > > > So this command gives me a file with all four trajectories, pasted > together. The combined trajectory has now got four sets of the same time > stamps. My question is how can I change the time stamps so that they appear > in chronological order, instead of repeated time stamps?. So I would have a > combined trajectory e.g. 20 to 200 ns. > > > > I hope I'm being clear about what I want to do and someone can guide me > on achieving this. > > > > Best wishes, > > > > Akash > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nelgho at gmail.com Thu Apr 9 22:25:41 2020 From: nelgho at gmail.com (Nadia Elghobashi-Meinhardt) Date: Thu, 09 Apr 2020 20:25:41 -0000 Subject: [gmx-users] Fwd: geometry optimization of metalloenzyme In-Reply-To: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> References: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> Message-ID: Thank you, Justin. I am still struggling with constraints. I am trying to use "freezegrps" and "freezedim" to run an NVT equilibration. However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" What do these messages indicate? Problem in memory allocation? On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: > > > On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: > > Hello everyone, > > > > I am trying to minimize the potential energy of a > > metalloenzyme containing Ni and Fe atoms. > > What is the best way to constrain (fix?) the position of the active site > > atoms > > during the geometry optimization? > > I have tried introducing bonds with relatively high force constants and > > alternatively, tried introducing a [constraints] section, > > but the atoms are still not staying put. > > Bonds or constraints will maintain distances between atoms (relative > position) but not absolute position. > > > Or should one use extra position restraints? > > If the absolute position matters, yes. I would think the approach of > adding restraints or constraints between atoms would be more meaningful > given that preserving coordination geometry is often the defect in MM > treatment of transition metals. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nelgho at gmail.com Thu Apr 9 22:25:41 2020 From: nelgho at gmail.com (Nadia Elghobashi-Meinhardt) Date: Thu, 09 Apr 2020 20:25:41 -0000 Subject: [gmx-users] Fwd: geometry optimization of metalloenzyme In-Reply-To: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> References: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> Message-ID: Thank you, Justin. I am still struggling with constraints. I am trying to use "freezegrps" and "freezedim" to run an NVT equilibration. However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" What do these messages indicate? Problem in memory allocation? On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: > > > On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: > > Hello everyone, > > > > I am trying to minimize the potential energy of a > > metalloenzyme containing Ni and Fe atoms. > > What is the best way to constrain (fix?) the position of the active site > > atoms > > during the geometry optimization? > > I have tried introducing bonds with relatively high force constants and > > alternatively, tried introducing a [constraints] section, > > but the atoms are still not staying put. > > Bonds or constraints will maintain distances between atoms (relative > position) but not absolute position. > > > Or should one use extra position restraints? > > If the absolute position matters, yes. I would think the approach of > adding restraints or constraints between atoms would be more meaningful > given that preserving coordination geometry is often the defect in MM > treatment of transition metals. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From Zuzana.Benkova at savba.sk Fri Apr 10 02:12:14 2020 From: Zuzana.Benkova at savba.sk (Zuzana Benkova) Date: Fri, 10 Apr 2020 00:12:14 -0000 Subject: [gmx-users] How to extend the force field by polariation parameters Message-ID: <1645121772.5078647.1586477186445.JavaMail.zimbra@savba.sk> Dear GROMACS users, I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each carbon atom, with length of 0.7 A? combined with a charge of 0.1 e, which yields a polarization of 0.910 A?^3 (GRAPPA). Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter 4.4. related to the polarization but it contains only information on simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field. Thank you for your answer in advance. Greetings Zuzana From parvezmh89 at gmail.com Fri Apr 10 08:17:01 2020 From: parvezmh89 at gmail.com (Parvez Mh) Date: Fri, 10 Apr 2020 06:17:01 -0000 Subject: [gmx-users] Buggy 2020? Message-ID: Hello All, I am wondering if gromacs-2020 is buggy? or I am missing something?. In gromacs-2020, for a certain setup, I got following warning, WARNING: There are no atom pairs for dispersion correction But, for same system, gromacs-2019 does not give warning. Apparently, gromacs-2020 gives zero in dispersion correction, whereas gormacs-2019 gives non-zero dispersion correction. Regards, Masrul From dave.gromax at gmail.com Fri Apr 10 08:26:45 2020 From: dave.gromax at gmail.com (Dave M) Date: Fri, 10 Apr 2020 06:26:45 -0000 Subject: [gmx-users] treating trajectory for diffusion calculations Message-ID: Hi All, I have a coarse-grained simulation box with water and oil phases. Just playing with the diffusion 'only on a single particle' (single martini coarse bead) gave me different results when I use -rmcomm on trajectories with and without -pbc nojump. NOTE: selected only single bead Same diffusion results: gmx msd -s md.tpr -n index.ndx -f md.xtc # D=2.8914 x1e-5 cm^2/s gmx msd -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s Different diffusion results: gmx msd -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5 cm^2/s gmx msd -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5 cm^2/s Also, I note that -rmcomm D values are very different (factor slow by e-15) from when I don't use rmcomm. What is the correct way to treat trajectory here before calculating msd? I have run my simulation as comm-grps whole system (default option). I am not sure when should I use -rmcomm option (in gmx msd) though the MSD numbers look more relevant if I don't use this. Thanks Dave From dave.gromax at gmail.com Fri Apr 10 09:08:36 2020 From: dave.gromax at gmail.com (Dave M) Date: Fri, 10 Apr 2020 07:08:36 -0000 Subject: [gmx-users] treating trajectory for diffusion calculations In-Reply-To: References: Message-ID: Ah! am sorry, I figured out. Please ignore my mail. I was using wrong group selection for rmcomm in the command line. Sorry to all! Dave On Thu, Apr 9, 2020 at 11:26 PM Dave M wrote: > Hi All, > > I have a coarse-grained simulation box with water and oil phases. Just > playing with the diffusion 'only on a single particle' (single martini > coarse bead) gave me different results when I use -rmcomm on trajectories > with and without -pbc nojump. > > NOTE: selected only single bead > > Same diffusion results: > gmx msd -s md.tpr -n index.ndx -f md.xtc # D=2.8914 x1e-5 cm^2/s > gmx msd -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s > > Different diffusion results: > gmx msd -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5 > cm^2/s > gmx msd -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5 > cm^2/s > > Also, I note that -rmcomm D values are very different (factor slow by > e-15) from when I don't use rmcomm. What is the correct way to treat > trajectory here before calculating msd? I have run my simulation as > comm-grps whole system (default option). I am not sure when should I use > -rmcomm option (in gmx msd) though the MSD numbers look more relevant if I > don't use this. > > Thanks > Dave > From paul.bauer.q at gmail.com Fri Apr 10 09:33:52 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Fri, 10 Apr 2020 07:33:52 -0000 Subject: [gmx-users] Converting a tpr file to an older version of gromacs In-Reply-To: References: Message-ID: Hello, there is no real supported way of doing this. You would need to re-create the TPR in the version you want to use it in. Can you use an external tool instead of g_mmpbsa that supports reading the newer file format? Cheers Paul On 09/04/2020 17:24, Mariem Ghoula wrote: > Hi, > > I would like to use g_mmpbsa on my protein-protein complex simulation. > However, after a few errors with the module due to tpr files version > mismatch and after reading some posts with the same issue, I came to the > conclusion that I need to convert my tpr file to an older version. Can you > please help me with this? After installing the old version of gromacs that > is compatible with the g_mmpbsa program, how can I convert my tpr file > issued from an 2019.5 version to an older one (5.0.7)? > > Thanks a lot. > > - Mariem -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From nelgho at gmail.com Fri Apr 10 10:18:32 2020 From: nelgho at gmail.com (Nadia Elghobashi-Meinhardt) Date: Fri, 10 Apr 2020 08:18:32 -0000 Subject: [gmx-users] Fwd: Fwd: geometry optimization of metalloenzyme In-Reply-To: References: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> Message-ID: Thank you, Justin. I am still struggling with constraints. I am trying to use "*freezegrps*" and "*freezedim*" to run an NVT equilibration of a structure (successfully geometry-optimized using freezegrps). However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" These messages seem to indicate a memory allocation problem, but I cannot isolate the problem. I am not sure of the correct combination of constraint (lincs) keywords in the nvt input, especially how to combine these with the freezegrps/freezedim commands. Do anybody have any tips or helpful examples? On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: > > > On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: > > Hello everyone, > > > > I am trying to minimize the potential energy of a > > metalloenzyme containing Ni and Fe atoms. > > What is the best way to constrain (fix?) the position of the active site > > atoms > > during the geometry optimization? > > I have tried introducing bonds with relatively high force constants and > > alternatively, tried introducing a [constraints] section, > > but the atoms are still not staying put. > > Bonds or constraints will maintain distances between atoms (relative > position) but not absolute position. > > > Or should one use extra position restraints? > > If the absolute position matters, yes. I would think the approach of > adding restraints or constraints between atoms would be more meaningful > given that preserving coordination geometry is often the defect in MM > treatment of transition metals. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From mariemghoula at gmail.com Fri Apr 10 13:57:30 2020 From: mariemghoula at gmail.com (Mariem Ghoula) Date: Fri, 10 Apr 2020 11:57:30 -0000 Subject: [gmx-users] Converting a tpr file to an older version of gromacs In-Reply-To: References: Message-ID: Hi Paul, Thank you for your reply. In fact, there is the GMXPBSA tool but I still have errors with that too when I run it on the examples provided in the installation folder. I tried to seek some help but the developers aren't responding. Thank you anyway! - Mariem Le ven. 10 avr. 2020 ? 09:34, Paul bauer a ?crit : > Hello, > > there is no real supported way of doing this. You would need to > re-create the TPR in the version you want to use it in. > Can you use an external tool instead of g_mmpbsa that supports reading > the newer file format? > > Cheers > > Paul > > On 09/04/2020 17:24, Mariem Ghoula wrote: > > Hi, > > > > I would like to use g_mmpbsa on my protein-protein complex simulation. > > However, after a few errors with the module due to tpr files version > > mismatch and after reading some posts with the same issue, I came to the > > conclusion that I need to convert my tpr file to an older version. Can > you > > please help me with this? After installing the old version of gromacs > that > > is compatible with the g_mmpbsa program, how can I convert my tpr file > > issued from an 2019.5 version to an older one (5.0.7)? > > > > Thanks a lot. > > > > - Mariem > > > -- > Paul Bauer, PhD > GROMACS Development Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From alexanderwien2k at gmail.com Fri Apr 10 14:14:00 2020 From: alexanderwien2k at gmail.com (Alex) Date: Fri, 10 Apr 2020 12:14:00 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> Message-ID: Dear Justin, Any comment please? Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the film. I even sometimes have > the same issue when I simulate the bulk of this system, I mean a cubic box > filled by this molecule and no water. > I got the force fields from the latest version of ATB repository by which > I have previously done some other simulation for the same molecule. > > https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb > > %--------mdp------- > title = Thin-Film > integrator = md > dt = 0.002 ; 2 fs ;0.001 1 fs > nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns > xtc-precision = 500 ; 1000 > ;nstlist = 40 > %----------------- > ;;in .trr file > nstxout = 3000 ; 6000 > nstvout = 0 > nstfout = 0 > ;;in energy file.log > nstlog = 2000 ; 4000 > nstcalcenergy = 2000 ;4000 > nstenergy = 2000 ;4000 > ;;in xtc file > nstxout-compressed = 0 > ;compressed-x-grps = non-Water > %----------------- > continuation = yes > gen-vel = no > constraint-algorithm = lincs > constraints = h-bonds > cutoff-scheme = Verlet > coulombtype = PME > rcoulomb = 1.4 > > vdwtype = Cut-off > rvdw = 1.4 > DispCorr = EnerPres > > tcoupl = v-rescale > tc-grps = system > tau-t = 1.5 > nhchainlength = 10 > ref-t = 298.15 > pbc = xyz > > pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > tau_p = 2.5 > compressibility = 4.5e-5 > ref_p = 1.0 > refcoord-scaling = com > energygrps = thin_film SOL > comm-mode = Linear > nstcomm = 100 > comm-grps = Thin_fiml SOL > %------------------------- > > Thank you > Alex > > On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > >> >> >> On 4/7/20 5:00 PM, Alex wrote: >> > Dear all, >> > After minimization and equalizations using nvt (v-rescale) and npt (both >> > berendsen and ;Parrinello-Rahman), a simulation of mine could run well >> for >> > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = >> 0.002 >> > with the particles communication fatal error. >> > >> > Fatal error: >> > 2 particles communicated to PME rank 12 are more than 2/3 times the >> cut-off >> > out of the domain decomposition cell of their charge group in dimension >> y. >> > This usually means that your system is not well equilibrated. >> > >> > So, if the system would not be well equlibrated, then I would expect >> that >> > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I >> expect >> > that it also crashes for example around 6 ns as the with the dt = 0.002 >> the >> > simulation last only 3 ns. >> > >> > Any comment that helps to understand the problem would be highly >> > appreciated. >> >> Please provide a description of what your system is and a full .mdp >> file. While most of the time these crashes come from poor equilibration, >> an inadequately parametrized topology or bad combination/misuse of >> algorithms can also cause crashes. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > From jalemkul at vt.edu Fri Apr 10 15:02:36 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 13:02:36 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> Message-ID: <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> On 4/10/20 8:13 AM, Alex wrote: > Dear Justin, > Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." I would also suggest you thoroughly validate the quality of the epoxy molecule topology against QM data and bulk-phase properties, if possible. -Justin > Regards, > Alex > > On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > >> Thanks Justin for the response. >> Please find below the mdp file. >> The system is a thin film made out of a epoxy molecule, picture in be >> below link, with water on top and bottom of the film. I even sometimes have >> the same issue when I simulate the bulk of this system, I mean a cubic box >> filled by this molecule and no water. >> I got the force fields from the latest version of ATB repository by which >> I have previously done some other simulation for the same molecule. >> >> https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb >> >> %--------mdp------- >> title = Thin-Film >> integrator = md >> dt = 0.002 ; 2 fs ;0.001 1 fs >> nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns >> xtc-precision = 500 ; 1000 >> ;nstlist = 40 >> %----------------- >> ;;in .trr file >> nstxout = 3000 ; 6000 >> nstvout = 0 >> nstfout = 0 >> ;;in energy file.log >> nstlog = 2000 ; 4000 >> nstcalcenergy = 2000 ;4000 >> nstenergy = 2000 ;4000 >> ;;in xtc file >> nstxout-compressed = 0 >> ;compressed-x-grps = non-Water >> %----------------- >> continuation = yes >> gen-vel = no >> constraint-algorithm = lincs >> constraints = h-bonds >> cutoff-scheme = Verlet >> coulombtype = PME >> rcoulomb = 1.4 >> >> vdwtype = Cut-off >> rvdw = 1.4 >> DispCorr = EnerPres >> >> tcoupl = v-rescale >> tc-grps = system >> tau-t = 1.5 >> nhchainlength = 10 >> ref-t = 298.15 >> pbc = xyz >> >> pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic >> tau_p = 2.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> refcoord-scaling = com >> energygrps = thin_film SOL >> comm-mode = Linear >> nstcomm = 100 >> comm-grps = Thin_fiml SOL >> %------------------------- >> >> Thank you >> Alex >> >> On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: >> >>> >>> On 4/7/20 5:00 PM, Alex wrote: >>>> Dear all, >>>> After minimization and equalizations using nvt (v-rescale) and npt (both >>>> berendsen and ;Parrinello-Rahman), a simulation of mine could run well >>> for >>>> 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = >>> 0.002 >>>> with the particles communication fatal error. >>>> >>>> Fatal error: >>>> 2 particles communicated to PME rank 12 are more than 2/3 times the >>> cut-off >>>> out of the domain decomposition cell of their charge group in dimension >>> y. >>>> This usually means that your system is not well equilibrated. >>>> >>>> So, if the system would not be well equlibrated, then I would expect >>> that >>>> with dt = 0.001 the simulation wouldn't run well for 200 ns. But I >>> expect >>>> that it also crashes for example around 6 ns as the with the dt = 0.002 >>> the >>>> simulation last only 3 ns. >>>> >>>> Any comment that helps to understand the problem would be highly >>>> appreciated. >>> Please provide a description of what your system is and a full .mdp >>> file. While most of the time these crashes come from poor equilibration, >>> an inadequately parametrized topology or bad combination/misuse of >>> algorithms can also cause crashes. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Office: 301 Fralin Hall >>> Lab: 303 Engel Hall >>> >>> Virginia Tech Department of Biochemistry >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalemkul at vt.edu | (540) 231-3129 >>> http://www.thelemkullab.com >>> >>> ================================================== >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 10 15:03:55 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 13:03:55 -0000 Subject: [gmx-users] Fwd: geometry optimization of metalloenzyme In-Reply-To: References: <53333cff-f995-4aba-e747-cc4fbfc033a0@vt.edu> Message-ID: <158ba13d-cd3f-47f6-57a6-1fde75bf1d64@vt.edu> On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote: > Thank you, Justin. > I am still struggling with constraints. > I am trying to use "freezegrps" and "freezedim" > to run an NVT equilibration. > However, when I try to build the binary using my optimized structure, I get > either "Segmentation fault" or the following error: > "free(): invalid next size (fast) > Aborted" > What do these messages indicate? Problem in memory allocation? All of this is probably a downstream effect of a simulation that is unstable and crashed. Freezing is totally artificial and I strongly discourage using it. The crash may be due to failure to use energygrp_exclusions when freezing or due to intrinsic instability of the system that even freezing cannot overcome. -Justin > On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: > >> >> On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: >>> Hello everyone, >>> >>> I am trying to minimize the potential energy of a >>> metalloenzyme containing Ni and Fe atoms. >>> What is the best way to constrain (fix?) the position of the active site >>> atoms >>> during the geometry optimization? >>> I have tried introducing bonds with relatively high force constants and >>> alternatively, tried introducing a [constraints] section, >>> but the atoms are still not staying put. >> Bonds or constraints will maintain distances between atoms (relative >> position) but not absolute position. >> >>> Or should one use extra position restraints? >> If the absolute position matters, yes. I would think the approach of >> adding restraints or constraints between atoms would be more meaningful >> given that preserving coordination geometry is often the defect in MM >> treatment of transition metals. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 10 15:05:59 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 13:05:59 -0000 Subject: [gmx-users] How to extend the force field by polariation parameters In-Reply-To: <1645121772.5078647.1586477186445.JavaMail.zimbra@savba.sk> References: <1645121772.5078647.1586477186445.JavaMail.zimbra@savba.sk> Message-ID: On 4/9/20 8:06 PM, Zuzana Benkova wrote: > Dear GROMACS users, > > I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each > carbon atom, with length of 0.7 A? combined with a charge of 0.1 e, which yields a polarization of 0.910 A?^3 (GRAPPA). > > Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter 4.4. related to the polarization but it contains only information on simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field. If your model has a fixed length between the core nucleus and the auxiliary particle, it's not a "polarizable" model because the dipoles cannot relax/change length, therefore nothing related to polarization options is relevant to you. You will have particles that are at a fixed distance from their nucleus (e.g. via [constraints]) -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ashmakhan200 at gmail.com Fri Apr 10 15:13:10 2020 From: ashmakhan200 at gmail.com (Ashma Khan) Date: Fri, 10 Apr 2020 13:13:10 -0000 Subject: [gmx-users] Regarding version of gromacs Message-ID: Dear all, I have run my simulation on gromacs 5.1.4 for 200ns but now I want to extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will there be problem during total simulation of 500ns in my systems. Please give me suggestion regarding this. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh From alexanderwien2k at gmail.com Fri Apr 10 15:17:16 2020 From: alexanderwien2k at gmail.com (Alex) Date: Fri, 10 Apr 2020 13:17:16 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> Message-ID: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fields are parametrized assuming all bonds are fixed, so > your constraints should be "all-bonds" not "h-bonds." > Interesting, hopefully that is the problem. > > I would also suggest you thoroughly validate the quality of the epoxy > molecule topology against QM data and bulk-phase properties, if possible. > As the ATB folks claim, the parameterization has been performed against a very high level DFT calculation, especially for the molecules with less than 50 atoms. I already have tested the density and it is in agreement with the experimental value. Regarding the "comm-grps = " , would you also please kindly let me know which one you would recommend for this system + plus a small single molecule called MOL_A which defuses from water inside the epoxy, specially for the PMF calculation of the Mol_A? comm-grps = Other SOL ;; (Other = thin_film and Mol_A) or comm-grps = system Thank you Alex > > -Justin > > > Regards, > > Alex > > > > On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > > > >> Thanks Justin for the response. > >> Please find below the mdp file. > >> The system is a thin film made out of a epoxy molecule, picture in be > >> below link, with water on top and bottom of the film. I even sometimes > have > >> the same issue when I simulate the bulk of this system, I mean a cubic > box > >> filled by this molecule and no water. > >> I got the force fields from the latest version of ATB repository by > which > >> I have previously done some other simulation for the same molecule. > >> > >> https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb > >> > >> %--------mdp------- > >> title = Thin-Film > >> integrator = md > >> dt = 0.002 ; 2 fs ;0.001 1 fs > >> nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns > >> xtc-precision = 500 ; 1000 > >> ;nstlist = 40 > >> %----------------- > >> ;;in .trr file > >> nstxout = 3000 ; 6000 > >> nstvout = 0 > >> nstfout = 0 > >> ;;in energy file.log > >> nstlog = 2000 ; 4000 > >> nstcalcenergy = 2000 ;4000 > >> nstenergy = 2000 ;4000 > >> ;;in xtc file > >> nstxout-compressed = 0 > >> ;compressed-x-grps = non-Water > >> %----------------- > >> continuation = yes > >> gen-vel = no > >> constraint-algorithm = lincs > >> constraints = h-bonds > >> cutoff-scheme = Verlet > >> coulombtype = PME > >> rcoulomb = 1.4 > >> > >> vdwtype = Cut-off > >> rvdw = 1.4 > >> DispCorr = EnerPres > >> > >> tcoupl = v-rescale > >> tc-grps = system > >> tau-t = 1.5 > >> nhchainlength = 10 > >> ref-t = 298.15 > >> pbc = xyz > >> > >> pcoupl = Parrinello-Rahman > >> Pcoupltype = isotropic > >> tau_p = 2.5 > >> compressibility = 4.5e-5 > >> ref_p = 1.0 > >> refcoord-scaling = com > >> energygrps = thin_film SOL > >> comm-mode = Linear > >> nstcomm = 100 > >> comm-grps = Thin_fiml SOL > >> %------------------------- > >> > >> Thank you > >> Alex > >> > >> On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > >> > >>> > >>> On 4/7/20 5:00 PM, Alex wrote: > >>>> Dear all, > >>>> After minimization and equalizations using nvt (v-rescale) and npt > (both > >>>> berendsen and ;Parrinello-Rahman), a simulation of mine could run well > >>> for > >>>> 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = > >>> 0.002 > >>>> with the particles communication fatal error. > >>>> > >>>> Fatal error: > >>>> 2 particles communicated to PME rank 12 are more than 2/3 times the > >>> cut-off > >>>> out of the domain decomposition cell of their charge group in > dimension > >>> y. > >>>> This usually means that your system is not well equilibrated. > >>>> > >>>> So, if the system would not be well equlibrated, then I would expect > >>> that > >>>> with dt = 0.001 the simulation wouldn't run well for 200 ns. But I > >>> expect > >>>> that it also crashes for example around 6 ns as the with the dt = > 0.002 > >>> the > >>>> simulation last only 3 ns. > >>>> > >>>> Any comment that helps to understand the problem would be highly > >>>> appreciated. > >>> Please provide a description of what your system is and a full .mdp > >>> file. While most of the time these crashes come from poor > equilibration, > >>> an inadequately parametrized topology or bad combination/misuse of > >>> algorithms can also cause crashes. > >>> > >>> -Justin > >>> > >>> -- > >>> ================================================== > >>> > >>> Justin A. Lemkul, Ph.D. > >>> Assistant Professor > >>> Office: 301 Fralin Hall > >>> Lab: 303 Engel Hall > >>> > >>> Virginia Tech Department of Biochemistry > >>> 340 West Campus Dr. > >>> Blacksburg, VA 24061 > >>> > >>> jalemkul at vt.edu | (540) 231-3129 > >>> http://www.thelemkullab.com > >>> > >>> ================================================== > >>> > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-request at gromacs.org. > >>> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Fri Apr 10 15:18:44 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 13:18:44 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> Message-ID: <81cbf4a1-4a7a-d0e9-a512-950544f2afb7@vt.edu> On 4/10/20 9:16 AM, Alex wrote: > Thank you for the response. > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > >> >> On 4/10/20 8:13 AM, Alex wrote: >>> Dear Justin, >>> Any comment please? >> Sorry, haven't had power/network for a while due to some bad storms here. >> >> GROMOS force fields are parametrized assuming all bonds are fixed, so >> your constraints should be "all-bonds" not "h-bonds." >> > Interesting, hopefully that is the problem. > > >> I would also suggest you thoroughly validate the quality of the epoxy >> molecule topology against QM data and bulk-phase properties, if possible. >> > As the ATB folks claim, the parameterization has been performed against a > very high level DFT calculation, especially for the molecules with less > than 50 atoms. > I already have tested the density and it is in agreement with the > experimental value. > > Regarding the "comm-grps = " , would you also please kindly let me know > which one you would recommend for this system + plus a small single > molecule called MOL_A which defuses from water inside the epoxy, specially > for the PMF calculation of the Mol_A? > comm-grps = Other SOL ;; (Other = thin_film and Mol_A) > or > comm-grps = system I saw the conversation with David about this. I have nothing to add that he hasn't already said. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From fnabi at myamu.ac.in Fri Apr 10 15:22:01 2020 From: fnabi at myamu.ac.in (FAISAL NABI) Date: Fri, 10 Apr 2020 13:22:01 -0000 Subject: [gmx-users] Regarding version of gromacs In-Reply-To: References: Message-ID: I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: > Dear all, > I have run my simulation on gromacs 5.1.4 for 200ns but now I want to > extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will > there be problem during total simulation of 500ns in my systems. Please > give me suggestion regarding this. > > -- > Ashma Khan > Research Scholar > Department of Chemistry > AMU, Aligarh > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Fri Apr 10 15:23:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 13:23:39 -0000 Subject: [gmx-users] Regarding version of gromacs In-Reply-To: References: Message-ID: <1e28d398-da6c-0e62-0eaa-dd3f6a241ea2@vt.edu> On 4/10/20 9:21 AM, FAISAL NABI wrote: > I have tried the same few days back but it didn't work. I have been using > gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. Switching between major versions that are years apart in their development will not work, and GROMACS has never guaranteed backwards compatibility between major versions. Patch releases in the same release series (e.g. 5.1.4 vs 5.1.2) should be compatible because the .tpr version will not have changed, but one needs to question why move backwards and potentially introduce bugs that were fixed between versions? -Justin > On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: > >> Dear all, >> I have run my simulation on gromacs 5.1.4 for 200ns but now I want to >> extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will >> there be problem during total simulation of 500ns in my systems. Please >> give me suggestion regarding this. >> >> -- >> Ashma Khan >> Research Scholar >> Department of Chemistry >> AMU, Aligarh >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From yasaman.karami at pasteur.fr Fri Apr 10 17:04:52 2020 From: yasaman.karami at pasteur.fr (Yasaman KARAMI) Date: Fri, 10 Apr 2020 15:04:52 -0000 Subject: [gmx-users] GROMACS version issue Message-ID: Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along the z-axis, for example dimensions are changing from 98.4 x 98.4 x 299.1 (A^3) to 116.8 x 116.8 x 212.9 (A^3). After trying so many possibilities, I've realised it is a version specific problem. Trying GROMACS 2019.4 the problem is totally solved. I was wondering if you could explain the reason. Thank you in advance. Best regards, Yasaman From jalemkul at vt.edu Fri Apr 10 17:20:31 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 15:20:31 -0000 Subject: [gmx-users] GROMACS version issue In-Reply-To: References: Message-ID: <5a2dd30a-1bf1-49ce-6a09-ebad2bedaa59@vt.edu> On 4/10/20 11:04 AM, Yasaman KARAMI wrote: > Dear GROMACS developers, > > > I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along the z-axis, for example dimensions are changing from 98.4 x 98.4 x 299.1 (A^3) to 116.8 x 116.8 x 212.9 (A^3). > > After trying so many possibilities, I've realised it is a version specific problem. Trying GROMACS 2019.4 the problem is totally solved. > > I was wondering if you could explain the reason. > If you're using the CHARMM force field, this was an issue related to incorrect treatment of CMAP terms when the protein crossed a periodic boundary. The issue was recently solved so you should use the newer GROMACS version. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From elham802011 at yahoo.com Fri Apr 10 18:15:41 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Fri, 10 Apr 2020 16:15:41 -0000 Subject: [gmx-users] Problem with pdb2gmx References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> Message-ID: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. From jalemkul at vt.edu Fri Apr 10 18:25:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 16:25:47 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> Message-ID: On 4/10/20 12:15 PM, Elham Taghikhani wrote: > Hi > > I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. > In the topology, I got this warning message : > Warning:long-bond... > I don't know what should I do to retain the covalent bond. > I will appreciate it if you help me with this problem. The full screen output of pdb2gmx would be informative here. If the long bond occurs between the residues flanking your modified residue, you forgot step 5 in http://manual.gromacs.org/documentation/current/how-to/topology.html#adding-a-new-residue If that doesn't solve it, please post the full screen output from pdb2gmx. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From rollyng at gmail.com Fri Apr 10 19:35:24 2020 From: rollyng at gmail.com (Rolly Ng) Date: Fri, 10 Apr 2020 17:35:24 -0000 Subject: [gmx-users] Protonated ligand free energy calculation in water Message-ID: <016a01d60f5e$678091f0$3681b5d0$@gmail.com> Dear GROMACS users, I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the webpage, http://www.mdtutorials.com/gmx/free_energy/index.html It is very helpful and easy to follow, but my ligand is protonated so the atomic charges in the topol.top are non-zero. The above tutorial also indicates that Coulombic interactions can be applied, but I would like to know how it can be done? vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 Here is the [ atoms ] in my topol.top and your advise is highly appreciated! [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 MT3 rtp MT3 q 2.0 1 nh 1 MT3 N1 1 -0.83505600 14.010000 ; qtot -0.835056 2 cz 1 MT3 C1 2 0.85138300 12.010000 ; qtot 0.016327 3 nh 1 MT3 N2 3 -0.51848300 14.010000 ; qtot -0.502156 4 nh 1 MT3 N3 4 -0.83505600 14.010000 ; qtot -1.337212 5 c3 1 MT3 C2 5 -0.34660600 12.010000 ; qtot -1.683818 6 nh 1 MT3 N4 6 0.02468700 14.010000 ; qtot -1.659131 7 nh 1 MT3 N5 7 -0.80566500 14.010000 ; qtot -2.464796 8 cz 1 MT3 C3 8 0.57808800 12.010000 ; qtot -1.886708 9 c3 1 MT3 C4 9 -0.34660600 12.010000 ; qtot -2.233314 10 hn 1 MT3 H1 10 0.47045200 1.008000 ; qtot -1.762862 11 hn 1 MT3 H2 11 0.47045200 1.008000 ; qtot -1.292410 12 hn 1 MT3 H3 12 0.38772400 1.008000 ; qtot -0.904686 13 hn 1 MT3 H4 13 0.47045200 1.008000 ; qtot -0.434234 14 h1 1 MT3 H5 14 0.17432200 1.008000 ; qtot -0.259912 15 h1 1 MT3 H6 15 0.17432200 1.008000 ; qtot -0.085590 16 h1 1 MT3 H7 16 0.17432200 1.008000 ; qtot 0.088732 17 hn 1 MT3 H8 17 0.45892600 1.008000 ; qtot 0.547658 18 h1 1 MT3 H9 18 0.17432200 1.008000 ; qtot 0.721980 19 h1 1 MT3 H10 19 0.17432200 1.008000 ; qtot 0.896302 20 h1 1 MT3 H11 20 0.17432200 1.008000 ; qtot 1.070624 21 hn 1 MT3 H12 21 0.45892600 1.008000 ; qtot 1.529550 22 hn 1 MT3 H13 22 0.47045200 1.008000 ; qtot 2.000002 Thank you, Rolly From alexanderwien2k at gmail.com Fri Apr 10 22:18:36 2020 From: alexanderwien2k at gmail.com (Alex) Date: Fri, 10 Apr 2020 20:18:36 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: <81cbf4a1-4a7a-d0e9-a512-950544f2afb7@vt.edu> References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> <81cbf4a1-4a7a-d0e9-a512-950544f2afb7@vt.edu> Message-ID: On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > > > On 4/10/20 9:16 AM, Alex wrote: > > Thank you for the response. > > > > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > >> > >> On 4/10/20 8:13 AM, Alex wrote: > >>> Dear Justin, > >>> Any comment please? > >> Sorry, haven't had power/network for a while due to some bad storms > here. > >> > >> GROMOS force fields are parametrized assuming all bonds are fixed, so > >> your constraints should be "all-bonds" not "h-bonds." > >> > > Interesting, hopefully that is the problem. > By constraining all the bonds "constraints = all-bonds", the simulation crashes in the first step immediately irrespective to the starting point of simulation, even if I continue the old working simulation. Regards, Alex > > > > > >> I would also suggest you thoroughly validate the quality of the epoxy > >> molecule topology against QM data and bulk-phase properties, if > possible. > >> > > As the ATB folks claim, the parameterization has been performed against a > > very high level DFT calculation, especially for the molecules with less > > than 50 atoms. > > I already have tested the density and it is in agreement with the > > experimental value. > > > > Regarding the "comm-grps = " , would you also please kindly let me know > > which one you would recommend for this system + plus a small single > > molecule called MOL_A which defuses from water inside the epoxy, > specially > > for the PMF calculation of the Mol_A? > > comm-grps = Other SOL ;; (Other = thin_film and Mol_A) > > or > > comm-grps = system > > I saw the conversation with David about this. I have nothing to add that > he hasn't already said. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Fri Apr 10 23:19:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 21:19:21 -0000 Subject: [gmx-users] dt in mdp In-Reply-To: References: <1c2496bf-afb1-466e-3685-b672a2b63758@vt.edu> <1f47fce1-ccc2-4572-646d-b2a6450ebc2f@vt.edu> <81cbf4a1-4a7a-d0e9-a512-950544f2afb7@vt.edu> Message-ID: <2ff1f26d-e227-99fe-4a41-216246e19db4@vt.edu> On 4/10/20 4:17 PM, Alex wrote: > On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > >> >> On 4/10/20 9:16 AM, Alex wrote: >>> Thank you for the response. >>> >>> >>> On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: >>> >>>> On 4/10/20 8:13 AM, Alex wrote: >>>>> Dear Justin, >>>>> Any comment please? >>>> Sorry, haven't had power/network for a while due to some bad storms >> here. >>>> GROMOS force fields are parametrized assuming all bonds are fixed, so >>>> your constraints should be "all-bonds" not "h-bonds." >>>> >>> Interesting, hopefully that is the problem. > By constraining all the bonds "constraints = all-bonds", the simulation > crashes in the first step immediately irrespective to the starting point of > simulation, even if I continue the old working simulation. Now we're getting somewhere. That suggests that at least one bond has deviated substantially from its equilibrium length, such that the constraint algorithm fails immediately. This also likely underlies the original failure - forces are building up on some atoms such that mdrun crashes. You have either a bad geometry, inadequate topology, or both. Inspect the molecule(s) that mdrun complains about to see if the molecules are distorted by computing bond lengths and comparing against the force field's parameters. It may be beneficial to re-minimize and equilibrate with the proper constraint scheme after validating that the topology is of sufficient quality. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sadafrani6 at gmail.com Fri Apr 10 23:48:38 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Fri, 10 Apr 2020 21:48:38 -0000 Subject: [gmx-users] segmentation fault gmx do_dssp Message-ID: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Not all residues were recognized (489 from 40652), the result may be inaccurate! Group 0 ( System) has 128526 elements Group 1 ( Protein) has 7893 elements Group 2 ( Protein-H) has 3971 elements Group 3 ( C-alpha) has 489 elements Group 4 ( Backbone) has 1467 elements Group 5 ( MainChain) has 1957 elements Group 6 ( MainChain+Cb) has 2415 elements Group 7 ( MainChain+H) has 2424 elements Group 8 ( SideChain) has 5469 elements Group 9 ( SideChain-H) has 2014 elements Group 10 ( Prot-Masses) has 7893 elements Group 11 ( non-Protein) has 120633 elements Group 12 ( Other) has 173 elements Group 13 ( G6P) has 27 elements Group 14 ( NAP) has 73 elements Group 15 ( NAS) has 73 elements Group 16 ( NA) has 10 elements Group 17 ( Water) has 120450 elements Group 18 ( SOL) has 120450 elements Group 19 ( non-Water) has 8076 elements Group 20 ( Ion) has 10 elements Group 21 ( G6P) has 27 elements Group 22 ( NAP) has 73 elements Group 23 ( NAS) has 73 elements Group 24 ( NA) has 10 elements Group 25 ( Water_and_ions) has 120460 elements Select a group: 5 Selected 5: 'MainChain' There are 489 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' Reading frame 0 time 0.000 Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# Segmentation fault (core dumped) How should I fix it. As my system is protein-ligand should I choose a group having protein and ligand together for this analysis? Any suggestions will really help. Thanks. Sadaf From scorpio.liao at gmail.com Fri Apr 10 23:53:03 2020 From: scorpio.liao at gmail.com (Qinghua Liao) Date: Fri, 10 Apr 2020 21:53:03 -0000 Subject: [gmx-users] segmentation fault gmx do_dssp In-Reply-To: References: Message-ID: Hello, I guess the problem is about memory. You could strip the water and ions first, then process the striped trajectory. All the best, Qinghua On 4/10/20 11:48 PM, Sadaf Rani wrote: > Dear Gromacs users > I am doing an analysis of protein-ligand MD simulation of 150ns. I am > trying to calculate secondary structure as below:- > gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 > > But I am getting segmentation fault error. > > Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) > Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) > Not all residues were recognized (489 from 40652), the result may be > inaccurate! > Group 0 ( System) has 128526 elements > Group 1 ( Protein) has 7893 elements > Group 2 ( Protein-H) has 3971 elements > Group 3 ( C-alpha) has 489 elements > Group 4 ( Backbone) has 1467 elements > Group 5 ( MainChain) has 1957 elements > Group 6 ( MainChain+Cb) has 2415 elements > Group 7 ( MainChain+H) has 2424 elements > Group 8 ( SideChain) has 5469 elements > Group 9 ( SideChain-H) has 2014 elements > Group 10 ( Prot-Masses) has 7893 elements > Group 11 ( non-Protein) has 120633 elements > Group 12 ( Other) has 173 elements > Group 13 ( G6P) has 27 elements > Group 14 ( NAP) has 73 elements > Group 15 ( NAS) has 73 elements > Group 16 ( NA) has 10 elements > Group 17 ( Water) has 120450 elements > Group 18 ( SOL) has 120450 elements > Group 19 ( non-Water) has 8076 elements > Group 20 ( Ion) has 10 elements > Group 21 ( G6P) has 27 elements > Group 22 ( NAP) has 73 elements > Group 23 ( NAS) has 73 elements > Group 24 ( NA) has 10 elements > Group 25 ( Water_and_ions) has 120460 elements > Select a group: 5 > Selected 5: 'MainChain' > There are 489 residues in your selected group > dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' > Reading frame 0 time 0.000 > Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# > Segmentation fault (core dumped) > How should I fix it. As my system is protein-ligand should I choose a group > having protein and ligand together for this analysis? > Any suggestions will really help. > Thanks. > Sadaf From jalemkul at vt.edu Fri Apr 10 23:54:43 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 21:54:43 -0000 Subject: [gmx-users] segmentation fault gmx do_dssp In-Reply-To: References: Message-ID: <1f25d365-8c18-f40e-4896-bbc3fdeaa39c@vt.edu> On 4/10/20 5:48 PM, Sadaf Rani wrote: > Dear Gromacs users > I am doing an analysis of protein-ligand MD simulation of 150ns. I am > trying to calculate secondary structure as below:- > gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 > > But I am getting segmentation fault error. > > Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) > Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) > Not all residues were recognized (489 from 40652), the result may be > inaccurate! > Group 0 ( System) has 128526 elements > Group 1 ( Protein) has 7893 elements > Group 2 ( Protein-H) has 3971 elements > Group 3 ( C-alpha) has 489 elements > Group 4 ( Backbone) has 1467 elements > Group 5 ( MainChain) has 1957 elements > Group 6 ( MainChain+Cb) has 2415 elements > Group 7 ( MainChain+H) has 2424 elements > Group 8 ( SideChain) has 5469 elements > Group 9 ( SideChain-H) has 2014 elements > Group 10 ( Prot-Masses) has 7893 elements > Group 11 ( non-Protein) has 120633 elements > Group 12 ( Other) has 173 elements > Group 13 ( G6P) has 27 elements > Group 14 ( NAP) has 73 elements > Group 15 ( NAS) has 73 elements > Group 16 ( NA) has 10 elements > Group 17 ( Water) has 120450 elements > Group 18 ( SOL) has 120450 elements > Group 19 ( non-Water) has 8076 elements > Group 20 ( Ion) has 10 elements > Group 21 ( G6P) has 27 elements > Group 22 ( NAP) has 73 elements > Group 23 ( NAS) has 73 elements > Group 24 ( NA) has 10 elements > Group 25 ( Water_and_ions) has 120460 elements > Select a group: 5 > Selected 5: 'MainChain' > There are 489 residues in your selected group > dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' > Reading frame 0 time 0.000 > Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# > Segmentation fault (core dumped) > How should I fix it. As my system is protein-ligand should I choose a group > having protein and ligand together for this analysis? The selection does not depend on the contents of the system; either MainChain or MainChain+H should work. You need to verify that your dssp binary works correctly and that its version matches what is expected by GROMACS. You may need to use the -ver option. See the many posts on this very topic in the archive. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From Zuzana.Benkova at savba.sk Sat Apr 11 00:44:58 2020 From: Zuzana.Benkova at savba.sk (Zuzana Benkova) Date: Fri, 10 Apr 2020 22:44:58 -0000 Subject: [gmx-users] How to extend the force field by polariation parameters In-Reply-To: References: <1645121772.5078647.1586477186445.JavaMail.zimbra@savba.sk> Message-ID: <2087965226.5180316.1586558681140.JavaMail.zimbra@savba.sk> Dear Justin, thank you for your answer. As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary particle, assumes rigid length between them. In this model, the virtual site has no van der Waals interactions, while it has a charge q and a mass m. Unlike the Drude oscillator, this rod a has a finite dipole moment = charge x length. Thus, it requires an orientational averaging (i.e., T > 0) to produce physically meaningful results. The rod involves three parameters: length, charge, and mass.The polarizability is (charge x length)^2/(3kbT) and the intrinsic time scale is given by (2kbT/(length^2 x mass)^0.5. Such a model has been already used. The authors carried out the simulations for graphene (GRAPPA FF) using GROMACS (Nanoscale, 2014, 6, 5438). I just wonder if I could adopt this model without changes in code by using virtual interaction sites. Thanks. Greetings Zuzana ----- Original Message ----- From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 10, 2020 3:05:47 PM Subject: Re: [gmx-users] How to extend the force field by polariation parameters On 4/9/20 8:06 PM, Zuzana Benkova wrote: > Dear GROMACS users, > > I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each > carbon atom, with length of 0.7 A? combined with a charge of 0.1 e, which yields a polarization of 0.910 A?^3 (GRAPPA). > > Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter 4.4. related to the polarization but it contains only information on simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field. If your model has a fixed length between the core nucleus and the auxiliary particle, it's not a "polarizable" model because the dipoles cannot relax/change length, therefore nothing related to polarization options is relevant to you. You will have particles that are at a fixed distance from their nucleus (e.g. via [constraints]) -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Sat Apr 11 00:49:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 10 Apr 2020 22:49:39 -0000 Subject: [gmx-users] How to extend the force field by polariation parameters In-Reply-To: <2087965226.5180316.1586558681140.JavaMail.zimbra@savba.sk> References: <1645121772.5078647.1586477186445.JavaMail.zimbra@savba.sk> <2087965226.5180316.1586558681140.JavaMail.zimbra@savba.sk> Message-ID: <1cec31da-1e15-1b2e-4b0e-03961d3b90a3@vt.edu> On 4/10/20 6:44 PM, Zuzana Benkova wrote: > Dear Justin, > > thank you for your answer. > As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary particle, assumes rigid length between them. > In this model, the virtual site has no van der Waals interactions, while it has a charge q and a mass m. Unlike the Drude oscillator, this rod a has a finite dipole moment = charge x length. Thus, it requires an orientational averaging (i.e., T > 0) to produce physically meaningful results. The rod involves three parameters: length, charge, and mass.The polarizability is (charge x length)^2/(3kbT) and the intrinsic time scale is given by (2kbT/(length^2 x mass)^0.5. Such a model has been already used. The authors carried out the simulations for graphene (GRAPPA FF) using GROMACS (Nanoscale, 2014, 6, 5438). > I just wonder if I could adopt this model without changes in code by using virtual interaction sites. No, Drude oscillators are not virtual sites, but you also do not need any code changes, either. If the study was published using GROMACS, you should contact the authors and ask for sample inputs. But it should be rather simple to set this up. I would argue this is not really a Drude model because the atom-"Drude" length is fixed. While the dipole can reorient, it cannot, by definition, oscillate if the length is constrained. All you have are additional atoms. They carry charge, have mass, and exist at fixed length from their parent atoms, which can be accomplished with [constraints] for all the dipoles. -Justin > Thanks. > > Greetings > > Zuzana > > > > > ----- Original Message ----- > From: "Justin Lemkul" > To: "gmx-users" > Sent: Friday, April 10, 2020 3:05:47 PM > Subject: Re: [gmx-users] How to extend the force field by polariation parameters > > On 4/9/20 8:06 PM, Zuzana Benkova wrote: >> Dear GROMACS users, >> >> I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each >> carbon atom, with length of 0.7 A? combined with a charge of 0.1 e, which yields a polarization of 0.910 A?^3 (GRAPPA). >> >> Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter 4.4. related to the polarization but it contains only information on simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field. > If your model has a fixed length between the core nucleus and the > auxiliary particle, it's not a "polarizable" model because the dipoles > cannot relax/change length, therefore nothing related to polarization > options is relevant to you. You will have particles that are at a fixed > distance from their nucleus (e.g. via [constraints]) > > -Justin > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From afsane_farhadi at yahoo.com Sat Apr 11 01:23:22 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Fri, 10 Apr 2020 23:23:22 -0000 Subject: [gmx-users] energy minimizing References: <637071192.2619091.1586557860833.ref@mail.yahoo.com> Message-ID: <637071192.2619091.1586557860833@mail.yahoo.com> hi friends?I generated a box of mixed gas with gmx insert-molecules....I ran an energy minimizing. ?the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization.?what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction ?is weaker than intramolecular interaction but I don't know how I can control this matter.?please help? Sent from Yahoo Mail on Android From sadafrani6 at gmail.com Sat Apr 11 02:07:19 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sat, 11 Apr 2020 00:07:19 -0000 Subject: [gmx-users] segmentation fault gmx do_dssp Message-ID: Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Qinghua, I am already using the stripped trajectory. Any suggestions would be appreciated. Thanks. Sadaf From jalemkul at vt.edu Sat Apr 11 02:39:49 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 00:39:49 -0000 Subject: [gmx-users] segmentation fault gmx do_dssp In-Reply-To: References: Message-ID: <4cd98a6c-f27a-82b6-7d13-e1da143ed7d6@vt.edu> On 4/10/20 8:07 PM, Sadaf Rani wrote: > Dear Justin and Qinghua > > I am using gromacs 2020 for analysis and dssp version on my system > is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Your version should be fine, but make sure the dssp binary works properly on its own (not via do_dssp) and try specifying -ver 2 when running do_dssp. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From fernando at hypernetlabs.io Sat Apr 11 03:03:40 2020 From: fernando at hypernetlabs.io (fernando at hypernetlabs.io) Date: Sat, 11 Apr 2020 01:03:40 -0000 Subject: [gmx-users] pdb2gmx: Selecting Force Field in first command Message-ID: <004501d60f9d$07506640$15f132c0$@hypernetlabs.io> Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Docker container with a Dockerfile (Dockerfile = instruction file for auto execution inside the container) containing the below: FROM mariojmdavid/gromacs-cuda:2019.3-runtime <-- thanks Mario! :) WORKDIR /usr/local/gromacs COPY . /usr/local/gromacs ENTRYPOINT ["/usr/local/gromacs/bin/gmx","pdb2gmx", "-f", "1aki.pdb", "-o", "1aki_processed.gro", "-water", "spce"] Problem Both simple examples ask to 'Select the Force Field' after the 1st command is executed. A Docker container is non-interactive so I can't really pass my option for Force Field after I send it off to auto-execute remotely. Question Does anyone know how I can pass my Force Field selection from the start? Many thanks in advance! Fernando From jalemkul at vt.edu Sat Apr 11 03:09:45 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 01:09:45 -0000 Subject: [gmx-users] pdb2gmx: Selecting Force Field in first command In-Reply-To: <004501d60f9d$07506640$15f132c0$@hypernetlabs.io> References: <004501d60f9d$07506640$15f132c0$@hypernetlabs.io> Message-ID: <4017a137-9259-ecc3-e1dc-05dbc501740c@vt.edu> On 4/10/20 9:03 PM, fernando at hypernetlabs.io wrote: > Hi all! > > Context > > I'm trying to run simple gromacs example commands below > > * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce > * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter > -water spc > > > > In a Docker container with a Dockerfile (Dockerfile = instruction file for > auto execution inside the container) containing the below: > > > > FROM mariojmdavid/gromacs-cuda:2019.3-runtime <-- thanks Mario! :) > > WORKDIR /usr/local/gromacs > > COPY . /usr/local/gromacs > > ENTRYPOINT ["/usr/local/gromacs/bin/gmx","pdb2gmx", "-f", "1aki.pdb", "-o", > "1aki_processed.gro", "-water", "spce"] > > > > Problem > > Both simple examples ask to 'Select the Force Field' after the 1st command > is executed. A Docker container is non-interactive so I can't really pass my > option for Force Field after I send it off to auto-execute remotely. > > > > Question > > Does anyone know how I can pass my Force Field selection from the start? That's what the -ff flag does. See gmx help pdb2gmx for all command-line options. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ashmakhan200 at gmail.com Sat Apr 11 03:21:07 2020 From: ashmakhan200 at gmail.com (Ashma Khan) Date: Sat, 11 Apr 2020 01:21:07 -0000 Subject: [gmx-users] Regarding version of gromacs Message-ID: Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh From jalemkul at vt.edu Sat Apr 11 03:22:14 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 01:22:14 -0000 Subject: [gmx-users] Regarding version of gromacs In-Reply-To: References: Message-ID: <960fa09f-738e-2db0-264b-a6619d8bc256@vt.edu> On 4/10/20 9:20 PM, Ashma Khan wrote: > Thank you Justin for your suggestion > As I run my simulation on supercomputer and there is availability of > gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it > has only 5.1.2 version. > You can always install the version you want in your home directory. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From mark.j.abraham at gmail.com Sat Apr 11 07:33:41 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 11 Apr 2020 05:33:41 -0000 Subject: [gmx-users] Buggy 2020? In-Reply-To: References: Message-ID: Hi, Based on what is in your system, what do you think the behavior should be? A change reflects that one of the versions may be wrong, but not that the new one is necessarily it. Mark On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote: > Hello All, > > I am wondering if gromacs-2020 is buggy? or I am missing something?. In > gromacs-2020, for a certain setup, I got following warning, > WARNING: There are no atom pairs for dispersion correction > > But, for same system, gromacs-2019 does not give warning. Apparently, > gromacs-2020 gives zero in dispersion correction, whereas > gormacs-2019 gives non-zero dispersion correction. > > Regards, > Masrul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From parvezmh89 at gmail.com Sat Apr 11 11:09:40 2020 From: parvezmh89 at gmail.com (Parvez Mh) Date: Sat, 11 Apr 2020 09:09:40 -0000 Subject: [gmx-users] Buggy 2020? In-Reply-To: References: Message-ID: Mark, I am expecting non-zero value. Looks like, the bugs is fixed in the latest version of gromacs-2020.1. I was trying gromacs-2020, which was giving zero dispersion, but 2020.1 is giving correct (non-zero). Sincerely, Masrul On Sat, Apr 11, 2020 at 12:33 AM Mark Abraham wrote: > Hi, > > Based on what is in your system, what do you think the behavior should be? > A change reflects that one of the versions may be wrong, but not that the > new one is necessarily it. > > Mark > > On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote: > > > Hello All, > > > > I am wondering if gromacs-2020 is buggy? or I am missing something?. In > > gromacs-2020, for a certain setup, I got following warning, > > WARNING: There are no atom pairs for dispersion correction > > > > But, for same system, gromacs-2019 does not give warning. Apparently, > > gromacs-2020 gives zero in dispersion correction, whereas > > gormacs-2019 gives non-zero dispersion correction. > > > > Regards, > > Masrul > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nt_mahmood at yahoo.com Sat Apr 11 11:26:06 2020 From: nt_mahmood at yahoo.com (Mahmood Naderan) Date: Sat, 11 Apr 2020 09:26:06 -0000 Subject: [gmx-users] Cannot run short-ranged nonbonded interactions on a GPU because there is none detected. References: <536493806.2714139.1586596434380.ref@mail.yahoo.com> Message-ID: <536493806.2714139.1586596434380@mail.yahoo.com> Hi Although I have built gromacs for 1080Ti and the device is working properly, I get this error when running gmx command $ ./gromacs-2019.4-1080ti/single/bin/gmx mdrun -nb gpu -v -deffnm nvt_5k ?..... GROMACS:????? gmx mdrun, version 2019.4 Executable:?? /storage/users/mnaderan/gromacs/./gromacs-2019.4-1080ti/single/bin/gmx Data prefix:? /storage/users/mnaderan/gromacs/./gromacs-2019.4-1080ti/single Working dir:? /storage/users/mnaderan/gromacs Command line: ? gmx mdrun -nb gpu -v -deffnm nvt_5k Back Off! I just backed up nvt_5k.log to ./#nvt_5k.log.1# Reading file nvt_5k.tpr, VERSION 2019.3 (single precision) Changing nstlist from 20 to 100, rlist from 1.023 to 1.147 Using 32 MPI threads Using 1 OpenMP thread per tMPI thread ------------------------------------------------------- Program:???? gmx mdrun, version 2019.4 Source file: src/gromacs/mdrun/runner.cpp (line 1041) MPI rank:??? 20 (out of 32) Fatal error: Cannot run short-ranged nonbonded interactions on a GPU because there is none detected. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ------------------------------------------------------- Program:???? gmx mdrun, version 2019.4 As I said, the device is working properly $ echo $CUDA_VISIBLE_DEVICES 0 $ ~/NVIDIA_CUDA-10.1_Samples/1_Utilities/deviceQuery/deviceQuery /storage/users/mnaderan/NVIDIA_CUDA-10.1_Samples/1_Utilities/deviceQuery/deviceQuery Starting... ?CUDA Device Query (Runtime API) version (CUDART static linking) Detected 1 CUDA Capable device(s) Device 0: "GeForce GTX 1080 Ti" ? CUDA Driver Version / Runtime Version????????? 10.0 / 10.0 ? CUDA Capability Major/Minor version number:??? 6.1 ? Total amount of global memory:???????????????? 11178 MBytes (11721506816 bytes) ? (28) Multiprocessors, (128) CUDA Cores/MP:???? 3584 CUDA Cores ? GPU Max Clock rate:??????????????????????????? 1683 MHz (1.68 GHz) ? Memory Clock rate:???????????????????????????? 5505 Mhz .... The configure command was cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/storage/users/mnaderan/gromacs/gromacs-2019.4-1080ti/single -DGMX_GPU=on -DGMX_CUDA_TARGET_SM=61 Any idea for fixing that? Regards, Mahmood From elham802011 at yahoo.com Sat Apr 11 11:38:57 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sat, 11 Apr 2020 09:38:57 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <1543342397.4042521.1586594738869@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> Message-ID: <605598567.4079627.1586597927263@mail.yahoo.com> Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 129 residues with 1971 atoms Chain time... Making bonds... Warning: Long Bond (1459-1462 = 0.259531 nm) Warning: Long Bond (1754-1757 = 0.259591 nm) Number of bonds was 1995, now 1995 Generating angles, dihedrals and pairs... Before cleaning: 5163 pairs Before cleaning: 5208 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 5208 dihedrals,? 429 impropers, 3556 angles ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites Total mass 14324.281 a.m.u. Total charge 19.000 e Writing topology Processing chain 2 (39 atoms, 1 residues) Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add FLO to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 39 atoms Chain time... Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions... There are??? 0 dihedrals,??? 0 impropers,??? 0 angles ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites Total mass 373.322 a.m.u. Total charge 0.000 e Writing topology Including chain 1 in system: 1971 atoms 129 residues Including chain 2 in system: 39 atoms 1 residues Now there are 2010 atoms and 130 residues Total mass in system 14697.603 a.m.u. Total charge in system 19.000 e Writing coordinate file... ?? ??? ?--------- PLEASE NOTE ------------ You have successfully generated a topology from: complex.pdb. The Oplsaa force field and the spc water model are used. ?? ??? ?--------- ETON ESAELP ------------ On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance. On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. From spoel at xray.bmc.uu.se Sat Apr 11 12:10:59 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 11 Apr 2020 10:10:59 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <605598567.4079627.1586597927263@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> Message-ID: <82a55314-e873-c4cf-29a5-6c761254b16c@xray.bmc.uu.se> Den 2020-04-11 kl. 11:38, skrev Elham Taghikhani: > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. > As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Give your ligand a different chain identifier such that gromacs knows these are different molecules. And make it a HETATM instead of ATOM. > Thank you in advance > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 129 residues with 1971 atoms > Chain time... > Making bonds... > Warning: Long Bond (1459-1462 = 0.259531 nm) > Warning: Long Bond (1754-1757 = 0.259591 nm) > Number of bonds was 1995, now 1995 > Generating angles, dihedrals and pairs... > Before cleaning: 5163 pairs > Before cleaning: 5208 dihedrals > Keeping all generated dihedrals > Making cmap torsions... > There are 5208 dihedrals,? 429 impropers, 3556 angles > ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites > Total mass 14324.281 a.m.u. > Total charge 19.000 e > Writing topology > Processing chain 2 (39 atoms, 1 residues) > > Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your structure, > and add FLO to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time... > Making bonds... > No bonds > Generating angles, dihedrals and pairs... > Making cmap torsions... > There are??? 0 dihedrals,??? 0 impropers,??? 0 angles > ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites > Total mass 373.322 a.m.u. > Total charge 0.000 e > Writing topology > Including chain 1 in system: 1971 atoms 129 residues > Including chain 2 in system: 39 atoms 1 residues > Now there are 2010 atoms and 130 residues > Total mass in system 14697.603 a.m.u. > Total charge in system 19.000 e > > Writing coordinate file... > ?? ??? ?--------- PLEASE NOTE ------------ > You have successfully generated a topology from: complex.pdb. > The Oplsaa force field and the spc water model are used. > ?? ??? ?--------- ETON ESAELP ------------ > > > On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: > > > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance. > On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: > > Hi > > I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. > In the topology, I got this warning message : > Warning:long-bond... > I don't know what should I do to retain the covalent bond. > I will appreciate it if you help me with this problem. > -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From jalemkul at vt.edu Sat Apr 11 13:06:36 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 11:06:36 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <605598567.4079627.1586597927263@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> Message-ID: <4b819740-e4ca-e627-2802-07ed603341db@vt.edu> On 4/11/20 5:38 AM, Elham Taghikhani wrote: > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. > As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 129 residues with 1971 atoms > Chain time... > Making bonds... > Warning: Long Bond (1459-1462 = 0.259531 nm) > Warning: Long Bond (1754-1757 = 0.259591 nm) > Number of bonds was 1995, now 1995 > Generating angles, dihedrals and pairs... > Before cleaning: 5163 pairs > Before cleaning: 5208 dihedrals > Keeping all generated dihedrals > Making cmap torsions... > There are 5208 dihedrals,? 429 impropers, 3556 angles > ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites > Total mass 14324.281 a.m.u. > Total charge 19.000 e > Writing topology > Processing chain 2 (39 atoms, 1 residues) > > Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your structure, > and add FLO to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time... > Making bonds... > No bonds > Generating angles, dihedrals and pairs... > Making cmap torsions... > There are??? 0 dihedrals,??? 0 impropers,??? 0 angles > ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites > Total mass 373.322 a.m.u. > Total charge 0.000 e > Writing topology > Including chain 1 in system: 1971 atoms 129 residues > Including chain 2 in system: 39 atoms 1 residues > Now there are 2010 atoms and 130 residues > Total mass in system 14697.603 a.m.u. > Total charge in system 19.000 e > > Writing coordinate file... > ?? ??? ?--------- PLEASE NOTE ------------ > You have successfully generated a topology from: complex.pdb. > The Oplsaa force field and the spc water model are used. > ?? ??? ?--------- ETON ESAELP ------------ There are two methods to handle this case: 1. Write an .rtp entry that encompasses both the ligand and the residue to which it is covalently linked, including the bond between the two entities. Add this new residue as Protein in residuetypes.dat. 2. As David suggested in his message, leave the ligand in a separate chain and deal with it as a separate species. This approach requires you to add an entry to specbonds.dat to generate the bond between the protein and the covalent ligand. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From zhangxuan7788 at gmail.com Sat Apr 11 14:04:20 2020 From: zhangxuan7788 at gmail.com (Xuan Zhang) Date: Sat, 11 Apr 2020 12:04:20 -0000 Subject: [gmx-users] Problem in energy minimization step Message-ID: Hi, I am a newer to GROMACS. I want to simulate the CO2 + Water + Surfactant system with GROMACS 2019.4. I generated the .pdb file with Packmol like below. After the 50000 steps steep EM, I want to run the cg EM, but it always had errors, One or more water molecules can not be settled. Is it because of the box size in Packmol? I have checked the all the .itp, .pdb files of surfactants, CO2 and H2O, and did not find error. Even I removed the surfacants, just mixing CO2 and H2O, it still did not work. However, when I exchange the surfactant type, sometimes it works. Thank you for all your kind reply very much. Looking forward any advice. Xuan tolerance 2.0 filetype pdb output mix.pdb structure CO2.pdb number 5400 inside box 0. 0. 0. 80. 80. 80. end structure structure C12.pdb number 30 inside box 0. 0. 82. 80. 80. 122. end structure structure H2O.pdb number 12000 inside box 0. 0. 130. 80. 80. 230. end structure structure C12.pdb number 30 inside box 0. 0. 238. 80. 80. 278. end structure structure CO22.pdb number 5400 inside box 0. 0. 280. 80. 80. 360. end structure step -1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. ------------------------------------------------------- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/mdrun/minimize.cpp (line 719) Fatal error: The coordinates could not be constrained. Minimizer 'cg' can not handle constraint failures, use minimizer 'steep' before using 'cg'. -- *Xuan Zhang* zhangxuan7788 at gmail.com From elham802011 at yahoo.com Sat Apr 11 18:18:59 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sat, 11 Apr 2020 16:18:59 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <605598567.4079627.1586597927263@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> Message-ID: <909802158.4236641.1586621815168@mail.yahoo.com> Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning: Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 129 residues with 1971 atoms Chain time... Making bonds... Warning: Long Bond (1459-1462 = 0.259531 nm) Warning: Long Bond (1754-1757 = 0.259591 nm) Number of bonds was 1995, now 1995 Generating angles, dihedrals and pairs... Before cleaning: 5163 pairs Before cleaning: 5208 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 5208 dihedrals,? 429 impropers, 3556 angles ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites Total mass 14324.281 a.m.u. Total charge 19.000 e Writing topology Processing chain 2 (39 atoms, 1 residues) Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add FLO to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 39 atoms Chain time... Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions... There are??? 0 dihedrals,??? 0 impropers,??? 0 angles ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites Total mass 373.322 a.m.u. Total charge 0.000 e Writing topology Including chain 1 in system: 1971 atoms 129 residues Including chain 2 in system: 39 atoms 1 residues Now there are 2010 atoms and 130 residues Total mass in system 14697.603 a.m.u. Total charge in system 19.000 e Writing coordinate file... ?? ??? ?--------- PLEASE NOTE ------------ You have successfully generated a topology from: complex.pdb. The Oplsaa force field and the spc water model are used. ?? ??? ?--------- ETON ESAELP ------------ On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance. On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. From jalemkul at vt.edu Sat Apr 11 18:26:32 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 16:26:32 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <909802158.4236641.1586621815168@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> <909802158.4236641.1586621815168@mail.yahoo.com> Message-ID: <600c821a-0b5f-1bb3-3640-5912ee04f048@vt.edu> On 4/11/20 12:16 PM, Elham Taghikhani wrote: > Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning: > > Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could either be > correct or a catastrophic error. Please check your structure, and add all > necessary residue names to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > The solution is to add FLO as a Protein residue in residuetypes.dat. -Justin > On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: > > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. > As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 129 residues with 1971 atoms > Chain time... > Making bonds... > Warning: Long Bond (1459-1462 = 0.259531 nm) > Warning: Long Bond (1754-1757 = 0.259591 nm) > Number of bonds was 1995, now 1995 > Generating angles, dihedrals and pairs... > Before cleaning: 5163 pairs > Before cleaning: 5208 dihedrals > Keeping all generated dihedrals > Making cmap torsions... > There are 5208 dihedrals,? 429 impropers, 3556 angles > ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites > Total mass 14324.281 a.m.u. > Total charge 19.000 e > Writing topology > Processing chain 2 (39 atoms, 1 residues) > > Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your structure, > and add FLO to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time... > Making bonds... > No bonds > Generating angles, dihedrals and pairs... > Making cmap torsions... > There are??? 0 dihedrals,??? 0 impropers,??? 0 angles > ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites > Total mass 373.322 a.m.u. > Total charge 0.000 e > Writing topology > Including chain 1 in system: 1971 atoms 129 residues > Including chain 2 in system: 39 atoms 1 residues > Now there are 2010 atoms and 130 residues > Total mass in system 14697.603 a.m.u. > Total charge in system 19.000 e > > Writing coordinate file... > ?? ??? ?--------- PLEASE NOTE ------------ > You have successfully generated a topology from: complex.pdb. > The Oplsaa force field and the spc water model are used. > ?? ??? ?--------- ETON ESAELP ------------ > > > On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: > > > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance. > On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: > > Hi > > I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. > In the topology, I got this warning message : > Warning:long-bond... > I don't know what should I do to retain the covalent bond. > I will appreciate it if you help me with this problem. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From elham802011 at yahoo.com Sat Apr 11 20:55:39 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sat, 11 Apr 2020 18:55:39 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <909802158.4236641.1586621815168@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> <909802158.4236641.1586621815168@mail.yahoo.com> Message-ID: <891501189.4285992.1586631333228@mail.yahoo.com> Thank you.? I did what you said and added new bond to specbond.dat file like this: 10 LYS???? CD????? 2?????? FLO???? NZ????? 2?????? 1.8???? LYS ?? FLO LYS???? NZ????? 2?????? FLO???? CX????? 2?????? 1.8???? LYS? ?? FLOCYS?? ?SG?? ?1?? ?CYS?? ?SG?? ?1?? ?0.2?? ?CYS2?? ?CYS2 CYS?? ?SG?? ?1?? ?HEM ?? ?FE?? ?2?? ?0.25?? ?CYS2?? ?HEME CYS?? ?SG?? ?1?? ?HEM ?? ?CAB?? ?1?? ?0.18?? ?CYS2?? ?HEME CYS?? ?SG?? ?1?? ?HEM ?? ?CAC?? ?1?? ?0.18?? ?CYS2?? ?HEME HIS?? ?NE2?? ?1?? ?HEM ?? ?FE?? ?1?? ?0.2?? ?HIS1?? ?HEME MET?? ?SD?? ?1?? ?HEM ?? ?FE?? ?1?? ?0.24?? ?MET?? ?HEME CO????? C?????? 1?????? HEME??? FE????? 1?????? 0.19??? CO????? HEME CYM???? SG????? 1?????? CYM???? SG????? 1?????? 0.2???? CYS2??? CYS2 but it seems that it doesn't read the lines of the specbond.dat file. 8 out of 8 lines of specbond.dat converted successfully...CASPH?? Protein CGLUH?? Protein FLO???? Other DA?? ?DNA DG?? ?DNA DC?? ?DNA..This is part of my residuetypes.dat file. I think there is some problem with my residuetypes.dat file but i don't what it is. nothing works i am so confused now. On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani wrote: Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning: Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 129 residues with 1971 atoms Chain time... Making bonds... Warning: Long Bond (1459-1462 = 0.259531 nm) Warning: Long Bond (1754-1757 = 0.259591 nm) Number of bonds was 1995, now 1995 Generating angles, dihedrals and pairs... Before cleaning: 5163 pairs Before cleaning: 5208 dihedrals Keeping all generated dihedrals Making cmap torsions... There are 5208 dihedrals,? 429 impropers, 3556 angles ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites Total mass 14324.281 a.m.u. Total charge 19.000 e Writing topology Processing chain 2 (39 atoms, 1 residues) Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add FLO to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 39 atoms Chain time... Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions... There are??? 0 dihedrals,??? 0 impropers,??? 0 angles ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites Total mass 373.322 a.m.u. Total charge 0.000 e Writing topology Including chain 1 in system: 1971 atoms 129 residues Including chain 2 in system: 39 atoms 1 residues Now there are 2010 atoms and 130 residues Total mass in system 14697.603 a.m.u. Total charge in system 19.000 e Writing coordinate file... ?? ??? ?--------- PLEASE NOTE ------------ You have successfully generated a topology from: complex.pdb. The Oplsaa force field and the spc water model are used. ?? ??? ?--------- ETON ESAELP ------------ On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: Hi Thank you for your response. I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. Thank you in advance. On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. From jalemkul at vt.edu Sat Apr 11 21:28:07 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 11 Apr 2020 19:28:07 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <891501189.4285992.1586631333228@mail.yahoo.com> References: <2F6D04A9-5552-47C2-86C6-664DA0B8EF06.ref@yahoo.com> <2F6D04A9-5552-47C2-86C6-664DA0B8EF06@yahoo.com> <1543342397.4042521.1586594738869@mail.yahoo.com> <605598567.4079627.1586597927263@mail.yahoo.com> <909802158.4236641.1586621815168@mail.yahoo.com> <891501189.4285992.1586631333228@mail.yahoo.com> Message-ID: <570ceca7-c418-fc93-8d98-c73c5f4d4bed@vt.edu> On 4/11/20 2:55 PM, Elham Taghikhani wrote: > Thank you. > I did what you said and added new bond to specbond.dat file like this: > 10 > LYS???? CD????? 2?????? FLO???? NZ????? 2?????? 1.8???? LYS ?? FLO > LYS???? NZ????? 2?????? FLO???? CX????? 2?????? 1.8???? LYS? ?? FLOCYS?? ?SG?? ?1?? ?CYS?? ?SG?? ?1?? ?0.2?? ?CYS2?? ?CYS2 I don't know whether it's your email formatting or the actual content of specbond.dat, but make sure you're using proper line endings. Also note that I doubt what you're doing is right. If you're simply asking for your residue to be bonded to NZ of LYS, that will generate a total of 5 bonds to NZ and not account for the change in charge. You should be generating a custom LYS residue and name it something else, which should be specified in the second-to-last column in specbond.dat. You will need to add it to residuetypes.dat, as well. > CYS?? ?SG?? ?1?? ?HEM ?? ?FE?? ?2?? ?0.25?? ?CYS2?? ?HEME > CYS?? ?SG?? ?1?? ?HEM ?? ?CAB?? ?1?? ?0.18?? ?CYS2?? ?HEME > CYS?? ?SG?? ?1?? ?HEM ?? ?CAC?? ?1?? ?0.18?? ?CYS2?? ?HEME > HIS?? ?NE2?? ?1?? ?HEM ?? ?FE?? ?1?? ?0.2?? ?HIS1?? ?HEME > MET?? ?SD?? ?1?? ?HEM ?? ?FE?? ?1?? ?0.24?? ?MET?? ?HEME > CO????? C?????? 1?????? HEME??? FE????? 1?????? 0.19??? CO????? HEME > CYM???? SG????? 1?????? CYM???? SG????? 1?????? 0.2???? CYS2??? CYS2 > > but it seems that it doesn't read the lines of the specbond.dat file. Which file did you modify? One in your local directory or the system-wide version in $GMXLIB? > 8 out of 8 lines of specbond.dat converted successfully...CASPH?? Protein > CGLUH?? Protein > FLO???? Other I suggested adding FLO as "Protein," not as "Other." > DA?? ?DNA > DG?? ?DNA > DC?? ?DNA..This is part of my residuetypes.dat file. > I think there is some problem with my residuetypes.dat file but i don't what it is. > nothing works i am so confused now. Please always provide the full screen output of pdb2gmx. There is a lot of diagnostic information it contains that may help. You may also want to post your PDB file and modified force field somewhere so we can better help in troubleshooting what is going on. -Justin > On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani wrote: > > Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning: > > Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could either be > correct or a catastrophic error. Please check your structure, and add all > necessary residue names to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > > On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: > > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. > As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 129 residues with 1971 atoms > Chain time... > Making bonds... > Warning: Long Bond (1459-1462 = 0.259531 nm) > Warning: Long Bond (1754-1757 = 0.259591 nm) > Number of bonds was 1995, now 1995 > Generating angles, dihedrals and pairs... > Before cleaning: 5163 pairs > Before cleaning: 5208 dihedrals > Keeping all generated dihedrals > Making cmap torsions... > There are 5208 dihedrals,? 429 impropers, 3556 angles > ????????? 5127 pairs,???? 1995 bonds and???? 0 virtual sites > Total mass 14324.281 a.m.u. > Total charge 19.000 e > Writing topology > Processing chain 2 (39 atoms, 1 residues) > > Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your structure, > and add FLO to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time... > Making bonds... > No bonds > Generating angles, dihedrals and pairs... > Making cmap torsions... > There are??? 0 dihedrals,??? 0 impropers,??? 0 angles > ???????????? 0 pairs,??????? 0 bonds and???? 0 virtual sites > Total mass 373.322 a.m.u. > Total charge 0.000 e > Writing topology > Including chain 1 in system: 1971 atoms 129 residues > Including chain 2 in system: 39 atoms 1 residues > Now there are 2010 atoms and 130 residues > Total mass in system 14697.603 a.m.u. > Total charge in system 19.000 e > > Writing coordinate file... > ?? ??? ?--------- PLEASE NOTE ------------ > You have successfully generated a topology from: complex.pdb. > The Oplsaa force field and the spc water model are used. > ?? ??? ?--------- ETON ESAELP ------------ > > > On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: > > > Hi > Thank you for your response. > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work.As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > Thank you in advance. > On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: > > Hi > > I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. > In the topology, I got this warning message : > Warning:long-bond... > I don't know what should I do to retain the covalent bond. > I will appreciate it if you help me with this problem. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From mohammad.madani at uconn.edu Sun Apr 12 05:41:04 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Sun, 12 Apr 2020 03:41:04 -0000 Subject: [gmx-users] Post processing REMD simulation Message-ID: Dear all, Hi. I have problems about the analysis of the REMD simulation. I run the remd for folding the protein. I have 191 replicas, the temperature range is 300K to 500K. I ran the simulation 16 ns for each replica. and the exchange rate is between 0.3-0.4. Now, I have one trr file and one log file for each replica in its temperature. I do not how can analysis these outputs. Could you please help me with this? Many thanks. Mohammad From mohammad.madani at uconn.edu Sun Apr 12 05:41:04 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Sun, 12 Apr 2020 03:41:04 -0000 Subject: [gmx-users] Post processing REMD simulation Message-ID: Dear all, Hi. I have problems about the analysis of the REMD simulation. I run the remd for folding the protein. I have 191 replicas, the temperature range is 300K to 500K. I ran the simulation 16 ns for each replica. and the exchange rate is between 0.3-0.4. Now, I have one trr file and one log file for each replica in its temperature. I do not how can analysis these outputs. Could you please help me with this? Many thanks. Mohammad From spoel at xray.bmc.uu.se Sun Apr 12 08:25:14 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 12 Apr 2020 06:25:14 -0000 Subject: [gmx-users] Post processing REMD simulation In-Reply-To: References: Message-ID: <4ff9e9ae-a03f-ef66-62c4-5eb85e7311da@xray.bmc.uu.se> Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: > Dear all, > Hi. > I have problems about the analysis of the REMD simulation. I run the remd > for folding the protein. > > I have 191 replicas, the temperature range is 300K to 500K. I ran the > simulation 16 ns for each replica. and the exchange rate is between > 0.3-0.4. > Now, I have one trr file and one log file for each replica in its > temperature. > I do not how can analysis these outputs. > > Could you please help me with this? What would you like to analyze? You will have to write a couple of scripts to plot potential energy as a function of T for instance. > > Many thanks. > > Mohammad > -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From mohammad.madani at uconn.edu Sun Apr 12 08:37:11 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Sun, 12 Apr 2020 06:37:11 -0000 Subject: [gmx-users] Post processing REMD simulation In-Reply-To: <4ff9e9ae-a03f-ef66-62c4-5eb85e7311da@xray.bmc.uu.se> References: <4ff9e9ae-a03f-ef66-62c4-5eb85e7311da@xray.bmc.uu.se> Message-ID: Dear Prof. Van der Spoel Many thanks for your email. In fact, I want to predict the structure of one highly disorder protein. I ran my Remd simulation for 16ns per each replica. I Checked the trajectory file of one of the replica randomly but I did not see any significant change in comparison with my initial Structure. I asked question about this issue from one of the professor in MIT, he suggest me that because the structure is disordered it will be important to characterize the ensemble you get out, rather than a single structure. Now, I do not know what should I do with this. Could you please help me with this? Many thanks On Sun, Apr 12, 2020 at 2:25 AM David van der Spoel wrote: > *Message sent from a system outside of UConn.* > > > Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: > > Dear all, > > Hi. > > I have problems about the analysis of the REMD simulation. I run the remd > > for folding the protein. > > > > I have 191 replicas, the temperature range is 300K to 500K. I ran the > > simulation 16 ns for each replica. and the exchange rate is between > > 0.3-0.4. > > Now, I have one trr file and one log file for each replica in its > > temperature. > > I do not how can analysis these outputs. > > > > Could you please help me with this? > > What would you like to analyze? > > You will have to write a couple of scripts to plot potential energy as a > function of T for instance. > > > > Many thanks. > > > > Mohammad > > > > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Sun Apr 12 08:52:02 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 12 Apr 2020 06:52:02 -0000 Subject: [gmx-users] Post processing REMD simulation In-Reply-To: References: <4ff9e9ae-a03f-ef66-62c4-5eb85e7311da@xray.bmc.uu.se> Message-ID: <8976c161-bb01-4db5-9fc0-8abdfd6afd65@xray.bmc.uu.se> Den 2020-04-12 kl. 08:36, skrev Mohammad Madani: > Dear Prof. Van der Spoel > Many thanks for your email. > In fact, I want to predict the structure of one highly disorder protein. I > ran my Remd simulation for 16ns per each replica. I Checked the trajectory > file of one of the replica randomly but I did not see any significant > change in comparison with my initial Structure. > I asked question about this issue from one of the professor in MIT, he > suggest me that because the structure is disordered it will be important to > characterize the ensemble you get out, rather than a single structure. > > Now, I do not know what should I do with this. > > Could you please help me with this? When you say you don't see any changes, have you visually inspected all the final structures? Another thing you can try is concatenate the trajectories from the 10 or 20 lowest temperature and run clustering analysis. Unfortunately 16 ns is not very long because it takes time to change conformation. It is also far from certain that your temperature exchange worked over the whole range, that is that structures cycled from 300K to 500K and back. The demux.pl script in the gromacs distribution may help analyzing that if it still works. > > Many thanks > > On Sun, Apr 12, 2020 at 2:25 AM David van der Spoel > wrote: > >> *Message sent from a system outside of UConn.* >> >> >> Den 2020-04-12 kl. 05:40, skrev Mohammad Madani: >>> Dear all, >>> Hi. >>> I have problems about the analysis of the REMD simulation. I run the remd >>> for folding the protein. >>> >>> I have 191 replicas, the temperature range is 300K to 500K. I ran the >>> simulation 16 ns for each replica. and the exchange rate is between >>> 0.3-0.4. >>> Now, I have one trr file and one log file for each replica in its >>> temperature. >>> I do not how can analysis these outputs. >>> >>> Could you please help me with this? >> >> What would you like to analyze? >> >> You will have to write a couple of scripts to plot potential energy as a >> function of T for instance. >>> >>> Many thanks. >>> >>> Mohammad >>> >> >> >> -- >> David van der Spoel, Ph.D., >> Professor of Biology >> Uppsala University. >> http://virtualchemistry.org >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From sadafrani6 at gmail.com Sun Apr 12 13:12:43 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 12 Apr 2020 11:12:43 -0000 Subject: [gmx-users] duplicate angle index- angle restraint Message-ID: Dear Gromacs users I am putting some restraints on bonds angles and dihedrals during free energy calculations for which the topology file section is as below:- ; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 7968 213 10 0.382 0.382 10.0 0.0 0.382 0.382 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 7959 7968 213 7968 1 89.40 0.0 1 89.40 41.840 1 213 7968 7922 7968 1 66.78 0.0 1 66.78 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7959 7968 213 218 1 174.86 0.0 0.0 174.86 0.0 41.840 7922 7968 213 211 1 149.95 0.0 0.0 149.95 0.0 41.840 7952 7968 213 211 1 167.76 0.0 0.0 167.76 0.0 41.840 grompp gives me warning that I have duplicate angle index when I remove column 4 (al) in angle restraints I get following message:- ERROR 1 [file topol.top, line 76867]: Incorrect number of parameters - found 5, expected 3 or 6 for Angle Rest. (after the function type). Could you please correct me in fixing this section, I followed table 5.14 of gromacs manual. Thanks in advance for your kind help. Regards. Sadaf From jalemkul at vt.edu Sun Apr 12 13:17:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 12 Apr 2020 11:17:35 -0000 Subject: [gmx-users] duplicate angle index- angle restraint In-Reply-To: References: Message-ID: <7ae2c974-69d6-2e09-0e29-7709718cb6ee@vt.edu> On 4/12/20 7:12 AM, Sadaf Rani wrote: > Dear Gromacs users > > I am putting some restraints on bonds angles and dihedrals during free > energy calculations for which the topology file section is as below:- > ; distance restraints > [ bonds ] > ; i j type r0A r1A r2A fcA r0B r1B r2B > fcB > 7968 213 10 0.382 0.382 10.0 0.0 0.382 0.382 10.0 > 4184.000 > > [ angle_restraints ] > ; ai aj ak al type thA fcA multA thB fcB > multB > 7959 7968 213 7968 1 89.40 0.0 1 89.40 41.840 > 1 > 213 7968 7922 7968 1 66.78 0.0 1 66.78 41.840 > 1 > > [ dihedral_restraints ] > ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB > 7959 7968 213 218 1 174.86 0.0 0.0 174.86 0.0 > 41.840 > 7922 7968 213 211 1 149.95 0.0 0.0 149.95 0.0 > 41.840 > 7952 7968 213 211 1 167.76 0.0 0.0 167.76 0.0 > 41.840 > > grompp gives me warning that I have duplicate angle index when I remove > column 4 (al) in angle restraints I get following message:- > > > ERROR 1 [file topol.top, line 76867]: > Incorrect number of parameters - found 5, expected 3 or 6 for Angle Rest. > (after the function type). > > Could you please correct me in fixing this section, I followed table 5.14 > of gromacs manual. Three atoms make an angle. You're specifying four, which is incorrect. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sadafrani6 at gmail.com Sun Apr 12 13:40:51 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 12 Apr 2020 11:40:51 -0000 Subject: [gmx-users] duplicate angle index- angle restraint Message-ID: Dear Justin As per table 5.14 in manual, For angle restraints it selects [image: image.png] Also in manual under heading *Angle restraints*, it is mentioned that these are used to restrain the angle between two pairs of particles or between one pair of particles and the ?-axis. Could you please correct me in setting this? Thanks. Sadaf From jalemkul at vt.edu Sun Apr 12 13:45:10 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 12 Apr 2020 11:45:10 -0000 Subject: [gmx-users] duplicate angle index- angle restraint In-Reply-To: References: Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66@vt.edu> On 4/12/20 7:40 AM, Sadaf Rani wrote: > Dear Justin > As per table 5.14 in manual, For angle restraints it selects > > [image: image.png] > Also in manual under heading *Angle restraints*, it is mentioned that these > are used to restrain the angle between two pairs of particles or between > one pair of particles and the ?-axis. > Could you please correct me in setting this? I've never used angle restraints, but clearly grompp is not expecting 4 atoms, as its error message clearly states. It is expecting to read 3 atoms, like a conventional angle. Either there is a bug in the code or a bad description in the manual; you'll need to look into which that is and please submit a bug report via https://gitlab.com/gromacs -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From prithwish.nandi at ichec.ie Sun Apr 12 15:16:43 2020 From: prithwish.nandi at ichec.ie (Prithwish Nandi) Date: Sun, 12 Apr 2020 13:16:43 -0000 Subject: [gmx-users] Electric field Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5@ichec.ie> Hi, I am trying to generate an alternating e-field using gromcas input as following: electric-field-x = 1.5 1 0 0 E0= 2 V/nm, omega = 1 cycle/ps This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. I ran this input with mdrun -field option for a sanity check. I plotted field.xvg . Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. It is only 1/4 cycle of a cosine wave. So, can you please point out what is that I am missing here? Thanks, PKN\\ From prithwish.nandi at ichec.ie Sun Apr 12 15:48:26 2020 From: prithwish.nandi at ichec.ie (Prithwish Nandi) Date: Sun, 12 Apr 2020 13:48:26 -0000 Subject: [gmx-users] Electric field In-Reply-To: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5@ichec.ie> References: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5@ichec.ie> Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325@ichec.ie> Please ignore my message. I figured it out. It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > On 12 Apr 2020, at 14:15, Prithwish Nandi wrote: > > Hi, > I am trying to generate an alternating e-field using gromcas input as following: > > electric-field-x = 1.5 1 0 0 > > E0= 2 V/nm, omega = 1 cycle/ps > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. > > I ran this input with mdrun -field option for a sanity check. > > I plotted field.xvg . > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. > It is only 1/4 cycle of a cosine wave. > > So, can you please point out what is that I am missing here? > > Thanks, > > PKN\\ > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From Lazaro.Castanedo at smu.ca Sun Apr 12 17:25:42 2020 From: Lazaro.Castanedo at smu.ca (Lazaro Castanedo) Date: Sun, 12 Apr 2020 15:25:42 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Message-ID: Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future. I have study from the manual and thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? I am attaching the .mdp and an image of the potential energy minimization from xmgrace. Appreciating any help in advance kindly, Lazaro From lamonteserincastanedo at gmail.com Sun Apr 12 17:42:20 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 12 Apr 2020 15:42:20 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Message-ID: Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future. I have study from the manual and the gromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? I am attaching an image of the potential energy minimization from xmgrace. Appreciating any help in advance kindly, Lazaro From lamonteserincastanedo at gmail.com Sun Apr 12 17:45:26 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 12 Apr 2020 15:45:26 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Message-ID: Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future. I have study from the manual and the gromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? Appreciating any help in advance kindly, Lazaro From jun.zhou at monash.edu Sun Apr 12 17:54:20 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Sun, 12 Apr 2020 15:54:20 -0000 Subject: [gmx-users] Triclinic box is too skewed Message-ID: Hi all, I want to simulate a liquid system with surfactant micelle in the middle, then I apply a velocity at xy direction. However, I always meet the error "triclinic box is too skewed" and the simulation will stop even using a very small shear rate. Have you met this simulation before, any suggestions will be appreciated. Thanks Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From johnwhittake at zedat.fu-berlin.de Sun Apr 12 18:42:38 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Sun, 12 Apr 2020 16:42:38 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: References: Message-ID: <51062.89.12.177.15.1586709754.webmail@webmail.zedat.fu-berlin.de> Hi Lazaro, > Hi, my name is Lazaro. I have done calculations using QM methods. But I > am > starting now to learn MD and I am using Gromacs 2020.1. I want to run > simulations in vacuum for small deoxynucleosides and ribonucleosides > (around 32 atoms) with the finality to initially optimize these molecules > relaxing all position (find the most stable structure) to use this > structure as input for DFT calculations in the future. > > I have study from the manual and the > gromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully > run a couple of simulations of the adenosine in water environment. > > But when I try to run the simulation in vacuum I have some problems. If I > create a box, but from there instead of fill it with water I go directly > and try to do an energy minimization, when I visualize the potential it > decrease but the curve does not look like the examples or like when I do > the simulation in vacuum. > > Do you think this is correct? or is correct how I am proceeding? No idea without more information. Does the simulation end with or without an error? > > Should I modified the .mdp? We have no way to tell if you don't post the contents of your .mdp file. > > I am attaching an image of the potential energy minimization from xmgrace. The mailing list does not accept attachments - You have to upload the plot to an external hosting site (google drive, dropbox, etc...) for us to be able to see it. > > Appreciating any help in advance > > kindly, > > Lazaro > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-request at gromacs.org. ---------------------------------------- John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universit?t Berlin +49 0160 936 04221 From neena.susaneappen at mail.utoronto.ca Sun Apr 12 18:59:09 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Sun, 12 Apr 2020 16:59:09 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: References: Message-ID: Hi Lazaro, Please upload your minim.mdp file and potential plot say on your google drive/ one drive/ dropbox. Make it shareable and provide the link to it here. I do vacuum simulations, so I can guide you. Neena ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se Sent: Sunday, April 12, 2020 3:25 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users at maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-request at maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-owner at maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: duplicate angle index- angle restraint (Sadaf Rani) 2. Re: duplicate angle index- angle restraint (Justin Lemkul) 3. Electric field (Prithwish Nandi) 4. Re: Electric field (Prithwish Nandi) 5. how to run a MD of a small molecule in vacuum in Gromacs (Lazaro Castanedo) ---------------------------------------------------------------------- Message: 1 Date: Sun, 12 Apr 2020 12:40:35 +0100 From: Sadaf Rani To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] duplicate angle index- angle restraint Message-ID: Content-Type: text/plain; charset="utf-8" Dear Justin As per table 5.14 in manual, For angle restraints it selects [image: image.png] Also in manual under heading *Angle restraints*, it is mentioned that these are used to restrain the angle between two pairs of particles or between one pair of particles and the ?-axis. Could you please correct me in setting this? Thanks. Sadaf ------------------------------ Message: 2 Date: Sun, 12 Apr 2020 07:44:57 -0400 From: Justin Lemkul To: gmx-users at gromacs.org Subject: Re: [gmx-users] duplicate angle index- angle restraint Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66 at vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 4/12/20 7:40 AM, Sadaf Rani wrote: > Dear Justin > As per table 5.14 in manual, For angle restraints it selects > > [image: image.png] > Also in manual under heading *Angle restraints*, it is mentioned that these > are used to restrain the angle between two pairs of particles or between > one pair of particles and the ?-axis. > Could you please correct me in setting this? I've never used angle restraints, but clearly grompp is not expecting 4 atoms, as its error message clearly states. It is expecting to read 3 atoms, like a conventional angle. Either there is a bug in the code or a bad description in the manual; you'll need to look into which that is and please submit a bug report via https://gitlab.com/gromacs -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== ------------------------------ Message: 3 Date: Sun, 12 Apr 2020 14:15:11 +0100 From: Prithwish Nandi To: gmx-users at gromacs.org Subject: [gmx-users] Electric field Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5 at ichec.ie> Content-Type: text/plain; charset=us-ascii Hi, I am trying to generate an alternating e-field using gromcas input as following: electric-field-x = 1.5 1 0 0 E0= 2 V/nm, omega = 1 cycle/ps This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. I ran this input with mdrun -field option for a sanity check. I plotted field.xvg . Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. It is only 1/4 cycle of a cosine wave. So, can you please point out what is that I am missing here? Thanks, PKN\\ ------------------------------ Message: 4 Date: Sun, 12 Apr 2020 14:48:20 +0100 From: Prithwish Nandi To: gmx-users at gromacs.org Subject: Re: [gmx-users] Electric field Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325 at ichec.ie> Content-Type: text/plain; charset=us-ascii Please ignore my message. I figured it out. It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > On 12 Apr 2020, at 14:15, Prithwish Nandi wrote: > > Hi, > I am trying to generate an alternating e-field using gromcas input as following: > > electric-field-x = 1.5 1 0 0 > > E0= 2 V/nm, omega = 1 cycle/ps > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. > > I ran this input with mdrun -field option for a sanity check. > > I plotted field.xvg . > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. > It is only 1/4 cycle of a cosine wave. > > So, can you please point out what is that I am missing here? > > Thanks, > > PKN\\ > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. ------------------------------ Message: 5 Date: Sun, 12 Apr 2020 15:25:36 +0000 From: Lazaro Castanedo To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future. I have study from the manual and thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? I am attaching the .mdp and an image of the potential energy minimization from xmgrace. Appreciating any help in advance kindly, Lazaro ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. End of gromacs.org_gmx-users Digest, Vol 192, Issue 36 ****************************************************** From lamonteserincastanedo at gmail.com Sun Apr 12 19:01:28 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 12 Apr 2020 17:01:28 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: <51062.89.12.177.15.1586709754.webmail@webmail.zedat.fu-berlin.de> References: <51062.89.12.177.15.1586709754.webmail@webmail.zedat.fu-berlin.de> Message-ID: The simulation ends without error. I am going to attach the files in Dropbox or google drive and send them in that format. Thank you for the guidance On Sun, Apr 12, 2020 at 1:42 PM John Whittaker < johnwhittake at zedat.fu-berlin.de> wrote: > Hi Lazaro, > > > Hi, my name is Lazaro. I have done calculations using QM methods. But I > > am > > starting now to learn MD and I am using Gromacs 2020.1. I want to run > > simulations in vacuum for small deoxynucleosides and ribonucleosides > > (around 32 atoms) with the finality to initially optimize these molecules > > relaxing all position (find the most stable structure) to use this > > structure as input for DFT calculations in the future. > > > > I have study from the manual and the > > gromacs.org_gmx-users at maillist.sys.kth.se tutorials and have > successfully > > run a couple of simulations of the adenosine in water environment. > > > > But when I try to run the simulation in vacuum I have some problems. If I > > create a box, but from there instead of fill it with water I go directly > > and try to do an energy minimization, when I visualize the potential it > > decrease but the curve does not look like the examples or like when I do > > the simulation in vacuum. > > > > Do you think this is correct? or is correct how I am proceeding? > > No idea without more information. Does the simulation end with or without > an error? > > > > > Should I modified the .mdp? > > We have no way to tell if you don't post the contents of your .mdp file. > > > > > I am attaching an image of the potential energy minimization from > xmgrace. > > The mailing list does not accept attachments - You have to upload the plot > to an external hosting site (google drive, dropbox, etc...) for us to be > able to see it. > > > > > Appreciating any help in advance > > > > kindly, > > > > Lazaro > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-request at gromacs.org. > > > ---------------------------------------- > > John Whittaker > Ph.D. Candidate > Department of Mathematics and Computer Science > Freie Universit?t Berlin > > +49 0160 936 04221 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From paolo.costa85 at gmail.com Sun Apr 12 19:19:10 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 12 Apr 2020 17:19:10 -0000 Subject: [gmx-users] Parametrization POM molecule Message-ID: Dear Gromacs users, I am new on Gromacs and in general on MD simulations. I am interested on simulating a POM (polyoxometallate) molecule in a water box. I could already find in literature works dealing with POM: - J. Phys. Chem. A 2005, 109, 1216-1222, Phys. Chem. Chem. Phys., 2008, 10, 6940?6953, J Comput Chem 32: 240?247, 2011, Chem. Eur. J. 2016, 22, 15280 ? 15289. By looking on those works, I could easily find the Lennard Jones parameters for the non bonded interactions. *However, I could not find the parameters for the bonded interactions.* Do I need such parameters? In case, how can I find them? Because by looking to this paper, Chem. Eur. J. 2016, 22, 15280 ? 15289, I will likely use AMBER99 force field which it does not include any parameters for such "exotic" molecule. Thanks a lot. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From lamonteserincastanedo at gmail.com Sun Apr 12 19:59:11 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 12 Apr 2020 17:59:11 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: References: Message-ID: Thank you very much Neena. I will do that On Sun, Apr 12, 2020 at 1:59 PM Neena Susan Eappen < neena.susaneappen at mail.utoronto.ca> wrote: > Hi Lazaro, > > Please upload your minim.mdp file and potential plot say on your google > drive/ one drive/ dropbox. Make it shareable and provide the link to it > here. I do vacuum simulations, so I can guide you. > > Neena > > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of > gromacs.org_gmx-users-request at maillist.sys.kth.se < > gromacs.org_gmx-users-request at maillist.sys.kth.se> > Sent: Sunday, April 12, 2020 3:25 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36 > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: duplicate angle index- angle restraint (Sadaf Rani) > 2. Re: duplicate angle index- angle restraint (Justin Lemkul) > 3. Electric field (Prithwish Nandi) > 4. Re: Electric field (Prithwish Nandi) > 5. how to run a MD of a small molecule in vacuum in Gromacs > (Lazaro Castanedo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 12 Apr 2020 12:40:35 +0100 > From: Sadaf Rani > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: > < > CAH9Uu9O85zXSA5uDg_MhSFtft3XHf6fakqRAvcxMmQ3b0N1EsQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Justin > As per table 5.14 in manual, For angle restraints it selects > > [image: image.png] > Also in manual under heading *Angle restraints*, it is mentioned that these > are used to restrain the angle between two pairs of particles or between > one pair of particles and the ?-axis. > Could you please correct me in setting this? > > Thanks. > Sadaf > > ------------------------------ > > Message: 2 > Date: Sun, 12 Apr 2020 07:44:57 -0400 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66 at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 4/12/20 7:40 AM, Sadaf Rani wrote: > > Dear Justin > > As per table 5.14 in manual, For angle restraints it selects > > > > [image: image.png] > > Also in manual under heading *Angle restraints*, it is mentioned that > these > > are used to restrain the angle between two pairs of particles or between > > one pair of particles and the ?-axis. > > Could you please correct me in setting this? > > I've never used angle restraints, but clearly grompp is not expecting 4 > atoms, as its error message clearly states. It is expecting to read 3 > atoms, like a conventional angle. > > Either there is a bug in the code or a bad description in the manual; > you'll need to look into which that is and please submit a bug report > via https://gitlab.com/gromacs > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Sun, 12 Apr 2020 14:15:11 +0100 > From: Prithwish Nandi > To: gmx-users at gromacs.org > Subject: [gmx-users] Electric field > Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5 at ichec.ie> > Content-Type: text/plain; charset=us-ascii > > Hi, > I am trying to generate an alternating e-field using gromcas input as > following: > > electric-field-x = 1.5 1 0 0 > > E0= 2 V/nm, omega = 1 cycle/ps > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per > pico-second. > > I ran this input with mdrun -field option for a sanity check. > > I plotted field.xvg . > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps > period. > It is only 1/4 cycle of a cosine wave. > > So, can you please point out what is that I am missing here? > > Thanks, > > PKN\\ > > > > > ------------------------------ > > Message: 4 > Date: Sun, 12 Apr 2020 14:48:20 +0100 > From: Prithwish Nandi > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Electric field > Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325 at ichec.ie> > Content-Type: text/plain; charset=us-ascii > > Please ignore my message. > I figured it out. > It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > > > > > On 12 Apr 2020, at 14:15, Prithwish Nandi > wrote: > > > > Hi, > > I am trying to generate an alternating e-field using gromcas input as > following: > > > > electric-field-x = 1.5 1 0 0 > > > > E0= 2 V/nm, omega = 1 cycle/ps > > > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per > pico-second. > > > > I ran this input with mdrun -field option for a sanity check. > > > > I plotted field.xvg . > > > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps > period. > > It is only 1/4 cycle of a cosine wave. > > > > So, can you please point out what is that I am missing here? > > > > Thanks, > > > > PKN\\ > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > > ------------------------------ > > Message: 5 > Date: Sun, 12 Apr 2020 15:25:36 +0000 > From: Lazaro Castanedo > To: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] how to run a MD of a small molecule in vacuum in > Gromacs > Message-ID: > < > QB1PR01MB337802A77869BE9DEB021AB6FCDC0 at QB1PR01MB3378.CANPRD01.PROD.OUTLOOK.COM > > > > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, my name is Lazaro. I have done calculations using QM methods. But I > am starting now to learn MD and I am using Gromacs 2020.1. I want to run > simulations in vacuum for small deoxynucleosides and ribonucleosides > (around 32 atoms) with the finality to initially optimize these molecules > relaxing all position (find the most stable structure) to use this > structure as input for DFT calculations in the future. > > I have study from the manual and > thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have > successfully run a couple of simulations of the adenosine in water > environment. > > But when I try to run the simulation in vacuum I have some problems. If I > create a box, but from there instead of fill it with water I go directly > and try to do an energy minimization, when I visualize the potential it > decrease but the curve does not look like the examples or like when I do > the simulation in vacuum. > > Do you think this is correct? or is correct how I am proceeding? > > Should I modified the .mdp? > > I am attaching the .mdp and an image of the potential energy minimization > from xmgrace. > > Appreciating any help in advance > > kindly, > > Lazaro > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 36 > ****************************************************** > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From dahal.udaya at gmail.com Sun Apr 12 20:31:19 2020 From: dahal.udaya at gmail.com (Udaya Dahal) Date: Sun, 12 Apr 2020 18:31:19 -0000 Subject: [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately Message-ID: Dear Gromacs Users, I am trying to understand the long-range dispersion interaction between two particles. I am trying to implement *LJPME *instead of *cut-off* for the vdW interaction. The simulation runs fine with *vdw-type=cut-off *but as soon as I changed to *LJPME *the simulation crashes after a few steps. Even decreasing the time-step to 0.5 femtoseconds doesn't lead to a stable simulation.Has anyone encountered similar problem? I appreciate your input. The version i am using is *gromacs-2018.3*. Thank you, Udaya Dahal From ekh58 at cornell.edu Sun Apr 12 20:42:06 2020 From: ekh58 at cornell.edu (Erik Henze) Date: Sun, 12 Apr 2020 18:42:06 -0000 Subject: [gmx-users] Same one lipid in bilayer causing LINCS crashing during minimization Message-ID: Hello, I am currently attempting an energy minimization of a water+ion+DSPC bilayer with an ion channel suspended in the bilayer. This was built using CHARMM GUI. When I run the simulation, one lipid in particular repeatedly keeps on causing the following error: "Step 17, time 0.017 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000144, max 0.034552 (between atoms 79632 and 79634) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 79632 79634 50.2 0.1104 0.1149 0.1111 Step= 17, Dmax= 7.7e-02 nm, Epot= -1.98890e+06 Fmax= 2.83841e+04, atom= 79638 Step 18, time 0.018 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000361, max 0.079519 (between atoms 79638 and 79640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 79632 79633 36.3 0.1101 0.1108 0.1111 79632 79634 43.1 0.1149 0.1132 0.1111 79638 79639 59.4 0.1119 0.1156 0.1111 79638 79640 59.3 0.1113 0.1199 0.1111 Step= 18, Dmax= 9.2e-02 nm, Epot= -2.03437e+06 Fmax= 5.35800e+05, atom= 79634 Step 19, time 0.019 (ps) LINCS WARNING relative constraint deviation after LINCS: rms -nan, max 0.019185 (between atoms 79638 and 79640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 79638 79639 33.6 0.1156 0.1121 0.1111" and then from here it just stops. I looked up these atoms and they correspond to one DSPC lipid which seems unexceptional (is located away from protein, just sitting in membrane). I tried removing the constraints in my .mdp file but this did not prevent the EM from crashing on this same lipid. Any advice on what might be causing this, or how to circumvent it, would be greatly appreciated, thank you! From elham802011 at yahoo.com Sun Apr 12 20:42:35 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sun, 12 Apr 2020 18:42:35 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <891501189.4285992.1586631333228@mail.yahoo.com> References: <891501189.4285992.1586631333228@mail.yahoo.com> Message-ID: <3F0E8912-4995-4B6B-9FAB-E14406E4CDE2@yahoo.com> Hi Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory. When it gives me topol.top file, it has another name (other_chain B) not FL. I think thats why it doesn't recognize my ligand as a Residue. > On Apr 11, 2020, at 11:25 PM, Elham Taghikhani wrote: > > ? > Thank you. > I did what you said and added new bond to specbond.dat file like this: > > 10 > LYS CD 2 FLO NZ 2 1.8 LYS FLO > LYS NZ 2 FLO CX 2 1.8 LYS FLO > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 > CYS SG 1 HEM FE 2 0.25 CYS2 HEME > CYS SG 1 HEM CAB 1 0.18 CYS2 HEME > CYS SG 1 HEM CAC 1 0.18 CYS2 HEME > HIS NE2 1 HEM FE 1 0.2 HIS1 HEME > MET SD 1 HEM FE 1 0.24 MET HEME > CO C 1 HEME FE 1 0.19 CO HEME > CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 > > but it seems that it doesn't read the lines of the specbond.dat file. > > 8 out of 8 lines of specbond.dat converted successfully. > . > . > CASPH Protein > CGLUH Protein > FLO Other > DA DNA > DG DNA > DC DNA > . > . > This is part of my residuetypes.dat file. > I think there is some problem with my residuetypes.dat file but i don't what it is. > nothing works i am so confused now. > On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani wrote: > > > Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file. > but still it has this warning: > > > Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could either be > correct or a catastrophic error. Please check your structure, and add all > necessary residue names to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > > On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: > > > Hi > > Thank you for your response. > > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. > As i said before I modified the rtp file too. > This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > > Thank you in advance > > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 129 residues with 1971 atoms > Chain time... > Making bonds... > Warning: Long Bond (1459-1462 = 0.259531 nm) > Warning: Long Bond (1754-1757 = 0.259591 nm) > Number of bonds was 1995, now 1995 > Generating angles, dihedrals and pairs... > Before cleaning: 5163 pairs > Before cleaning: 5208 dihedrals > Keeping all generated dihedrals > Making cmap torsions... > There are 5208 dihedrals, 429 impropers, 3556 angles > 5127 pairs, 1995 bonds and 0 virtual sites > Total mass 14324.281 a.m.u. > Total charge 19.000 e > Writing topology > Processing chain 2 (39 atoms, 1 residues) > > Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your structure, > and add FLO to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time... > Making bonds... > No bonds > Generating angles, dihedrals and pairs... > Making cmap torsions... > There are 0 dihedrals, 0 impropers, 0 angles > 0 pairs, 0 bonds and 0 virtual sites > Total mass 373.322 a.m.u. > Total charge 0.000 e > Writing topology > Including chain 1 in system: 1971 atoms 129 residues > Including chain 2 in system: 39 atoms 1 residues > Now there are 2010 atoms and 130 residues > Total mass in system 14697.603 a.m.u. > Total charge in system 19.000 e > > Writing coordinate file... > --------- PLEASE NOTE ------------ > You have successfully generated a topology from: complex.pdb. > The Oplsaa force field and the spc water model are used. > --------- ETON ESAELP ------------ > > > On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: > > > > Hi > > Thank you for your response. > > I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work. > As i said before I modified the rtp file too. > This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. > > Thank you in advance. > > On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: > > > Hi > > I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. > In the topology, I got this warning message : > Warning:long-bond... > I don't know what should I do to retain the covalent bond. > I will appreciate it if you help me with this problem. From lamonteserincastanedo at gmail.com Mon Apr 13 01:05:38 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 12 Apr 2020 23:05:38 -0000 Subject: [gmx-users] about simulation of small molecules in vacuum. link to dropbox Message-ID: Dear all I am trying to simulate in Gromacs 2020.1 small molecules nucleosides (32 atoms) in vacuum. I have try to follow the tutorial steps, so I created a box and followed did an energy minimization. But the graph from potential.xvg doesn't look similar to the ones on the tutorials. Somebody could guide on how to do this kind of simulation properly? or if I am doing things right? This is the link to the files minim.mdp, potential.xvg and .top related to my simulations in vacuum in dropbox: Kindly, Lazaro vacuum_MD Abrir el v?nculo en Dropbox From dahal.udaya at gmail.com Mon Apr 13 01:18:14 2020 From: dahal.udaya at gmail.com (Udaya Dahal) Date: Sun, 12 Apr 2020 23:18:14 -0000 Subject: [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately Message-ID: Dear Gromacs Users, I am trying to understand the long-range dispersion interaction between two particles. I am trying to implement *LJPME *instead of *cut-off* for the vdW interaction. The simulation runs fine with *vdw-type=cut-off *but as soon as I changed to *LJPME *the simulation crashes after a few steps. Even decreasing the time-step to 0.5 femtoseconds doesn't lead to a stable simulation.Has anyone encountered similar problem? I appreciate your input. The version i am using is *gromacs-2018.3*. Thank you, Udaya Dahal From neena.susaneappen at mail.utoronto.ca Mon Apr 13 04:51:59 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Mon, 13 Apr 2020 02:51:59 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: References: , Message-ID: Try the below minim.mdp parameters which has worked well for vacuum simulations. Proper way to do vacuum simulations: no PBC, PME and cutoffs. To reduce computation time, Konermann Lab solved it by implementing pseudo-PBC conditions. Their paper explains it very clearly (link here): https://www.ncbi.nlm.nih.gov/pubmed/29678588 ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steep descent energy minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 50000 ; Maximum number of (minimization) steps to perform nstxout = 100 ; Number of steps to elapse between writing coordinates to output trajectory file ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = cutoff ; Treatment of long range electrostatic interactions rcoulomb = 333.3 ; Short-range electrostatic cut-off vdwtype = cutoff ; Treatment of long range Van der Waals interactions rvdw = 333.3 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions rlist = 333.3 ; short-range neighbour list cut-off ________________________________ From: Neena Susan Eappen Sent: Sunday, April 12, 2020 4:59 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Hi Lazaro, Please upload your minim.mdp file and potential plot say on your google drive/ one drive/ dropbox. Make it shareable and provide the link to it here. I do vacuum simulations, so I can guide you. Neena ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se Sent: Sunday, April 12, 2020 3:25 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users at maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-request at maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-owner at maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: duplicate angle index- angle restraint (Sadaf Rani) 2. Re: duplicate angle index- angle restraint (Justin Lemkul) 3. Electric field (Prithwish Nandi) 4. Re: Electric field (Prithwish Nandi) 5. how to run a MD of a small molecule in vacuum in Gromacs (Lazaro Castanedo) ---------------------------------------------------------------------- Message: 1 Date: Sun, 12 Apr 2020 12:40:35 +0100 From: Sadaf Rani To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] duplicate angle index- angle restraint Message-ID: Content-Type: text/plain; charset="utf-8" Dear Justin As per table 5.14 in manual, For angle restraints it selects [image: image.png] Also in manual under heading *Angle restraints*, it is mentioned that these are used to restrain the angle between two pairs of particles or between one pair of particles and the ?-axis. Could you please correct me in setting this? Thanks. Sadaf ------------------------------ Message: 2 Date: Sun, 12 Apr 2020 07:44:57 -0400 From: Justin Lemkul To: gmx-users at gromacs.org Subject: Re: [gmx-users] duplicate angle index- angle restraint Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66 at vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 4/12/20 7:40 AM, Sadaf Rani wrote: > Dear Justin > As per table 5.14 in manual, For angle restraints it selects > > [image: image.png] > Also in manual under heading *Angle restraints*, it is mentioned that these > are used to restrain the angle between two pairs of particles or between > one pair of particles and the ?-axis. > Could you please correct me in setting this? I've never used angle restraints, but clearly grompp is not expecting 4 atoms, as its error message clearly states. It is expecting to read 3 atoms, like a conventional angle. Either there is a bug in the code or a bad description in the manual; you'll need to look into which that is and please submit a bug report via https://gitlab.com/gromacs -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== ------------------------------ Message: 3 Date: Sun, 12 Apr 2020 14:15:11 +0100 From: Prithwish Nandi To: gmx-users at gromacs.org Subject: [gmx-users] Electric field Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5 at ichec.ie> Content-Type: text/plain; charset=us-ascii Hi, I am trying to generate an alternating e-field using gromcas input as following: electric-field-x = 1.5 1 0 0 E0= 2 V/nm, omega = 1 cycle/ps This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. I ran this input with mdrun -field option for a sanity check. I plotted field.xvg . Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. It is only 1/4 cycle of a cosine wave. So, can you please point out what is that I am missing here? Thanks, PKN\\ ------------------------------ Message: 4 Date: Sun, 12 Apr 2020 14:48:20 +0100 From: Prithwish Nandi To: gmx-users at gromacs.org Subject: Re: [gmx-users] Electric field Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325 at ichec.ie> Content-Type: text/plain; charset=us-ascii Please ignore my message. I figured it out. It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > On 12 Apr 2020, at 14:15, Prithwish Nandi wrote: > > Hi, > I am trying to generate an alternating e-field using gromcas input as following: > > electric-field-x = 1.5 1 0 0 > > E0= 2 V/nm, omega = 1 cycle/ps > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per pico-second. > > I ran this input with mdrun -field option for a sanity check. > > I plotted field.xvg . > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps period. > It is only 1/4 cycle of a cosine wave. > > So, can you please point out what is that I am missing here? > > Thanks, > > PKN\\ > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. ------------------------------ Message: 5 Date: Sun, 12 Apr 2020 15:25:36 +0000 From: Lazaro Castanedo To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, my name is Lazaro. I have done calculations using QM methods. But I am starting now to learn MD and I am using Gromacs 2020.1. I want to run simulations in vacuum for small deoxynucleosides and ribonucleosides (around 32 atoms) with the finality to initially optimize these molecules relaxing all position (find the most stable structure) to use this structure as input for DFT calculations in the future. I have study from the manual and thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully run a couple of simulations of the adenosine in water environment. But when I try to run the simulation in vacuum I have some problems. If I create a box, but from there instead of fill it with water I go directly and try to do an energy minimization, when I visualize the potential it decrease but the curve does not look like the examples or like when I do the simulation in vacuum. Do you think this is correct? or is correct how I am proceeding? Should I modified the .mdp? I am attaching the .mdp and an image of the potential energy minimization from xmgrace. Appreciating any help in advance kindly, Lazaro ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. End of gromacs.org_gmx-users Digest, Vol 192, Issue 36 ****************************************************** From prithwish.nandi at ichec.ie Mon Apr 13 12:27:45 2020 From: prithwish.nandi at ichec.ie (Prithwish Nandi) Date: Mon, 13 Apr 2020 10:27:45 -0000 Subject: [gmx-users] Error message Message-ID: Hi, I am simulating a water droplet in gas phase using Gromacs. Basically, this is a water droplet kept at the centre of a large box of dimension 100 nm. The problem is that the run ended with an error message as shown below: ?8 particles communicated to PME rank 14 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.? Any suggestion on how to resolve this error? Thanks, PKN\\ From jalemkul at vt.edu Mon Apr 13 13:17:53 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 13 Apr 2020 11:17:53 -0000 Subject: [gmx-users] Problem with pdb2gmx In-Reply-To: <3F0E8912-4995-4B6B-9FAB-E14406E4CDE2@yahoo.com> References: <891501189.4285992.1586631333228@mail.yahoo.com> <3F0E8912-4995-4B6B-9FAB-E14406E4CDE2@yahoo.com> Message-ID: <106b7bde-2ffb-ecc1-6f9b-f9a12499b851@vt.edu> On 4/12/20 2:42 PM, Elham Taghikhani wrote: > Hi > Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory. These files should be in the working directory, not in the force field subdirectory. This is why they are not being read. > When it gives me topol.top file, it has another name (other_chain B) not FL. > I think thats why it doesn't recognize my ligand as a Residue. Merge the chains with the -merge command. -Justin > >> On Apr 11, 2020, at 11:25 PM, Elham Taghikhani wrote: >> >> ? >> Thank you. >> I did what you said and added new bond to specbond.dat file like this: >> >> 10 >> LYS CD 2 FLO NZ 2 1.8 LYS FLO >> LYS NZ 2 FLO CX 2 1.8 LYS FLO >> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 >> CYS SG 1 HEM FE 2 0.25 CYS2 HEME >> CYS SG 1 HEM CAB 1 0.18 CYS2 HEME >> CYS SG 1 HEM CAC 1 0.18 CYS2 HEME >> HIS NE2 1 HEM FE 1 0.2 HIS1 HEME >> MET SD 1 HEM FE 1 0.24 MET HEME >> CO C 1 HEME FE 1 0.19 CO HEME >> CYM SG 1 CYM SG 1 0.2 CYS2 CYS2 >> >> but it seems that it doesn't read the lines of the specbond.dat file. >> >> 8 out of 8 lines of specbond.dat converted successfully. >> . >> . >> CASPH Protein >> CGLUH Protein >> FLO Other >> DA DNA >> DG DNA >> DC DNA >> . >> . >> This is part of my residuetypes.dat file. >> I think there is some problem with my residuetypes.dat file but i don't what it is. >> nothing works i am so confused now. >> On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani wrote: >> >> >> Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file. >> but still it has this warning: >> >> >> Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA. >> This makes it impossible to link them into a molecule, which could either be >> correct or a catastrophic error. Please check your structure, and add all >> necessary residue names to residuetypes.dat if this was not correct. >> >> Problem with chain definition, or missing terminal residues. >> This chain does not appear to contain a recognized chain molecule. >> If this is incorrect, you can edit residuetypes.dat to modify the behavior. >> 8 out of 8 lines of specbond.dat converted successfully >> >> >> On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani wrote: >> >> >> Hi >> >> Thank you for your response. >> >> I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case. >> As i said before I modified the rtp file too. >> This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. >> >> Thank you in advance >> >> Checking for duplicate atoms.... >> Generating any missing hydrogen atoms and/or adding termini. >> Now there are 129 residues with 1971 atoms >> Chain time... >> Making bonds... >> Warning: Long Bond (1459-1462 = 0.259531 nm) >> Warning: Long Bond (1754-1757 = 0.259591 nm) >> Number of bonds was 1995, now 1995 >> Generating angles, dihedrals and pairs... >> Before cleaning: 5163 pairs >> Before cleaning: 5208 dihedrals >> Keeping all generated dihedrals >> Making cmap torsions... >> There are 5208 dihedrals, 429 impropers, 3556 angles >> 5127 pairs, 1995 bonds and 0 virtual sites >> Total mass 14324.281 a.m.u. >> Total charge 19.000 e >> Writing topology >> Processing chain 2 (39 atoms, 1 residues) >> >> Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA. >> This chain lacks identifiers, which makes it impossible to do strict >> classification of the start/end residues. Here we need to guess this residue >> should not be part of the chain and instead introduce a break, but that will >> be catastrophic if they should in fact be linked. Please check your structure, >> and add FLO to residuetypes.dat if this was not correct. >> >> Problem with chain definition, or missing terminal residues. >> This chain does not appear to contain a recognized chain molecule. >> If this is incorrect, you can edit residuetypes.dat to modify the behavior. >> 8 out of 8 lines of specbond.dat converted successfully >> Checking for duplicate atoms.... >> Generating any missing hydrogen atoms and/or adding termini. >> Now there are 1 residues with 39 atoms >> Chain time... >> Making bonds... >> No bonds >> Generating angles, dihedrals and pairs... >> Making cmap torsions... >> There are 0 dihedrals, 0 impropers, 0 angles >> 0 pairs, 0 bonds and 0 virtual sites >> Total mass 373.322 a.m.u. >> Total charge 0.000 e >> Writing topology >> Including chain 1 in system: 1971 atoms 129 residues >> Including chain 2 in system: 39 atoms 1 residues >> Now there are 2010 atoms and 130 residues >> Total mass in system 14697.603 a.m.u. >> Total charge in system 19.000 e >> >> Writing coordinate file... >> --------- PLEASE NOTE ------------ >> You have successfully generated a topology from: complex.pdb. >> The Oplsaa force field and the spc water model are used. >> --------- ETON ESAELP ------------ >> >> >> On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani wrote: >> >> >> >> Hi >> >> Thank you for your response. >> >> I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it doesn't work. >> As i said before I modified the rtp file too. >> This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command. >> >> Thank you in advance. >> >> On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani wrote: >> >> >> Hi >> >> I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. >> In the topology, I got this warning message : >> Warning:long-bond... >> I don't know what should I do to retain the covalent bond. >> I will appreciate it if you help me with this problem. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Mon Apr 13 16:37:14 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Mon, 13 Apr 2020 14:37:14 -0000 Subject: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment? Message-ID: Dear Gromacs users I have three questions about the details of running MD of small molecules in gromacs: 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the carbons in the sugar) with genrestr, should I use temperature coupling groups? 2) Now, if I freeze in the nucleoside again the carbons from the sugar but the calculation is in water, should I use temperature coupling?, should I put the nucleoside in one group and the solvent in another group? What temperature coupling methodology would be more recommended? 3) For these type of small molecules (around 32 atoms) what would be the best time to run the MD, e.x. 5ns, 10ns, 20ns, etc? Kindly, Lazaro From lamonteserincastanedo at gmail.com Mon Apr 13 16:37:31 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Mon, 13 Apr 2020 14:37:31 -0000 Subject: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs In-Reply-To: References: Message-ID: Thank you very much Neena. I will try these parameters. Kindly, Lazaro El dom., 12 de abr. de 2020 a la(s) 23:53, Neena Susan Eappen ( neena.susaneappen at mail.utoronto.ca) escribi?: > Try the below minim.mdp parameters which has worked well for vacuum > simulations. Proper way to do vacuum simulations: no PBC, PME and cutoffs. > To reduce computation time, Konermann Lab solved it by implementing > pseudo-PBC conditions. Their paper explains it very clearly (link here): > https://www.ncbi.nlm.nih.gov/pubmed/29678588 > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steep descent energy > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 50000 ; Maximum number of (minimization) steps to > perform > nstxout = 100 ; Number of steps to elapse between writing > coordinates to output trajectory file > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 10 ; Frequency to update the neighbor list and > long range forces > cutoff-scheme = Verlet ; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, > grid) > coulombtype = cutoff ; Treatment of long range electrostatic > interactions > rcoulomb = 333.3 ; Short-range electrostatic cut-off > vdwtype = cutoff ; Treatment of long range Van der Waals > interactions > rvdw = 333.3 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions in all 3 > dimensions > rlist = 333.3 ; short-range neighbour list cut-off > > > ________________________________ > From: Neena Susan Eappen > Sent: Sunday, April 12, 2020 4:59 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: Re: [gmx-users] how to run a MD of a small molecule in vacuum in > Gromacs > > Hi Lazaro, > > Please upload your minim.mdp file and potential plot say on your google > drive/ one drive/ dropbox. Make it shareable and provide the link to it > here. I do vacuum simulations, so I can guide you. > > Neena > > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of > gromacs.org_gmx-users-request at maillist.sys.kth.se < > gromacs.org_gmx-users-request at maillist.sys.kth.se> > Sent: Sunday, April 12, 2020 3:25 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: gromacs.org_gmx-users Digest, Vol 192, Issue 36 > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: duplicate angle index- angle restraint (Sadaf Rani) > 2. Re: duplicate angle index- angle restraint (Justin Lemkul) > 3. Electric field (Prithwish Nandi) > 4. Re: Electric field (Prithwish Nandi) > 5. how to run a MD of a small molecule in vacuum in Gromacs > (Lazaro Castanedo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 12 Apr 2020 12:40:35 +0100 > From: Sadaf Rani > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: > < > CAH9Uu9O85zXSA5uDg_MhSFtft3XHf6fakqRAvcxMmQ3b0N1EsQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Justin > As per table 5.14 in manual, For angle restraints it selects > > [image: image.png] > Also in manual under heading *Angle restraints*, it is mentioned that these > are used to restrain the angle between two pairs of particles or between > one pair of particles and the ?-axis. > Could you please correct me in setting this? > > Thanks. > Sadaf > > ------------------------------ > > Message: 2 > Date: Sun, 12 Apr 2020 07:44:57 -0400 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] duplicate angle index- angle restraint > Message-ID: <9759f6db-9aa5-67b3-f253-bdef82ce5c66 at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 4/12/20 7:40 AM, Sadaf Rani wrote: > > Dear Justin > > As per table 5.14 in manual, For angle restraints it selects > > > > [image: image.png] > > Also in manual under heading *Angle restraints*, it is mentioned that > these > > are used to restrain the angle between two pairs of particles or between > > one pair of particles and the ?-axis. > > Could you please correct me in setting this? > > I've never used angle restraints, but clearly grompp is not expecting 4 > atoms, as its error message clearly states. It is expecting to read 3 > atoms, like a conventional angle. > > Either there is a bug in the code or a bad description in the manual; > you'll need to look into which that is and please submit a bug report > via https://gitlab.com/gromacs > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Sun, 12 Apr 2020 14:15:11 +0100 > From: Prithwish Nandi > To: gmx-users at gromacs.org > Subject: [gmx-users] Electric field > Message-ID: <46810BF1-EFC3-4E89-82C3-CB22198D3CD5 at ichec.ie> > Content-Type: text/plain; charset=us-ascii > > Hi, > I am trying to generate an alternating e-field using gromcas input as > following: > > electric-field-x = 1.5 1 0 0 > > E0= 2 V/nm, omega = 1 cycle/ps > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per > pico-second. > > I ran this input with mdrun -field option for a sanity check. > > I plotted field.xvg . > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps > period. > It is only 1/4 cycle of a cosine wave. > > So, can you please point out what is that I am missing here? > > Thanks, > > PKN\\ > > > > > ------------------------------ > > Message: 4 > Date: Sun, 12 Apr 2020 14:48:20 +0100 > From: Prithwish Nandi > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Electric field > Message-ID: <61883BAE-5DAC-46B1-AD2D-64EE5EC34325 at ichec.ie> > Content-Type: text/plain; charset=us-ascii > > Please ignore my message. > I figured it out. > It should be 2*pi*1 = 6.28 for omega to generate a full cycle. > > > > > On 12 Apr 2020, at 14:15, Prithwish Nandi > wrote: > > > > Hi, > > I am trying to generate an alternating e-field using gromcas input as > following: > > > > electric-field-x = 1.5 1 0 0 > > > > E0= 2 V/nm, omega = 1 cycle/ps > > > > This means a cosine wave of magnitude 1.5 eV/nm and 1 cycle per > pico-second. > > > > I ran this input with mdrun -field option for a sanity check. > > > > I plotted field.xvg . > > > > Surprisingly, the plot (attached) is NOT showing 1 full cycle in a 1-ps > period. > > It is only 1/4 cycle of a cosine wave. > > > > So, can you please point out what is that I am missing here? > > > > Thanks, > > > > PKN\\ > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > > ------------------------------ > > Message: 5 > Date: Sun, 12 Apr 2020 15:25:36 +0000 > From: Lazaro Castanedo > To: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] how to run a MD of a small molecule in vacuum in > Gromacs > Message-ID: > < > QB1PR01MB337802A77869BE9DEB021AB6FCDC0 at QB1PR01MB3378.CANPRD01.PROD.OUTLOOK.COM > > > > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, my name is Lazaro. I have done calculations using QM methods. But I > am starting now to learn MD and I am using Gromacs 2020.1. I want to run > simulations in vacuum for small deoxynucleosides and ribonucleosides > (around 32 atoms) with the finality to initially optimize these molecules > relaxing all position (find the most stable structure) to use this > structure as input for DFT calculations in the future. > > I have study from the manual and > thegromacs.org_gmx-users at maillist.sys.kth.se tutorials and have > successfully run a couple of simulations of the adenosine in water > environment. > > But when I try to run the simulation in vacuum I have some problems. If I > create a box, but from there instead of fill it with water I go directly > and try to do an energy minimization, when I visualize the potential it > decrease but the curve does not look like the examples or like when I do > the simulation in vacuum. > > Do you think this is correct? or is correct how I am proceeding? > > Should I modified the .mdp? > > I am attaching the .mdp and an image of the potential energy minimization > from xmgrace. > > Appreciating any help in advance > > kindly, > > Lazaro > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 36 > ****************************************************** > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Mon Apr 13 17:51:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 13 Apr 2020 15:51:47 -0000 Subject: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment? In-Reply-To: References: Message-ID: <54add009-1c6c-f6f1-61a6-17c7cdc5f7d2@vt.edu> On 4/13/20 10:37 AM, lazaro monteserin wrote: > Dear Gromacs users > > I have three questions about the details of running MD of small molecules > in gromacs: > > 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the > carbons in the sugar) with genrestr, should I use temperature coupling > groups? Freezing and restraining are different; don't use the terms interchangeably. Freezing means the atoms are never updated (position or velocity), and I don't recommend using this approach as it is entirely unphysical. What you're talking about is applying a restraint. You need to assign all atoms to a temperature-coupling bath. If you don't, that's also completely unphysical. > 2) Now, if I freeze in the nucleoside again the carbons from the sugar but > the calculation is in water, should I use temperature coupling?, should I > put the nucleoside in one group and the solvent in another group? What > temperature coupling methodology would be more recommended? For a small solute in water, couple the whole system together. > 3) For these type of small molecules (around 32 atoms) what would be the > best time to run the MD, e.x. 5ns, 10ns, 20ns, etc? You should base this conclusion on your examination of the literature. What are the time scales of the dynamics you are interested in? What have previous studies on similar systems demonstrated? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From afsane_farhadi at yahoo.com Mon Apr 13 17:59:39 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Mon, 13 Apr 2020 15:59:39 -0000 Subject: [gmx-users] energy minimization References: <1267325081.3286158.1586793572943.ref@mail.yahoo.com> Message-ID: <1267325081.3286158.1586793572943@mail.yahoo.com> hi friends?I generated a box of mixed gas with gmx insert-molecules....I ran an energy minimizing. ?the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization.?what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction ?is weaker than intramolecular interaction but I don't know how I can control this matter.?please help? Sent from Yahoo Mail on Android From carlheroneme at ku.edu Mon Apr 13 20:41:50 2020 From: carlheroneme at ku.edu (Heroneme, Carl Joseph) Date: Mon, 13 Apr 2020 18:41:50 -0000 Subject: [gmx-users] Polarization assistance request Message-ID: Hello GROMACS Users, I was wondering if anyone who has experience with simulations using polarization would be willing to take a look at what I?ve tried that so far hasn?t worked and give some tips and perhaps share their topology files and run settings. I am attempting to model a 3-atom molecule with polarizability of the partial charge on each atom. The only examples I have found so far through the other posts have been for Justin Lemkul?s DrudeFF branch, but I was hoping to just use the regular release if that is possible. I have included my .itp files for things I have tried that have not worked- Version 1, no explicitly defined shell particles ? made with the assumption that Gromacs would handle generating the shell particles for me given the host and a polarizability. [ moleculetype ] ; molname nrexcl ozone 2 [ atoms ] ; id at type res nr res name at name cg nr charge mass 1 OzCs94e8 1 OZO OzC 1 0.3 15.9994 2 OzSs94e8 1 OZO OzS1 1 -0.15 15.9994 3 OzSs94e8 1 OZO OzS2 1 -0.15 15.9994 [ bonds ] ; i j funct length force.c. 1 2 1 0.1278 182000 1 3 1 0.1278 182000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 116.8 587.7 [ polarization ] ; atom i j type alpha 1 2 1 0.00095 2 3 1 0.00095 3 1 1 0.00095 Version 2, explicitly assigned shell particles (shell atoms defined as shell type in the ffnonbonded.itp file) [ atomtypes ] OzCs94e8 8 15.9994 1.30 A 3.02e-01 5.2216e-01 OzSs94e8 8 15.9994 0.85 A 3.02e-01 5.2216e-01 OzCs94e8s 8 0 -1 S 0 0 OzSs94e8s 8 0 -1 S 0 0 [ moleculetype ] ; molname nrexcl ozone 2 [ atoms ] ; id at type res nr res name at name cg nr charge mass 1 OzCs94e8 1 OZO OzC 1 1.3 15.9994 2 OzCs94e8s 1 OZO OzCs 1 -1 0 3 OzSs94e8 1 OZO OzS1 1 0.85 15.9994 4 OzSs94e8s 1 OZO OzS1s 1 -1 0 5 OzSs94e8 1 OZO OzS2 1 0.85 15.9994 6 OzSs94e8s 1 OZO OzS2s 1 -1 0 [ bonds ] ; i j funct length force.c. 1 2 1 0.1278 182000 1 3 1 0.1278 182000 [ angles ] ; i j k funct angle force.c. 2 1 3 1 116.8 587.7 [ polarization ] ; atom i j type alpha 1 2 1 0.00095 3 4 1 0.00095 5 6 1 0.00095 Thanks, From leandro.obt at gmail.com Mon Apr 13 22:39:15 2020 From: leandro.obt at gmail.com (Leandro Bortot) Date: Mon, 13 Apr 2020 20:39:15 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" In-Reply-To: References: Message-ID: Dear Szil?rd, Thank you for your answer. I'm already exporting the three variables as separate commands (maybe what you saw was some formatting problem with the email? I'm not sure). For clarity, I just tested the following line: export GMX_GPU_DD_COMMS=true ; export GMX_GPU_PME_PP_COMMS=true ; export GMX_FORCE_UPDATE_DEFAULT_GPU=true ; mpirun -np 16 gmx_mpi mdrun -s md.tpr -v -deffnm md -ntomp 3 -nstlist 400 -nb gpu -bonded gpu -pme gpu -pin on -npme 1 And I still have the same problem: " *Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable, but the following condition(s) were not satisfied:Domain decomposition without GPU halo exchange is not supported. With separate PME rank(s), PME must use direct communication.Will use CPU version of update.* " Any ideas about what may be happening? Best regards, Leandro ------- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational Biology Brazilian Biosciences National Laboratory (LNBio) Brazilian Center for Research in Energy and Materials (CNPEM) Zip Code 13083-970, Campinas, S?o Paulo, Brazil. On Mon, Apr 6, 2020 at 10:25 AM Szil?rd P?ll wrote: > On Fri, Mar 27, 2020 at 8:30 PM Leandro Bortot > wrote: > > > Dear users, > > > > I'm trying to optimize the execution of a system composed by 10 > > million atoms on a multi-GPU machine with GROMACS 2020.1. > > I've followed the instructions given at > > > > > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ > > . However, when I run my simulation, mdrun tells me this: > > > > " > > > > *Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU > > environment variable, but the following condition(s) were not > > satisfied:Domain decomposition without GPU halo exchange is not > supported.* > > " > > > > My understanding was that exporting *GMX_GPU_DD_COMMS=true* would > > enable such halo communications. > > My simulation runs, however the performance is not scaling well with > > the number of GPUs. > > > > I've done the following: > > " > > > > *export GMX_GPU_DD_COMMS=trueexport GMX_GPU_PME_PP_COMMS=trueexport > > GMX_FORCE_UPDATE_DEFAULT_GPU=true*" > > > > You are getting the error below because you did not export all three > variables there. Those exports are separate commands and need to be issued > with some separator, e.g. semicolon or newline. > > > > And my execution line is: > > "*mpirun -np 4 gmx_mpi mdrun -s eq.1.tpr -v -deffnm eq.1 -pin on -ntomp 6 > > -npme 1 -nb gpu -bonded gpu -pme gpu -nstlist 400*" > > > > Beware that this command line is specific for one use-case presented in > your source (i.e. that very hardware and input system) and may not be fully > transferable (e.g. "-ntomp 6" or "-nstlist 400"). > > Cheers, > -- > Szil?rd > > > > > > If I add "-update gpu" to this same line I have the following error: > > " > > > > > > > > > > *Inconsistency in user input:Update task on the GPU was required,but the > > following condition(s) were not satisfied:Domain decomposition without > GPU > > halo exchange is not supported. With separate PME rank(s), PME must use > > direct communication.*" > > > > Also, I'm using constraints = h-bonds in my .mdp file. > > > > Am I doing something wrong? > > > > Thank you for your attention, > > Leandro > > ------- > > Leandro Oliveira Bortot > > Postdoctoral Fellow > > https://www.linkedin.com/in/leandro-obt/ > > Laboratory of Computational Biology > > Brazilian Biosciences National Laboratory (LNBio) > > Brazilian Center for Research in Energy and Materials (CNPEM) > > Zip Code 13083-970, Campinas, S?o Paulo, Brazil. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From lamonteserincastanedo at gmail.com Mon Apr 13 22:40:45 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Mon, 13 Apr 2020 20:40:45 -0000 Subject: [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment? In-Reply-To: <54add009-1c6c-f6f1-61a6-17c7cdc5f7d2@vt.edu> References: <54add009-1c6c-f6f1-61a6-17c7cdc5f7d2@vt.edu> Message-ID: Dear Dr. Lemkul thank you very much for your answer. I will look on the literature. El lun., 13 de abr. de 2020 a la(s) 12:55, Justin Lemkul (jalemkul at vt.edu) escribi?: > > > On 4/13/20 10:37 AM, lazaro monteserin wrote: > > Dear Gromacs users > > > > I have three questions about the details of running MD of small molecules > > in gromacs: > > > > 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say > the > > carbons in the sugar) with genrestr, should I use temperature coupling > > groups? > > Freezing and restraining are different; don't use the terms > interchangeably. Freezing means the atoms are never updated (position or > velocity), and I don't recommend using this approach as it is entirely > unphysical. What you're talking about is applying a restraint. You need > to assign all atoms to a temperature-coupling bath. If you don't, that's > also completely unphysical. > > > 2) Now, if I freeze in the nucleoside again the carbons from the sugar > but > > the calculation is in water, should I use temperature coupling?, should I > > put the nucleoside in one group and the solvent in another group? What > > temperature coupling methodology would be more recommended? > > For a small solute in water, couple the whole system together. > > > 3) For these type of small molecules (around 32 atoms) what would be the > > best time to run the MD, e.x. 5ns, 10ns, 20ns, etc? > > You should base this conclusion on your examination of the literature. > What are the time scales of the dynamics you are interested in? What > have previous studies on similar systems demonstrated? > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pganguly at chem.ucsb.edu Tue Apr 14 02:00:41 2020 From: pganguly at chem.ucsb.edu (Pritam Ganguly) Date: Tue, 14 Apr 2020 00:00:41 -0000 Subject: [gmx-users] Replica exchange probabilities beyond version 2016 Message-ID: <19587795-4e28-887c-ead3-e06c7ee41e38@chem.ucsb.edu> Hello, I have noticed that the average exchange probability for a replica exchange run increases significantly if I use Gromacs versions 2018, as compared to versions 2016 or earlier. I have tested that by simulating the same system with versions 2016.4 and 2018.3 and the average probabilities I find are: Version 2016.4: Replica exchange statistics Repl? 1666 attempts, 833 odd, 833 even Repl? average probabilities: Repl???? 0??? 1??? 2??? 3??? 4??? 5??? 6??? 7??? 8??? 9?? 10 11 12?? 13?? 14?? 15?? 16?? 17?? 18?? 19?? 20?? 21?? 22?? 23 24 25?? 26?? 27?? 28?? 29?? 30?? 31?? 32?? 33?? 34?? 35?? 36 37 38?? 39?? 40?? 41?? 42?? 43?? 44?? 45?? 46?? 47?? 48?? 49 50 51?? 52?? 53?? 54?? 55?? 56?? 57?? 58?? 59?? 60?? 61?? 62 63 Repl????? .29? .33? .29? .30? .28? .30? .30? .29? .29? .29? .30 .26? .29? .30? .28? .29? .26? .26? .29? .28? .26? .27? .27? .27 .27? .28? .26? .27? .26? .25? .27? .25? .26? .27? .25? .24? .25 .26? .27? .25? .27? .26? .26? .26? .25? .26? .26? .24? .25? .27 .26? .27? .26? .25? .27? .27? .28? .26? .27? .26? .27? .27? .28 Version 2018.3: Replica exchange statistics Repl? 1666 attempts, 833 odd, 833 even Repl? average probabilities: Repl???? 0??? 1??? 2??? 3??? 4??? 5??? 6??? 7??? 8??? 9?? 10 11 12?? 13?? 14?? 15?? 16?? 17?? 18?? 19?? 20?? 21?? 22?? 23 24 25?? 26?? 27?? 28?? 29?? 30?? 31?? 32?? 33?? 34?? 35?? 36 37 38?? 39?? 40?? 41?? 42?? 43?? 44?? 45?? 46?? 47?? 48?? 49 50 51?? 52?? 53?? 54?? 55?? 56?? 57?? 58?? 59?? 60?? 61?? 62 63 Repl????? .39? .39? .37? .42? .38? .38? .39? .36? .36? .38? .40 .39? .40? .39? .37? .35? .40? .39? .35? .38? .40? .35? .38? .35 .36? .35? .36? .36? .38? .36? .37? .36? .35? .36? .36? .37? .35 .35? .35? .37? .37? .35? .37? .36? .37? .34? .36? .38? .38? .38 .35? .37? .36? .39? .36? .40? .38? .38? .40? .36? .37? .36? .33 These are test runs for 5 ns with exchange frequencies of 3 ps. I have used the same input parameters for both of these runs (mdp is attached). I actually observed this with many other systems and I was looking for any relevant gromacs release note for versions 2018 or beyond related to the replica exchange algorithm or the way the energies are calculated, but I could not figure it out. Regards, Pritam -- Pritam Ganguly Department of Chemistry and Biochemistry University of California at Santa Barbara Santa Barbara, CA, USA 93106 Office: PSBN 3606 Phone: +1-805-893-2767 http://people.chem.ucsb.edu/ganguly/pritam -------------- next part -------------- ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/roe include = ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 2500000 ; For exact run continuation or redoing part of a run init-step = 0 ; Part index is updated automatically on checkpointing (keeps files separate) simulation-part = 1 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 100 ; group(s) for center of mass motion removal comm_grps = system ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = -1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax-shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 100000 nstcalcenergy = 100 nstenergy = 10000 ; Output frequency and precision for .xtc file nstxout-compressed = 100000 compressed-x-precision = 1000 ; This selects the subset of atoms for the compressed ; trajectory file. You can select multiple groups. By ; default, all atoms will be written. compressed-x-grps = System ; Selection of energy groups energygrps = System ; NEIGHBORSEARCHING PARAMETERS ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) cutoff-scheme = Verlet ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic-molecules = no ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist verlet-buffer-tolerance = 0.005 ; nblist cut-off rlist = 1.2 ; long-range cut-off for switched potentials ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME coulomb-modifier = Potential-shift-Verlet rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon-r = 1 epsilon-rf = 0 ; Method for doing Van der Waals vdwtype = cut-off vdw-modifier = Potential-shift-Verlet ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = enerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Separate tables between energy group pairs energygrp-table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 ; IMPLICIT SOLVENT ALGORITHM implicit-solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb-algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 1 ; Dielectric coefficient of the implicit solvent gb-epsilon-solvent = 80 ; Salt concentration in M for Generalized Born models gb-saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa-surface-tension = -1 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.5 ref_t = 300 ; pressure coupling Pcoupl = no pcoupltype = Isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = No ; OPTIONS FOR QMMM calculations QMMM = no ; Groups treated Quantum Mechanically QMMM-grps = ; QM method QMmethod = ; QMMM scheme QMMMscheme = normal ; QM basisset QMbasis = ; QM charge QMcharge = ; QM multiplicity QMmult = ; Surface Hopping SH = ; CAS space options CASorbitals = CASelectrons = SAon = SAoff = SAsteps = ; Scale factor for MM charges MMChargeScaleFactor = 1 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing-npoints = ; List of times at the annealing points for each group annealing-time = ; Temp. at each annealing point, for each group. annealing-temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 300 gen_seed = 182756 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp-excl = ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype = wall-density = wall-ewald-zfac = 3 ; COM PULLING pull = no ; AWH biasing awh = no ; ENFORCED ROTATION ; Enforced rotation: No or Yes rotation = no ; Group to display and/or manipulate in interactive MD session IMD-group = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no disre-fc = 1000 disre-tau = 0 ; Output frequency for pair distances to energy file nstdisreout = 100 ; Orientation restraints: No or Yes orire = no ; Orientation restraints force constant and tau for time averaging orire-fc = 0 orire-tau = 0 orire-fitgrp = ; Output frequency for trace(SD) and S to energy file nstorireout = 100 ; Free energy variables free-energy = no couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no init-lambda = -1 init-lambda-state = -1 delta-lambda = 0 nstdhdl = 50 fep-lambdas = mass-lambdas = coul-lambdas = vdw-lambdas = bonded-lambdas = restraint-lambdas = temperature-lambdas = calc-lambda-neighbors = 1 init-lambda-weights = dhdl-print-energy = no sc-alpha = 0 sc-power = 1 sc-r-power = 6 sc-sigma = 0.3 sc-coul = no separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 ; Non-equilibrium MD stuff acc-grps = accelerate = freezegrps = freezedim = cos-acceleration = 0 deform = ; simulated tempering variables simulated-tempering = no simulated-tempering-scaling = geometric sim-temp-low = 300 sim-temp-high = 300 ; Ion/water position swapping for computational electrophysiology setups ; Swap positions along direction: no, X, Y, Z swapcoords = no adress = no ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 ; Electric fields ; Format for electric-field-x, etc. is: four real variables: ; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), ; and sigma (ps) width of the pulse. Omega = 0 means static field, ; sigma = 0 means no pulse, leaving the field to be a cosine function. electric-field-x = 0 0 0 0 electric-field-y = 0 0 0 0 electric-field-z = 0 0 0 0 From jun.zhou at monash.edu Tue Apr 14 03:39:39 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Tue, 14 Apr 2020 01:39:39 -0000 Subject: [gmx-users] Ways to calculate shear viscosity Message-ID: Hi all, I have sent this before but no one answers. I want to simulate a couvette flow using gromacs by applying a deform velocity at xz direction. For a pure water box, it works well though there are warnings "the box is too skewed". When I put a surfactant micelle in the middle, that warning still occurs and also terminates the simulation. Does anyone have any suggestions about this? Also, I read some paper they said they apply *the Lees?Edwards sliding brick boundary conditions *to get a shear flow (10.1039/c7cp08349a), and when I search the mailing list, Berk Hess also says he has a patch for this. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-October/009325.html. Can anyone show me how to do this? Thanks. -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From mohammad.madani at uconn.edu Tue Apr 14 04:03:21 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Tue, 14 Apr 2020 02:03:21 -0000 Subject: [gmx-users] Basic question about command line Message-ID: Dear all Hi, I have a basic question about the using the gromacs. I want to use gmx cluster for clustering. I use the cluster hpc. When I run the this command: gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg I receive the error that I should select the group for least rmsd. Could you please help me how can I add this part to the command line? Can I do this?? Many thanks From mohammad.madani at uconn.edu Tue Apr 14 04:03:22 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Tue, 14 Apr 2020 02:03:22 -0000 Subject: [gmx-users] Basic question about command line Message-ID: Dear all Hi, I have a basic question about the using the gromacs. I want to use gmx cluster for clustering. I use the cluster hpc. When I run the this command: gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg I receive the error that I should select the group for least rmsd. Could you please help me how can I add this part to the command line? Can I do this?? Many thanks From h.gul.ozer at gmail.com Tue Apr 14 04:55:50 2020 From: h.gul.ozer at gmail.com (=?UTF-8?Q?G=C3=BCl_Zerze?=) Date: Tue, 14 Apr 2020 02:55:50 -0000 Subject: [gmx-users] Replica exchange probabilities beyond version 2016 In-Reply-To: <19587795-4e28-887c-ead3-e06c7ee41e38@chem.ucsb.edu> References: <19587795-4e28-887c-ead3-e06c7ee41e38@chem.ucsb.edu> Message-ID: Hi Pritam, Did you check your energy fluctuations? Looks like you are using NH thermostat, you might be suffering from the interaction of NH thermostat oscillations with resonance modes in the system, which makes energy fluctuations substantially larger (compared to fluctuations with NH in older versions of Gromacs). As a result of amplified fluctuations, you have higher exchange probability. See here for a previous relevant exchange: https://redmine.gromacs.org/issues/2904 For my system, making tau_t=10 helped to recover the old behavior. Best, G?l *--* *G?l H. Zerze* Postdoctoral Research Associate Chemical and Biological Engineering Princeton University http://pablonet.princeton.edu/ On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly wrote: > Hello, > > I have noticed that the average exchange probability for a replica > exchange run increases significantly if I use Gromacs versions 2018, as > compared to versions 2016 or earlier. I have tested that by simulating > the same system with versions 2016.4 and 2018.3 and the average > probabilities I find are: > > Version 2016.4: > > Replica exchange statistics > Repl 1666 attempts, 833 odd, 833 even > Repl average probabilities: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 > 58 59 60 61 62 63 > Repl .29 .33 .29 .30 .28 .30 .30 .29 .29 .29 .30 .26 > .29 .30 .28 .29 .26 .26 .29 .28 .26 .27 .27 .27 .27 .28 > .26 .27 .26 .25 .27 .25 .26 .27 .25 .24 .25 .26 .27 .25 > .27 .26 .26 .26 .25 .26 .26 .24 .25 .27 .26 .27 .26 .25 > .27 .27 .28 .26 .27 .26 .27 .27 .28 > > > Version 2018.3: > > Replica exchange statistics > Repl 1666 attempts, 833 odd, 833 even > Repl average probabilities: > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 > 58 59 60 61 62 63 > Repl .39 .39 .37 .42 .38 .38 .39 .36 .36 .38 .40 .39 > .40 .39 .37 .35 .40 .39 .35 .38 .40 .35 .38 .35 .36 .35 > .36 .36 .38 .36 .37 .36 .35 .36 .36 .37 .35 .35 .35 .37 > .37 .35 .37 .36 .37 .34 .36 .38 .38 .38 .35 .37 .36 .39 > .36 .40 .38 .38 .40 .36 .37 .36 .33 > > These are test runs for 5 ns with exchange frequencies of 3 ps. I have > used the same input parameters for both of these runs (mdp is attached). > I actually observed this with many other systems and I was looking for > any relevant gromacs release note for versions 2018 or beyond related to > the replica exchange algorithm or the way the energies are calculated, > but I could not figure it out. > > Regards, > > Pritam > > -- > Pritam Ganguly > Department of Chemistry and Biochemistry > University of California at Santa Barbara > Santa Barbara, CA, USA 93106 > > Office: PSBN 3606 > Phone: +1-805-893-2767 > http://people.chem.ucsb.edu/ganguly/pritam > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From byunjy0614 at gmail.com Tue Apr 14 08:31:05 2020 From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=) Date: Tue, 14 Apr 2020 06:31:05 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem Message-ID: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> Dear GROMACS users, Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below Step 231785, time 463.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000176, max 0.003912 (between atoms 3035 and 3037) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3035 3036 34.0 0.1090 0.1087 0.1090 ?. Step 231825, time 463.65 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3024 3025 90.0 0.1090 0.1236 0.1090 3026 3027 100.8 0.1090 6.6242 0.1090 3028 3029 162.5 1.7683 5245.4102 0.1090 3033 3034 106.7 0.1090 426.5654 0.1090 3035 3037 90.0 0.3851 0.7991 0.1090 3038 3039 90.0 0.6045 0.4497 0.1090 3038 3040 90.0 0.1123 0.2833 0.1090 3041 3042 59.0 0.1020 0.1020 0.1020 Wrote pdb files with previous and current coordinates Step 231826, time 463.652 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1423 1424 140.4 0.1000 503.9983 0.1000 3024 3025 61.1 0.1236 223337872.0000 0.1090 3026 3027 168.8 6.6242 149263.5000 0.1090 3028 3029 165.8 5245.4102 263929.4375 0.1090 3031 3032 116.2 0.1090 223428336.0000 0.1090 3033 3034 179.9 426.5654 446766720.0000 0.1090 3035 3036 35.3 29.6105 831.0708 0.1090 3035 3037 102.9 0.7991 775.3371 0.1090 3038 3039 90.0 0.4497 0.6355 0.1090 3038 3040 47.7 0.2833 0.1111 0.1090 step 231826: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. Why does the LINCS warning occurs? and How I solve this problem? Many Thanks Jinyoung From ydu-sci at outlook.com Tue Apr 14 10:08:27 2020 From: ydu-sci at outlook.com (Yu Du) Date: Tue, 14 Apr 2020 08:08:27 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> Message-ID: Hi Jinyoung, I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring. After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? Sent: Tuesday, April 14, 2020 14:32 To: gmx-users at gromacs.org Subject: [gmx-users] How to solve the "LINCS WARNING" problem Dear GROMACS users, Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below Step 231785, time 463.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000176, max 0.003912 (between atoms 3035 and 3037) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3035 3036 34.0 0.1090 0.1087 0.1090 ?. Step 231825, time 463.65 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3024 3025 90.0 0.1090 0.1236 0.1090 3026 3027 100.8 0.1090 6.6242 0.1090 3028 3029 162.5 1.7683 5245.4102 0.1090 3033 3034 106.7 0.1090 426.5654 0.1090 3035 3037 90.0 0.3851 0.7991 0.1090 3038 3039 90.0 0.6045 0.4497 0.1090 3038 3040 90.0 0.1123 0.2833 0.1090 3041 3042 59.0 0.1020 0.1020 0.1020 Wrote pdb files with previous and current coordinates Step 231826, time 463.652 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1423 1424 140.4 0.1000 503.9983 0.1000 3024 3025 61.1 0.1236 223337872.0000 0.1090 3026 3027 168.8 6.6242 149263.5000 0.1090 3028 3029 165.8 5245.4102 263929.4375 0.1090 3031 3032 116.2 0.1090 223428336.0000 0.1090 3033 3034 179.9 426.5654 446766720.0000 0.1090 3035 3036 35.3 29.6105 831.0708 0.1090 3035 3037 102.9 0.7991 775.3371 0.1090 3038 3039 90.0 0.4497 0.6355 0.1090 3038 3040 47.7 0.2833 0.1111 0.1090 step 231826: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. Why does the LINCS warning occurs? and How I solve this problem? Many Thanks Jinyoung -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From olayiwolateslim9 at gmail.com Tue Apr 14 10:35:20 2020 From: olayiwolateslim9 at gmail.com (Teslim Olayiwola) Date: Tue, 14 Apr 2020 08:35:20 -0000 Subject: [gmx-users] Basic question about command line (Mohammad Madani) Message-ID: Hi Mohammed Madani, Your command is missing the group as mentioned in the error message. While correct for periodic error, you should ensure that you extract (that's if your top/file has more than one groups) the appropriate group (not system) from the production file (xtc) by using trjconv option. After extracting with trj, you can regenerate the tpr file for the select groups. After doing this, you can then use the following command gmxi clustsize -f file.nojump.mol.xtc -n group.ndx -s group.tpr -mol yes -cut 0.35 -pbc yes On Tue, 14 Apr 2020 at 11:09, < gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Basic question about command line (Mohammad Madani) > 2. Basic question about command line (Mohammad Madani) > 3. Re: Replica exchange probabilities beyond version 2016 (G?l Zerze) > 4. How to solve the "LINCS WARNING" problem (???) > 5. Re: How to solve the "LINCS WARNING" problem (Yu Du) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Apr 2020 22:03:07 -0400 > From: Mohammad Madani > To: "gmx-users at gromacs.org" , > "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] Basic question about command line > Message-ID: > < > CABaRwomJ3AV7nFPr4cJNbqThWeEBL9wGBrMhWTAu2yEJoxX6-A at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all > Hi, > I have a basic question about the using the gromacs. > I want to use gmx cluster for clustering. I use the cluster hpc. > When I run the this command: > gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg > I receive the error that I should select the group for least rmsd. > Could you please help me how can I add this part to the command line? > Can I do this?? > > Many thanks > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Apr 2020 22:03:07 -0400 > From: Mohammad Madani > To: "gmx-users at gromacs.org" , > "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] Basic question about command line > Message-ID: > < > CABaRwomJ3AV7nFPr4cJNbqThWeEBL9wGBrMhWTAu2yEJoxX6-A at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all > Hi, > I have a basic question about the using the gromacs. > I want to use gmx cluster for clustering. I use the cluster hpc. > When I run the this command: > gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg > I receive the error that I should select the group for least rmsd. > Could you please help me how can I add this part to the command line? > Can I do this?? > > Many thanks > > > ------------------------------ > > Message: 3 > Date: Mon, 13 Apr 2020 22:55:35 -0400 > From: G?l Zerze > To: gmx-users at gromacs.org, pganguly at chem.ucsb.edu > Subject: Re: [gmx-users] Replica exchange probabilities beyond version > 2016 > Message-ID: > 6t8zvBHHpgN_w1WZQ at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi Pritam, > > Did you check your energy fluctuations? Looks like you are using NH > thermostat, you might be suffering from the interaction of NH thermostat > oscillations with resonance modes in the system, which makes energy > fluctuations substantially larger (compared to fluctuations with NH in > older versions of Gromacs). As a result of amplified fluctuations, you have > higher exchange probability. See here for a previous relevant exchange: > https://redmine.gromacs.org/issues/2904 For my system, making tau_t=10 > helped to recover the old behavior. > > Best, > G?l > *--* > *G?l H. Zerze* > Postdoctoral Research Associate > > Chemical and Biological Engineering > Princeton University > http://pablonet.princeton.edu/ > > > > On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly > wrote: > > > Hello, > > > > I have noticed that the average exchange probability for a replica > > exchange run increases significantly if I use Gromacs versions 2018, as > > compared to versions 2016 or earlier. I have tested that by simulating > > the same system with versions 2016.4 and 2018.3 and the average > > probabilities I find are: > > > > Version 2016.4: > > > > Replica exchange statistics > > Repl 1666 attempts, 833 odd, 833 even > > Repl average probabilities: > > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > > 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 > > 58 59 60 61 62 63 > > Repl .29 .33 .29 .30 .28 .30 .30 .29 .29 .29 .30 .26 > > .29 .30 .28 .29 .26 .26 .29 .28 .26 .27 .27 .27 .27 .28 > > .26 .27 .26 .25 .27 .25 .26 .27 .25 .24 .25 .26 .27 .25 > > .27 .26 .26 .26 .25 .26 .26 .24 .25 .27 .26 .27 .26 .25 > > .27 .27 .28 .26 .27 .26 .27 .27 .28 > > > > > > Version 2018.3: > > > > Replica exchange statistics > > Repl 1666 attempts, 833 odd, 833 even > > Repl average probabilities: > > Repl 0 1 2 3 4 5 6 7 8 9 10 11 12 > > 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 > > 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 > > 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 > > 58 59 60 61 62 63 > > Repl .39 .39 .37 .42 .38 .38 .39 .36 .36 .38 .40 .39 > > .40 .39 .37 .35 .40 .39 .35 .38 .40 .35 .38 .35 .36 .35 > > .36 .36 .38 .36 .37 .36 .35 .36 .36 .37 .35 .35 .35 .37 > > .37 .35 .37 .36 .37 .34 .36 .38 .38 .38 .35 .37 .36 .39 > > .36 .40 .38 .38 .40 .36 .37 .36 .33 > > > > These are test runs for 5 ns with exchange frequencies of 3 ps. I have > > used the same input parameters for both of these runs (mdp is attached). > > I actually observed this with many other systems and I was looking for > > any relevant gromacs release note for versions 2018 or beyond related to > > the replica exchange algorithm or the way the energies are calculated, > > but I could not figure it out. > > > > Regards, > > > > Pritam > > > > -- > > Pritam Ganguly > > Department of Chemistry and Biochemistry > > University of California at Santa Barbara > > Santa Barbara, CA, USA 93106 > > > > Office: PSBN 3606 > > Phone: +1-805-893-2767 > > http://people.chem.ucsb.edu/ganguly/pritam > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > ------------------------------ > > Message: 4 > Date: Tue, 14 Apr 2020 15:32:37 +0900 > From: ??? > To: gmx-users at gromacs.org > Subject: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2 at gmail.com> > Content-Type: text/plain; charset=utf-8 > > Dear GROMACS users, > > Since I have run the nvt and npt processes for the protein-ligand > interaction, I met the the warning messages below > > Step 231785, time 463.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3035 3036 34.0 0.1090 0.1087 0.1090 > > ?. > > Step 231825, time 463.65 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3024 3025 90.0 0.1090 0.1236 0.1090 > 3026 3027 100.8 0.1090 6.6242 0.1090 > 3028 3029 162.5 1.7683 5245.4102 0.1090 > 3033 3034 106.7 0.1090 426.5654 0.1090 > 3035 3037 90.0 0.3851 0.7991 0.1090 > 3038 3039 90.0 0.6045 0.4497 0.1090 > 3038 3040 90.0 0.1123 0.2833 0.1090 > 3041 3042 59.0 0.1020 0.1020 0.1020 > Wrote pdb files with previous and current coordinates > > Step 231826, time 463.652 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1423 1424 140.4 0.1000 503.9983 0.1000 > 3024 3025 61.1 0.1236 223337872.0000 0.1090 > 3026 3027 168.8 6.6242 149263.5000 0.1090 > 3028 3029 165.8 5245.4102 263929.4375 0.1090 > 3031 3032 116.2 0.1090 223428336.0000 0.1090 > 3033 3034 179.9 426.5654 446766720.0000 0.1090 > 3035 3036 35.3 29.6105 831.0708 0.1090 > 3035 3037 102.9 0.7991 775.3371 0.1090 > 3038 3039 90.0 0.4497 0.6355 0.1090 > 3038 3040 47.7 0.2833 0.1111 0.1090 > step 231826: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > So I checked the my input configuration. the 3035, 3028, 3035 atoms are > ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > Why does the LINCS warning occurs? and How I solve this problem? > > Many Thanks > > Jinyoung > > ------------------------------ > > Message: 5 > Date: Tue, 14 Apr 2020 08:08:20 +0000 > From: Yu Du > To: "gmx-users at gromacs.org" > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > < > SL2PR04MB30336C02709B0CDE69A04AF1E0DA0 at SL2PR04MB3033.apcprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="ks_c_5601-1987" > > Hi Jinyoung, > > I guess that the LINCS WARNING you encountered maybe came from hiden > errors in the configuration of either protein or ligand OR more directly > from the ligand's topology. You need to carefully check the configuration > of protein and ligand, e.g. side chain goes through benzene ring. > > After a careful check, If you want more suggestion, you need to provide > some details of the generation of ligand's topology. > > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < > byunjy0614 at gmail.com> > Sent: Tuesday, April 14, 2020 14:32 > To: gmx-users at gromacs.org > Subject: [gmx-users] How to solve the "LINCS WARNING" problem > > Dear GROMACS users, > > Since I have run the nvt and npt processes for the protein-ligand > interaction, I met the the warning messages below > > Step 231785, time 463.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3035 3036 34.0 0.1090 0.1087 0.1090 > > ?. > > Step 231825, time 463.65 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3024 3025 90.0 0.1090 0.1236 0.1090 > 3026 3027 100.8 0.1090 6.6242 0.1090 > 3028 3029 162.5 1.7683 5245.4102 0.1090 > 3033 3034 106.7 0.1090 426.5654 0.1090 > 3035 3037 90.0 0.3851 0.7991 0.1090 > 3038 3039 90.0 0.6045 0.4497 0.1090 > 3038 3040 90.0 0.1123 0.2833 0.1090 > 3041 3042 59.0 0.1020 0.1020 0.1020 > Wrote pdb files with previous and current coordinates > > Step 231826, time 463.652 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1423 1424 140.4 0.1000 503.9983 0.1000 > 3024 3025 61.1 0.1236 223337872.0000 0.1090 > 3026 3027 168.8 6.6242 149263.5000 0.1090 > 3028 3029 165.8 5245.4102 263929.4375 0.1090 > 3031 3032 116.2 0.1090 223428336.0000 0.1090 > 3033 3034 179.9 426.5654 446766720.0000 0.1090 > 3035 3036 35.3 29.6105 831.0708 0.1090 > 3035 3037 102.9 0.7991 775.3371 0.1090 > 3038 3039 90.0 0.4497 0.6355 0.1090 > 3038 3040 47.7 0.2833 0.1111 0.1090 > step 231826: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > So I checked the my input configuration. the 3035, 3028, 3035 atoms are > ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > Why does the LINCS warning occurs? and How I solve this problem? > > Many Thanks > > Jinyoung > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 43 > ****************************************************** > From tamas at hegelab.org Tue Apr 14 16:52:07 2020 From: tamas at hegelab.org (Tamas Hegedus) Date: Tue, 14 Apr 2020 14:52:07 -0000 Subject: [gmx-users] gromacs 2020, bug? high total energy Message-ID: <7ac2cc8a-2729-f549-4d47-ee6de8a23951@hegelab.org> Hi, There might be some bug(?) in gromacs 2020. I can not decide. I just installed 2020.1 today using the same script (and libraries) what I have used for gromacs 2019. After energy minimization, in the nvt equilibration run, it stops: Fatal error: Step 0: The total potential energy is 1.99295e+23, which is extremely high. The LJ and electrostatic contributions to the energy are 73028.7 and -712615, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. I tried two different systems (two different soluble proteins, ff charmm-36m). However, if I start the simulations with 2019.4, there is no problem at all. Have a nice day, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas at hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org From tamas at hegelab.org Tue Apr 14 17:07:05 2020 From: tamas at hegelab.org (Tamas Hegedus) Date: Tue, 14 Apr 2020 15:07:05 -0000 Subject: [gmx-users] gromacs 2020, bug? high total energy In-Reply-To: <7ac2cc8a-2729-f549-4d47-ee6de8a23951@hegelab.org> References: <7ac2cc8a-2729-f549-4d47-ee6de8a23951@hegelab.org> Message-ID: <488b599d-57c6-1fd9-4e82-85f7f7e116d0@hegelab.org> Hi, It was not gromacs 2020, but my fault and mixing up various tools (grompp, mdrun) from 2019 and 2020 versions. I am sorry. Bests, Tamas On 4/14/20 4:44 PM, Tamas Hegedus wrote: > Hi, > > There might be some bug(?) in gromacs 2020. I can not decide. > > I just installed 2020.1 today using the same script (and libraries) > what I have used for gromacs 2019. > After energy minimization, in the nvt equilibration run, it stops: > Fatal error: > Step 0: The total potential energy is 1.99295e+23, which is extremely > high. > The LJ and electrostatic contributions to the energy are 73028.7 and > -712615, > respectively. A very high potential energy can be caused by overlapping > interactions in bonded interactions or very large coordinate values. > Usually > this is caused by a badly- or non-equilibrated initial configuration, > incorrect interactions or parameters in the topology. > > I tried two different systems (two different soluble proteins, ff > charmm-36m). > > However, if I start the simulations with 2019.4, there is no problem > at all. > > Have a nice day, > Tamas > -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas at hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org From jalemkul at vt.edu Tue Apr 14 18:32:54 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 14 Apr 2020 16:32:54 -0000 Subject: [gmx-users] Basic question about command line In-Reply-To: References: Message-ID: On 4/13/20 10:03 PM, Mohammad Madani wrote: > Dear all > Hi, > I have a basic question about the using the gromacs. > I want to use gmx cluster for clustering. I use the cluster hpc. > When I run the this command: > gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg > I receive the error that I should select the group for least rmsd. > Could you please help me how can I add this part to the command line? > Can I do this?? http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From shubhadip022 at gmail.com Tue Apr 14 20:06:25 2020 From: shubhadip022 at gmail.com (shubhadip das) Date: Tue, 14 Apr 2020 18:06:25 -0000 Subject: [gmx-users] Basic question about command line In-Reply-To: References: Message-ID: In Bob I'm _ bk no ??llkmjk mm lll look okk jul ki o ki olk by hmm j by by he On Tue, 14 Apr 2020, 6:33 pm Justin Lemkul, wrote: > > > On 4/13/20 10:03 PM, Mohammad Madani wrote: > > Dear all > > Hi, > > I have a basic question about the using the gromacs. > > I want to use gmx cluster for clustering. I use the cluster hpc. > > When I run the this command: > > gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg > > I receive the error that I should select the group for least rmsd. > > Could you please help me how can I add this part to the command line? > > Can I do this?? > > http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From m.b.abdelaal at gmail.com Tue Apr 14 22:55:58 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 14 Apr 2020 20:55:58 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: Sorry for writing again in the same topic but I couldn't solve the velocity problem. I am trying to reproduce a paper written by: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. Powell Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films It was mentioned in the paper that " The molecule was inserted into the system such that the x and y coordinates of the centre of mass were sampled from a uniform distribution covering the entire box while the z coordinate of the centre of mass was set to 2.0 nm above the current surface. The initial orientation of the molecule was randomised. *The velocities of each atom within the inserted molecule in x and y were sampled from a Gaussian distribution with a mean of 0.0 nm/ps and a standard deviation appropriate for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T is the temperature and m is the mass of the atom). The velocities in z were sampled from the distribution with the same standard deviation as x and y but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in the direction opposite to the surface) were rectified by taking the absolute value. This ensured all molecules moved toward the surface.* I have read the section 3.4.1 of the manual version 5.1.2 as recommended above and I have also read all the velocity related topics in the manual and user guide. (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file and then I inserted the molecule in a box using insert-molecules, However after the insertion process is completed I opened the output .gro file but the velocity was not read. This means that I can only generate the velocity through the .mdp file. If I am going to generate the velocity using my .mdp file, is it possible to change the standard deviation and the mean ? if yes, how can I modify them ? (I can't find any way to modify the parameters of the Maxwell distribution) I want to have velocity distributions with means equal to 0,0,0.5 nmps in the x,y,z directions respectively. You wrote in your last email that, "A 3D Maxwell Boltzmann velocity distribution corresponds to three identical gaussian speed distributions in vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). Just change the standard deviation of the velocity distribution sqrt(kT/m) for each velocity component if you want them to be different. If you don't want the mean to be zero for whatever reason, add a constant." If the velocity will not be read from the .gro file where should I add the constant to change the mean? Many thanks, Mohamed On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal wrote: > Many thanks for your reply :) > > All your language assumptions are true and that is exactly what I wanted > to communicate, next time I will try to be more precise and sorry for the > confusion ? > > I will read section 3.4.1 again carefully. > > Thanks again and sorry for the inconvenience. > > Mohamed > > On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal >> wrote: >> >> > Many thanks for your reply ? >> > >> > The limitation in the generate velocity using the .mdp file, is that >> while >> > I can generate the velocity from Maxwell distribution, I will have the >> > same velocities in the x, y and z directions. >> > >> >> I think you mean "same velocity *distributions* in the x, y, and z >> directions." The distributions will be approximately the same but each >> atom will have a different velocity. >> >> > >> > On the other hand, generating the velocity from the .gro file will let >> me >> > specify different velocities in the x,y and z directions but they will >> be >> > the same velocities for all the atoms (will not be taken from a maxwell >> > distribution with variation in the atoms velocities). >> > >> >> I think you mean "specify different velocity *distributions* in the x, y, >> and z directions" >> >> > >> > Is it possible to generate different velocities in the x,y and z >> directions >> > >> >> I think you mean "generate different velocity *distributions* in the x, y, >> and z directions." If so, the answer is obviously yes. Because you can >> type in each individual vxi, vyi, and vzi for every atom i, you can >> generate different velocity distributions in the x, y, and z directions. >> >> >> > from a maxwell distribution ? >> >> >> I am not sure what this part of the sentence means. If you do what you >> are >> suggesting, you will not be working with a maxwell distribution because >> all >> three directions should have identical distributions. See comment below. >> If there is another misunderstanding, you need to spend more time crafting >> precise sentences to communicate what you are after. >> >> >> > (for example the velocities to be taken from >> > a maxwell distribution with a mean of 0.1 in the x direction and with a >> > mean of 0.2 in the y direction and with mean of 0.3 in the z direction?) >> > >> >> In my last email I suggested reading section 3.4.1 of the manual version >> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity >> distribution >> corresponds to three identical gaussian speed distributions in vx, vy, and >> vz centered at zero (mean should be zero for vx, vy, vz). Just change the >> standard deviation of the velocity distribution sqrt(kT/m) for each >> velocity component if you want them to be different. If you don't want >> the >> mean to be zero for whatever reason, add a constant. However, a non-zero >> mean for any of the velocity components will generate center of mass >> motion. If you want center of mass motion, turn off center of mass motion >> removal in the mdp file. >> >> >> > Thanks for your help :) >> > Mohamed >> > >> > On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: >> > >> > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < >> m.b.abdelaal at gmail.com> >> > > wrote: >> > > >> > > > No, I use the generate velocity option in the .mdp files. >> > > > >> > > > However I want now to assign different velocities in the x,y,z >> > > directions. >> > > > Which I thought it could only be done through the .gro file, but I >> > don't >> > > > know If I did that, should I change the value of the generate >> velocity >> > to >> > > > be = NO in the .mdp files ? (otherwise I would have generated the >> > > > velocities twice). >> > > > >> > > >> > > That sounds logical. Set it to no if you provide your own initial >> > > velocities. >> > > >> > > > >> > > > Moreover, if I added the velocities in the .gro file how can I >> generate >> > > the >> > > > velocities in the .gro file from a distribution (Maxwell) with a >> > specific >> > > > mean and standard deviation ? >> > > > >> > > > I have tried to search in different sources (the user list, manual, >> > user >> > > > guide, research gate and other platforms) how to solve this velocity >> > > > problem but I didn't find a clear way to insert different >> velocities in >> > > the >> > > > x,y,z directions using distribution rater than constant velocities. >> > > > >> > > > There is a good section on this in the manual. For example, section >> > > 3.4.1 >> > > in the Gromacs 5.1.2 manual. >> > > >> > > Also, you know that the generate velocities option assigns velocities >> to >> > > atoms from an approximate MB distribution at whatever temperature you >> > > specify in the MDP file, right? If I understand you correctly, the >> > > generate velocities options should do exactly what you want. With no >> > extra >> > > work. >> > > >> > > >> > > > Please guide me how to do it as I am a little bit confused in the >> > > velocity >> > > > generation mechanisms. >> > > > >> > > > Many thanks, >> > > > Mohamed >> > > > >> > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul >> wrote: >> > > > >> > > > > >> > > > > >> > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: >> > > > > > Hello everybody :) >> > > > > > >> > > > > > Can I use the gmx insert-molecules to insert molecules in my box >> > with >> > > > > > velocities by adding the velocities in t >> he >> .gro file and insert the >> > > > > > molecules from this .gro file ? >> > > > > >> > > > > Have you tried it? >> > > > > >> > > > > -Justin >> > > > > >> > > > > -- >> > > > > ================================================== >> > > > > >> > > > > Justin A. Lemkul, Ph.D. >> > > > > Assistant Professor >> > > > > Office: 301 Fralin Hall >> > > > > Lab: 303 Engel Hall >> > > > > >> > > > > Virginia Tech Department of Biochemistry >> > > > > 340 West Campus Dr. >> > > > > Blacksburg, VA 24061 >> > > > > >> > > > > jalemkul at vt.edu | (540) 231-3129 >> > > > > http://www.thelemkullab.com >> > > > > >> > > > > ================================================== >> > > > > >> > > > > -- >> > > > > Gromacs Users mailing list >> > > > > >> > > > > * Please search the archive at >> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> before >> > > > > posting! >> > > > > >> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > >> > > > > * For (un)subscribe requests visit >> > > > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> > or >> > > > > send a mail to gmx-users-request at gromacs.org. >> > > > > >> > > > -- >> > > > Gromacs Users mailing list >> > > > >> > > > * Please search the archive at >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > > posting! >> > > > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > >> > > > * For (un)subscribe requests visit >> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >> > > > send a mail to gmx-users-request at gromacs.org. >> > > > >> > > -- >> > > Gromacs Users mailing list >> > > >> > > * Please search the archive at >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > posting! >> > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > > send a mail to gmx-users-request at gromacs.org. >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > > From jalemkul at vt.edu Tue Apr 14 23:09:27 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 14 Apr 2020 21:09:27 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: On 4/14/20 4:55 PM, Mohamed Abdelaal wrote: > Sorry for writing again in the same topic but I couldn't solve > the velocity problem. > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > Powell > Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic > Light-Emitting Diode Films > > It was mentioned in the paper that " The molecule was inserted into the > system such that the x and y coordinates of the centre of mass were sampled > from a uniform distribution covering the entire box while the z coordinate > of the centre of mass was set to 2.0 nm above the current surface. The > initial orientation of the molecule was randomised. *The velocities of each > atom within the inserted molecule in x and y were sampled from a Gaussian > distribution with a mean of 0.0 nm/ps and a standard deviation appropriate > for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T > is the temperature and m is the mass of the atom). The velocities in z were > sampled from the distribution with the same standard deviation as x and y > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in > the direction opposite to the surface) were rectified by taking the > absolute value. This ensured all molecules moved toward the surface.* Presumably the authors used different software; GROMACS does not allow such granular control of velocities. > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > above and I have also read all the velocity related topics in the manual > and user guide. > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > and then I inserted the molecule in a box using insert-molecules, However > after the insertion process is completed I opened the output .gro file but > the velocity was not read. This means that I can only generate the velocity > through the .mdp file. That's not true. If you know what velocities you want to assign, do so *after* building the whole system by writing the velocities to the .gro file (you will need your own code/script to do this). Then do not generate velocities in the .mdp file and they will be read from the .gro file. > If I am going to generate the velocity using my .mdp file, is it possible > to change the standard deviation and the mean ? if yes, how can I modify > them ? (I can't find any way to modify the parameters of the Maxwell > distribution) No, GROMACS has no such capability. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From m.b.abdelaal at gmail.com Tue Apr 14 23:13:25 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 14 Apr 2020 21:13:25 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: Many thanks for your quick reply :) On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul wrote: > > > On 4/14/20 4:55 PM, Mohamed Abdelaal wrote: > > Sorry for writing again in the same topic but I couldn't solve > > the velocity problem. > > > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, > Alpeshkumar > > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > > Powell > > Title: Elucidating the Spatial Arrangement of Emitter Molecules in > Organic > > Light-Emitting Diode Films > > > > It was mentioned in the paper that " The molecule was inserted into the > > system such that the x and y coordinates of the centre of mass were > sampled > > from a uniform distribution covering the entire box while the z > coordinate > > of the centre of mass was set to 2.0 nm above the current surface. The > > initial orientation of the molecule was randomised. *The velocities of > each > > atom within the inserted molecule in x and y were sampled from a Gaussian > > distribution with a mean of 0.0 nm/ps and a standard deviation > appropriate > > for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T > > is the temperature and m is the mass of the atom). The velocities in z > were > > sampled from the distribution with the same standard deviation as x and y > > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving > in > > the direction opposite to the surface) were rectified by taking the > > absolute value. This ensured all molecules moved toward the surface.* > > Presumably the authors used different software; GROMACS does not allow > such granular control of velocities. > > > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > > above and I have also read all the velocity related topics in the manual > > and user guide. > > > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > > and then I inserted the molecule in a box using insert-molecules, However > > after the insertion process is completed I opened the output .gro file > but > > the velocity was not read. This means that I can only generate the > velocity > > through the .mdp file. > > That's not true. If you know what velocities you want to assign, do so > *after* building the whole system by writing the velocities to the .gro > file (you will need your own code/script to do this). Then do not > generate velocities in the .mdp file and they will be read from the .gro > file. > > > If I am going to generate the velocity using my .mdp file, is it possible > > to change the standard deviation and the mean ? if yes, how can I modify > > them ? (I can't find any way to modify the parameters of the Maxwell > > distribution) > > No, GROMACS has no such capability. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From ericsmoll at gmail.com Tue Apr 14 23:14:23 2020 From: ericsmoll at gmail.com (Eric Smoll) Date: Tue, 14 Apr 2020 21:14:23 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: No problem. Now it is clear what you are trying to do. The previous description of your goals did not make much physical sense. The initial velocities are such that all three dimensions are sampled from the same 3D velocity distribution (gaussian with the same width). The difference is that there is a constant velocity added in the z-direction so there is net motion in the z-direction. One way to do this is to use gen-vel as usual and just add the constant to the z-coordinate. The velocities were probably read in. By default, the velocities may not be printed in the gro. What matters is that they were loaded in the tpr. Try a simulation to see if the molecule is moving as expected. Alternatively, dump the contents of the tpr and make sure the velocities you created were read in. -Eric On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal wrote: > Sorry for writing again in the same topic but I couldn't solve > the velocity problem. > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > Powell > Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic > Light-Emitting Diode Films > > It was mentioned in the paper that " The molecule was inserted into the > system such that the x and y coordinates of the centre of mass were sampled > from a uniform distribution covering the entire box while the z coordinate > of the centre of mass was set to 2.0 nm above the current surface. The > initial orientation of the molecule was randomised. *The velocities of each > atom within the inserted molecule in x and y were sampled from a Gaussian > distribution with a mean of 0.0 nm/ps and a standard deviation appropriate > for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T > is the temperature and m is the mass of the atom). The velocities in z were > sampled from the distribution with the same standard deviation as x and y > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving in > the direction opposite to the surface) were rectified by taking the > absolute value. This ensured all molecules moved toward the surface.* > > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > above and I have also read all the velocity related topics in the manual > and user guide. > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > and then I inserted the molecule in a box using insert-molecules, However > after the insertion process is completed I opened the output .gro file but > the velocity was not read. This means that I can only generate the velocity > through the .mdp file. > > If I am going to generate the velocity using my .mdp file, is it possible > to change the standard deviation and the mean ? if yes, how can I modify > them ? (I can't find any way to modify the parameters of the Maxwell > distribution) > > I want to have velocity distributions with means equal to 0,0,0.5 nmps in > the x,y,z directions respectively. > > You wrote in your last email that, "A 3D Maxwell Boltzmann velocity > distribution corresponds to three identical gaussian speed distributions in > vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). Just > change the standard deviation of the velocity distribution sqrt(kT/m) for > each velocity component if you want them to be different. If you don't > want the mean to be zero for whatever reason, add a constant." > > If the velocity will not be read from the .gro file where should I add the > constant to change the mean? > > Many thanks, > Mohamed > > > On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal > wrote: > > > Many thanks for your reply :) > > > > All your language assumptions are true and that is exactly what I wanted > > to communicate, next time I will try to be more precise and sorry for the > > confusion ? > > > > I will read section 3.4.1 again carefully. > > > > Thanks again and sorry for the inconvenience. > > > > Mohamed > > > > On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: > > > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal > > >> wrote: > >> > >> > Many thanks for your reply ? > >> > > >> > The limitation in the generate velocity using the .mdp file, is that > >> while > >> > I can generate the velocity from Maxwell distribution, I will have > the > >> > same velocities in the x, y and z directions. > >> > > >> > >> I think you mean "same velocity *distributions* in the x, y, and z > >> directions." The distributions will be approximately the same but each > >> atom will have a different velocity. > >> > >> > > >> > On the other hand, generating the velocity from the .gro file will let > >> me > >> > specify different velocities in the x,y and z directions but they will > >> be > >> > the same velocities for all the atoms (will not be taken from a > maxwell > >> > distribution with variation in the atoms velocities). > >> > > >> > >> I think you mean "specify different velocity *distributions* in the x, > y, > >> and z directions" > >> > >> > > >> > Is it possible to generate different velocities in the x,y and z > >> directions > >> > > >> > >> I think you mean "generate different velocity *distributions* in the x, > y, > >> and z directions." If so, the answer is obviously yes. Because you can > >> type in each individual vxi, vyi, and vzi for every atom i, you can > >> generate different velocity distributions in the x, y, and z directions. > >> > >> > >> > from a maxwell distribution ? > >> > >> > >> I am not sure what this part of the sentence means. If you do what you > >> are > >> suggesting, you will not be working with a maxwell distribution because > >> all > >> three directions should have identical distributions. See comment > below. > >> If there is another misunderstanding, you need to spend more time > crafting > >> precise sentences to communicate what you are after. > >> > >> > >> > (for example the velocities to be taken from > >> > a maxwell distribution with a mean of 0.1 in the x direction and with > a > >> > mean of 0.2 in the y direction and with mean of 0.3 in the z > direction?) > >> > > >> > >> In my last email I suggested reading section 3.4.1 of the manual version > >> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity > >> distribution > >> corresponds to three identical gaussian speed distributions in vx, vy, > and > >> vz centered at zero (mean should be zero for vx, vy, vz). Just change > the > >> standard deviation of the velocity distribution sqrt(kT/m) for each > >> velocity component if you want them to be different. If you don't want > >> the > >> mean to be zero for whatever reason, add a constant. However, a > non-zero > >> mean for any of the velocity components will generate center of mass > >> motion. If you want center of mass motion, turn off center of mass > motion > >> removal in the mdp file. > >> > >> > >> > Thanks for your help :) > >> > Mohamed > >> > > >> > On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: > >> > > >> > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < > >> m.b.abdelaal at gmail.com> > >> > > wrote: > >> > > > >> > > > No, I use the generate velocity option in the .mdp files. > >> > > > > >> > > > However I want now to assign different velocities in the x,y,z > >> > > directions. > >> > > > Which I thought it could only be done through the .gro file, but I > >> > don't > >> > > > know If I did that, should I change the value of the generate > >> velocity > >> > to > >> > > > be = NO in the .mdp files ? (otherwise I would have generated the > >> > > > velocities twice). > >> > > > > >> > > > >> > > That sounds logical. Set it to no if you provide your own initial > >> > > velocities. > >> > > > >> > > > > >> > > > Moreover, if I added the velocities in the .gro file how can I > >> generate > >> > > the > >> > > > velocities in the .gro file from a distribution (Maxwell) with a > >> > specific > >> > > > mean and standard deviation ? > >> > > > > >> > > > I have tried to search in different sources (the user list, > manual, > >> > user > >> > > > guide, research gate and other platforms) how to solve this > velocity > >> > > > problem but I didn't find a clear way to insert different > >> velocities in > >> > > the > >> > > > x,y,z directions using distribution rater than constant > velocities. > >> > > > > >> > > > There is a good section on this in the manual. For example, > section > >> > > 3.4.1 > >> > > in the Gromacs 5.1.2 manual. > >> > > > >> > > Also, you know that the generate velocities option assigns > velocities > >> to > >> > > atoms from an approximate MB distribution at whatever temperature > you > >> > > specify in the MDP file, right? If I understand you correctly, the > >> > > generate velocities options should do exactly what you want. With > no > >> > extra > >> > > work. > >> > > > >> > > > >> > > > Please guide me how to do it as I am a little bit confused in the > >> > > velocity > >> > > > generation mechanisms. > >> > > > > >> > > > Many thanks, > >> > > > Mohamed > >> > > > > >> > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul > >> wrote: > >> > > > > >> > > > > > >> > > > > > >> > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > >> > > > > > Hello everybody :) > >> > > > > > > >> > > > > > Can I use the gmx insert-molecules to insert molecules in my > box > >> > with > >> > > > > > velocities by adding the velocities in t > >> < > https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g > >he > >> .gro file and insert the > >> > > > > > molecules from this .gro file ? > >> > > > > > >> > > > > Have you tried it? > >> > > > > > >> > > > > -Justin > >> > > > > > >> > > > > -- > >> > > > > ================================================== > >> > > > > > >> > > > > Justin A. Lemkul, Ph.D. > >> > > > > Assistant Professor > >> > > > > Office: 301 Fralin Hall > >> > > > > Lab: 303 Engel Hall > >> > > > > > >> > > > > Virginia Tech Department of Biochemistry > >> > > > > 340 West Campus Dr. > >> > > > > Blacksburg, VA 24061 > >> > > > > > >> > > > > jalemkul at vt.edu | (540) 231-3129 > >> > > > > http://www.thelemkullab.com > >> > > > > > >> > > > > ================================================== > >> > > > > > >> > > > > -- > >> > > > > Gromacs Users mailing list > >> > > > > > >> > > > > * Please search the archive at > >> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >> before > >> > > > > posting! > >> > > > > > >> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > >> > > > > * For (un)subscribe requests visit > >> > > > > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> > or > >> > > > > send a mail to gmx-users-request at gromacs.org. > >> > > > > > >> > > > -- > >> > > > Gromacs Users mailing list > >> > > > > >> > > > * Please search the archive at > >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > >> > > > posting! > >> > > > > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > >> > > > * For (un)subscribe requests visit > >> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > >> > > > send a mail to gmx-users-request at gromacs.org. > >> > > > > >> > > -- > >> > > Gromacs Users mailing list > >> > > > >> > > * Please search the archive at > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > > posting! > >> > > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > >> > > * For (un)subscribe requests visit > >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> > > send a mail to gmx-users-request at gromacs.org. > >> > > > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-request at gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From m.b.abdelaal at gmail.com Tue Apr 14 23:49:02 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 14 Apr 2020 21:49:02 -0000 Subject: [gmx-users] How to prevent velocity generation for my position restrained molecules ? Message-ID: Hello everybody, I am simulating the evaporation process for different atoms on a graphene sheet and the z-coordinate of each graphene carbon atom was restrained (using position restrain). The energy minimization was successfully done without any errors Then I started the equilibration, I have done the NVT. My nvt.mdp file is written below. I have added the -DPOSRES to enable the position restrain and I added temperature coupling for both the GRM (the graphene sheet molecules) and the G8LE (The residue molecules; the molecules I am evaporating) then I wrote generate velocity = yes. After finishing the NVT equilibration, I checked the nvt.gro file and the problem now is that, I have velocity for both the graphene molecules (which supposed to be position restrained) and for the residue. How can I generate velocity for the residue only (G8LE) and make sure that the graphene sheet is restrained. title = NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.0005 ; 0.5 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings all-angles cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = G8LE GRM ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed periodic_molecules = yes Many thanks, Mohamed From jalemkul at vt.edu Wed Apr 15 00:01:51 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 14 Apr 2020 22:01:51 -0000 Subject: [gmx-users] How to prevent velocity generation for my position restrained molecules ? In-Reply-To: References: Message-ID: <67082b23-a779-14bf-435a-3fefe7ac0ada@vt.edu> On 4/14/20 5:48 PM, Mohamed Abdelaal wrote: > Hello everybody, > > I am simulating the evaporation process for different atoms on a graphene > sheet and the z-coordinate of each graphene carbon atom was restrained > (using position restrain). > > The energy minimization was successfully done without any errors > > Then I started the equilibration, I have done the NVT. My nvt.mdp file > is written below. I have added the -DPOSRES to enable the position > restrain and I added temperature > > coupling for both the GRM (the graphene sheet molecules) and the G8LE > (The residue molecules; the molecules I am evaporating) then I wrote > generate velocity = yes. > > After finishing the NVT equilibration, I checked the nvt.gro file and > the problem now is that, I have velocity for both the graphene > molecules (which supposed to be position > > restrained) and for the residue. How can I generate velocity for the > residue only (G8LE) and make sure that the graphene sheet is > restrained. > Applying restraints does not prevent dynamics; your restrained atoms will have velocities. There will be a "Position Rest." term written to the .log and .edr files that is a clear signal your restraints were on and working. If you want the group completely frozen (no position or velocity updates), that's what freezegrps is for, but freezing anything is highly artificial. -Justin > title = NVT equilibration > define = -DPOSRES ; position restrain the protein > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 50000 ; 2 * 50000 = 100 ps > dt = 0.0005 ; 0.5 fs > ; Output control > nstxout = 500 ; save coordinates every 1.0 ps > nstvout = 500 ; save velocities every 1.0 ps > nstenergy = 500 ; save energies every 1.0 ps > nstlog = 500 ; update log file every 1.0 ps > ; Bond parameters > continuation = no ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = h-bonds ; bonds involving H are constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Nonbonded settings all-angles > cutoff-scheme = Verlet ; Buffered neighbor searching > ns_type = grid ; search neighboring grid cells > nstlist = 10 ; 20 fs, largely irrelevant with Verlet > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Electrostatics > coulombtype = cut-off ; Particle Mesh Ewald for > long-range electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = G8LE GRM ; two coupling groups - more accurate > tau_t = 0.1 0.1 ; time constant, in ps > ref_t = 300 300 ; reference temperature, one for > each group, in K > ; Pressure coupling is off > pcoupl = no ; no pressure coupling in NVT > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Velocity generation > gen_vel = yes ; assign velocities from Maxwell > distribution > gen_temp = 300 ; temperature for Maxwell distribution > gen_seed = -1 ; generate a random seed > periodic_molecules = yes > > > Many thanks, > > Mohamed -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From m.b.abdelaal at gmail.com Wed Apr 15 00:02:26 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 14 Apr 2020 22:02:26 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: Many thanks Dr. Erik for your reply :) On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll wrote: > No problem. > > Now it is clear what you are trying to do. The previous description of > your goals did not make much physical sense. The initial velocities are > such that all three dimensions are sampled from the same 3D velocity > distribution (gaussian with the same width). The difference is that there > is a constant velocity added in the z-direction so there is net motion in > the z-direction. > One way to do this is to use gen-vel as usual and just add the constant to > the z-coordinate. > *Can you please tell me more details how to add the constant to the z-coordinate ? If I will generate the velocity from the .mdp file, in which file should I add the constant to the z-coordinate ? * > The velocities were probably read in. By default, the velocities may not > be printed in the gro. What matters is that they were loaded in the tpr. > Try a simulation to see if the molecule is moving as expected. > I will complete the simulation to the end to check whether or not the velocity was added from my .gro file. > Alternatively, dump the contents of the tpr and make sure the velocities > you created were read in. > > Do you mean that I should manually edit the .tpr file ? I have tried to open it with text editor but it can't be open. > -Eric > > On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal > wrote: > > > Sorry for writing again in the same topic but I couldn't solve > > the velocity problem. > > > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, > Alpeshkumar > > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > > Powell > > Title: Elucidating the Spatial Arrangement of Emitter Molecules in > Organic > > Light-Emitting Diode Films > > > > It was mentioned in the paper that " The molecule was inserted into the > > system such that the x and y coordinates of the centre of mass were > sampled > > from a uniform distribution covering the entire box while the z > coordinate > > of the centre of mass was set to 2.0 nm above the current surface. The > > initial orientation of the molecule was randomised. *The velocities of > each > > atom within the inserted molecule in x and y were sampled from a Gaussian > > distribution with a mean of 0.0 nm/ps and a standard deviation > appropriate > > for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T > > is the temperature and m is the mass of the atom). The velocities in z > were > > sampled from the distribution with the same standard deviation as x and y > > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving > in > > the direction opposite to the surface) were rectified by taking the > > absolute value. This ensured all molecules moved toward the surface.* > > > > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > > above and I have also read all the velocity related topics in the manual > > and user guide. > > > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > > and then I inserted the molecule in a box using insert-molecules, However > > after the insertion process is completed I opened the output .gro file > but > > the velocity was not read. This means that I can only generate the > velocity > > through the .mdp file. > > > > If I am going to generate the velocity using my .mdp file, is it possible > > to change the standard deviation and the mean ? if yes, how can I modify > > them ? (I can't find any way to modify the parameters of the Maxwell > > distribution) > > > > I want to have velocity distributions with means equal to 0,0,0.5 nmps in > > the x,y,z directions respectively. > > > > You wrote in your last email that, "A 3D Maxwell Boltzmann velocity > > distribution corresponds to three identical gaussian speed distributions > in > > vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). > Just > > change the standard deviation of the velocity distribution sqrt(kT/m) for > > each velocity component if you want them to be different. If you don't > > want the mean to be zero for whatever reason, add a constant." > > > > If the velocity will not be read from the .gro file where should I add > the > > constant to change the mean? > > > > Many thanks, > > Mohamed > > > > > > On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal > > wrote: > > > > > Many thanks for your reply :) > > > > > > All your language assumptions are true and that is exactly what I > wanted > > > to communicate, next time I will try to be more precise and sorry for > the > > > confusion ? > > > > > > I will read section 3.4.1 again carefully. > > > > > > Thanks again and sorry for the inconvenience. > > > > > > Mohamed > > > > > > On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: > > > > > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal < > m.b.abdelaal at gmail.com > > > > > >> wrote: > > >> > > >> > Many thanks for your reply ? > > >> > > > >> > The limitation in the generate velocity using the .mdp file, is that > > >> while > > >> > I can generate the velocity from Maxwell distribution, I will have > > the > > >> > same velocities in the x, y and z directions. > > >> > > > >> > > >> I think you mean "same velocity *distributions* in the x, y, and z > > >> directions." The distributions will be approximately the same but > each > > >> atom will have a different velocity. > > >> > > >> > > > >> > On the other hand, generating the velocity from the .gro file will > let > > >> me > > >> > specify different velocities in the x,y and z directions but they > will > > >> be > > >> > the same velocities for all the atoms (will not be taken from a > > maxwell > > >> > distribution with variation in the atoms velocities). > > >> > > > >> > > >> I think you mean "specify different velocity *distributions* in the x, > > y, > > >> and z directions" > > >> > > >> > > > >> > Is it possible to generate different velocities in the x,y and z > > >> directions > > >> > > > >> > > >> I think you mean "generate different velocity *distributions* in the > x, > > y, > > >> and z directions." If so, the answer is obviously yes. Because you > can > > >> type in each individual vxi, vyi, and vzi for every atom i, you can > > >> generate different velocity distributions in the x, y, and z > directions. > > >> > > >> > > >> > from a maxwell distribution ? > > >> > > >> > > >> I am not sure what this part of the sentence means. If you do what > you > > >> are > > >> suggesting, you will not be working with a maxwell distribution > because > > >> all > > >> three directions should have identical distributions. See comment > > below. > > >> If there is another misunderstanding, you need to spend more time > > crafting > > >> precise sentences to communicate what you are after. > > >> > > >> > > >> > (for example the velocities to be taken from > > >> > a maxwell distribution with a mean of 0.1 in the x direction and > with > > a > > >> > mean of 0.2 in the y direction and with mean of 0.3 in the z > > direction?) > > >> > > > >> > > >> In my last email I suggested reading section 3.4.1 of the manual > version > > >> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity > > >> distribution > > >> corresponds to three identical gaussian speed distributions in vx, vy, > > and > > >> vz centered at zero (mean should be zero for vx, vy, vz). Just change > > the > > >> standard deviation of the velocity distribution sqrt(kT/m) for each > > >> velocity component if you want them to be different. If you don't > want > > >> the > > >> mean to be zero for whatever reason, add a constant. However, a > > non-zero > > >> mean for any of the velocity components will generate center of mass > > >> motion. If you want center of mass motion, turn off center of mass > > motion > > >> removal in the mdp file. > > >> > > >> > > >> > Thanks for your help :) > > >> > Mohamed > > >> > > > >> > On Wed, Apr 8, 2020 at 05:48 Eric Smoll > wrote: > > >> > > > >> > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < > > >> m.b.abdelaal at gmail.com> > > >> > > wrote: > > >> > > > > >> > > > No, I use the generate velocity option in the .mdp files. > > >> > > > > > >> > > > However I want now to assign different velocities in the x,y,z > > >> > > directions. > > >> > > > Which I thought it could only be done through the .gro file, > but I > > >> > don't > > >> > > > know If I did that, should I change the value of the generate > > >> velocity > > >> > to > > >> > > > be = NO in the .mdp files ? (otherwise I would have generated > the > > >> > > > velocities twice). > > >> > > > > > >> > > > > >> > > That sounds logical. Set it to no if you provide your own initial > > >> > > velocities. > > >> > > > > >> > > > > > >> > > > Moreover, if I added the velocities in the .gro file how can I > > >> generate > > >> > > the > > >> > > > velocities in the .gro file from a distribution (Maxwell) with a > > >> > specific > > >> > > > mean and standard deviation ? > > >> > > > > > >> > > > I have tried to search in different sources (the user list, > > manual, > > >> > user > > >> > > > guide, research gate and other platforms) how to solve this > > velocity > > >> > > > problem but I didn't find a clear way to insert different > > >> velocities in > > >> > > the > > >> > > > x,y,z directions using distribution rater than constant > > velocities. > > >> > > > > > >> > > > There is a good section on this in the manual. For example, > > section > > >> > > 3.4.1 > > >> > > in the Gromacs 5.1.2 manual. > > >> > > > > >> > > Also, you know that the generate velocities option assigns > > velocities > > >> to > > >> > > atoms from an approximate MB distribution at whatever temperature > > you > > >> > > specify in the MDP file, right? If I understand you correctly, > the > > >> > > generate velocities options should do exactly what you want. With > > no > > >> > extra > > >> > > work. > > >> > > > > >> > > > > >> > > > Please guide me how to do it as I am a little bit confused in > the > > >> > > velocity > > >> > > > generation mechanisms. > > >> > > > > > >> > > > Many thanks, > > >> > > > Mohamed > > >> > > > > > >> > > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul > > >> wrote: > > >> > > > > > >> > > > > > > >> > > > > > > >> > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > >> > > > > > Hello everybody :) > > >> > > > > > > > >> > > > > > Can I use the gmx insert-molecules to insert molecules in my > > box > > >> > with > > >> > > > > > velocities by adding the velocities in t > > >> < > > > https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g > > >he > > >> .gro file and insert the > > >> > > > > > molecules from this .gro file ? > > >> > > > > > > >> > > > > Have you tried it? > > >> > > > > > > >> > > > > -Justin > > >> > > > > > > >> > > > > -- > > >> > > > > ================================================== > > >> > > > > > > >> > > > > Justin A. Lemkul, Ph.D. > > >> > > > > Assistant Professor > > >> > > > > Office: 301 Fralin Hall > > >> > > > > Lab: 303 Engel Hall > > >> > > > > > > >> > > > > Virginia Tech Department of Biochemistry > > >> > > > > 340 West Campus Dr. > > >> > > > > Blacksburg, VA 24061 > > >> > > > > > > >> > > > > jalemkul at vt.edu | (540) 231-3129 > > >> > > > > http://www.thelemkullab.com > > >> > > > > > > >> > > > > ================================================== > > >> > > > > > > >> > > > > -- > > >> > > > > Gromacs Users mailing list > > >> > > > > > > >> > > > > * Please search the archive at > > >> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > >> before > > >> > > > > posting! > > >> > > > > > > >> > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > >> > > > > > > >> > > > > * For (un)subscribe requests visit > > >> > > > > > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > >> > or > > >> > > > > send a mail to gmx-users-request at gromacs.org. > > >> > > > > > > >> > > > -- > > >> > > > Gromacs Users mailing list > > >> > > > > > >> > > > * Please search the archive at > > >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > >> > > > posting! > > >> > > > > > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > > > >> > > > * For (un)subscribe requests visit > > >> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > >> or > > >> > > > send a mail to gmx-users-request at gromacs.org. > > >> > > > > > >> > > -- > > >> > > Gromacs Users mailing list > > >> > > > > >> > > * Please search the archive at > > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > >> > > posting! > > >> > > > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > > >> > > * For (un)subscribe requests visit > > >> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > >> > > send a mail to gmx-users-request at gromacs.org. > > >> > > > > >> > -- > > >> > Gromacs Users mailing list > > >> > > > >> > * Please search the archive at > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> > posting! > > >> > > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > > >> > * For (un)subscribe requests visit > > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > >> > send a mail to gmx-users-request at gromacs.org. > > >> -- > > >> Gromacs Users mailing list > > >> > > >> * Please search the archive at > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >> posting! > > >> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >> > > >> * For (un)subscribe requests visit > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > >> send a mail to gmx-users-request at gromacs.org. > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From ericsmoll at gmail.com Wed Apr 15 00:26:11 2020 From: ericsmoll at gmail.com (Eric Smoll) Date: Tue, 14 Apr 2020 22:26:11 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> Message-ID: <276CD4BE-ECF1-411E-9B03-3D250763450A@gmail.com> My knowledge is a bit old. Tpr files are binary so you cannot read them without a special tool. In gromacs 2018, there was a tool that would spit out the contents of a tpr file in a readable format. Execute ?gmx dump -h? to learn more. Justin is correct. There is no tool or file that will allow you to add a constant velocity in the z direction to a set of atoms. I would suggest writing a program to build a custom gro file from the start that has everything you want. If that is not possible for you, you could use gen-vel and attempt to export a gro with the resulting velocities at some point afterward (e.g., use gen-vel tpr for a 1 step simulation writing coordinates and velocities to the trr at every step and then extract gro with velocities from the trr). Then go through the gro file and add a constant z-velocity to all the atoms that need it. Then read the edited gro file in again and proceed. -Eric Sent from my iPhone > On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal wrote: > > Many thanks Dr. Erik for your reply :) > > >> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll wrote: >> >> No problem. >> >> Now it is clear what you are trying to do. The previous description of >> your goals did not make much physical sense. The initial velocities are >> such that all three dimensions are sampled from the same 3D velocity >> distribution (gaussian with the same width). The difference is that there >> is a constant velocity added in the z-direction so there is net motion in >> the z-direction. > > > >> One way to do this is to use gen-vel as usual and just add the constant to >> the z-coordinate. >> > > *Can you please tell me more details how to add the constant to the > z-coordinate ? If I will generate the velocity from the .mdp file, in which > file should I add the constant to the z-coordinate ? * > >> > > The velocities were probably read in. By default, the velocities may not >> be printed in the gro. What matters is that they were loaded in the tpr. >> Try a simulation to see if the molecule is moving as expected. >> > > I will complete the simulation to the end to check whether or not the > velocity was added from my .gro file. > > >> Alternatively, dump the contents of the tpr and make sure the velocities >> you created were read in. >> >> Do you mean that I should manually edit the .tpr file ? I have tried to > open it with text editor but it can't be open. > > >> -Eric >> >> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal >> wrote: >> >>> Sorry for writing again in the same topic but I couldn't solve >>> the velocity problem. >>> >>> I am trying to reproduce a paper written by: Claire Tonnel + , Martin >>> Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, >> Alpeshkumar >>> K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. >>> Powell >>> Title: Elucidating the Spatial Arrangement of Emitter Molecules in >> Organic >>> Light-Emitting Diode Films >>> >>> It was mentioned in the paper that " The molecule was inserted into the >>> system such that the x and y coordinates of the centre of mass were >> sampled >>> from a uniform distribution covering the entire box while the z >> coordinate >>> of the centre of mass was set to 2.0 nm above the current surface. The >>> initial orientation of the molecule was randomised. *The velocities of >> each >>> atom within the inserted molecule in x and y were sampled from a Gaussian >>> distribution with a mean of 0.0 nm/ps and a standard deviation >> appropriate >>> for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s , T >>> is the temperature and m is the mass of the atom). The velocities in z >> were >>> sampled from the distribution with the same standard deviation as x and y >>> but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving >> in >>> the direction opposite to the surface) were rectified by taking the >>> absolute value. This ensured all molecules moved toward the surface.* >>> >>> I have read the section 3.4.1 of the manual version 5.1.2 as recommended >>> above and I have also read all the velocity related topics in the manual >>> and user guide. >>> >>> (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file >>> and then I inserted the molecule in a box using insert-molecules, However >>> after the insertion process is completed I opened the output .gro file >> but >>> the velocity was not read. This means that I can only generate the >> velocity >>> through the .mdp file. >>> >>> If I am going to generate the velocity using my .mdp file, is it possible >>> to change the standard deviation and the mean ? if yes, how can I modify >>> them ? (I can't find any way to modify the parameters of the Maxwell >>> distribution) >>> >>> I want to have velocity distributions with means equal to 0,0,0.5 nmps in >>> the x,y,z directions respectively. >>> >>> You wrote in your last email that, "A 3D Maxwell Boltzmann velocity >>> distribution corresponds to three identical gaussian speed distributions >> in >>> vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). >> Just >>> change the standard deviation of the velocity distribution sqrt(kT/m) for >>> each velocity component if you want them to be different. If you don't >>> want the mean to be zero for whatever reason, add a constant." >>> >>> If the velocity will not be read from the .gro file where should I add >> the >>> constant to change the mean? >>> >>> Many thanks, >>> Mohamed >>> >>> >>> On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal >>> wrote: >>> >>>> Many thanks for your reply :) >>>> >>>> All your language assumptions are true and that is exactly what I >> wanted >>>> to communicate, next time I will try to be more precise and sorry for >> the >>>> confusion ? >>>> >>>> I will read section 3.4.1 again carefully. >>>> >>>> Thanks again and sorry for the inconvenience. >>>> >>>> Mohamed >>>> >>>>> On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: >>>>> >>>>> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal < >> m.b.abdelaal at gmail.com >>>> >>>>> wrote: >>>>> >>>>>> Many thanks for your reply ? >>>>>> >>>>>> The limitation in the generate velocity using the .mdp file, is that >>>>> while >>>>>> I can generate the velocity from Maxwell distribution, I will have >>> the >>>>>> same velocities in the x, y and z directions. >>>>>> >>>>> >>>>> I think you mean "same velocity *distributions* in the x, y, and z >>>>> directions." The distributions will be approximately the same but >> each >>>>> atom will have a different velocity. >>>>> >>>>>> >>>>>> On the other hand, generating the velocity from the .gro file will >> let >>>>> me >>>>>> specify different velocities in the x,y and z directions but they >> will >>>>> be >>>>>> the same velocities for all the atoms (will not be taken from a >>> maxwell >>>>>> distribution with variation in the atoms velocities). >>>>>> >>>>> >>>>> I think you mean "specify different velocity *distributions* in the x, >>> y, >>>>> and z directions" >>>>> >>>>>> >>>>>> Is it possible to generate different velocities in the x,y and z >>>>> directions >>>>>> >>>>> >>>>> I think you mean "generate different velocity *distributions* in the >> x, >>> y, >>>>> and z directions." If so, the answer is obviously yes. Because you >> can >>>>> type in each individual vxi, vyi, and vzi for every atom i, you can >>>>> generate different velocity distributions in the x, y, and z >> directions. >>>>> >>>>> >>>>>> from a maxwell distribution ? >>>>> >>>>> >>>>> I am not sure what this part of the sentence means. If you do what >> you >>>>> are >>>>> suggesting, you will not be working with a maxwell distribution >> because >>>>> all >>>>> three directions should have identical distributions. See comment >>> below. >>>>> If there is another misunderstanding, you need to spend more time >>> crafting >>>>> precise sentences to communicate what you are after. >>>>> >>>>> >>>>>> (for example the velocities to be taken from >>>>>> a maxwell distribution with a mean of 0.1 in the x direction and >> with >>> a >>>>>> mean of 0.2 in the y direction and with mean of 0.3 in the z >>> direction?) >>>>>> >>>>> >>>>> In my last email I suggested reading section 3.4.1 of the manual >> version >>>>> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity >>>>> distribution >>>>> corresponds to three identical gaussian speed distributions in vx, vy, >>> and >>>>> vz centered at zero (mean should be zero for vx, vy, vz). Just change >>> the >>>>> standard deviation of the velocity distribution sqrt(kT/m) for each >>>>> velocity component if you want them to be different. If you don't >> want >>>>> the >>>>> mean to be zero for whatever reason, add a constant. However, a >>> non-zero >>>>> mean for any of the velocity components will generate center of mass >>>>> motion. If you want center of mass motion, turn off center of mass >>> motion >>>>> removal in the mdp file. >>>>> >>>>> >>>>>> Thanks for your help :) >>>>>> Mohamed >>>>>> >>>>>> On Wed, Apr 8, 2020 at 05:48 Eric Smoll >> wrote: >>>>>> >>>>>>> On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < >>>>> m.b.abdelaal at gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> No, I use the generate velocity option in the .mdp files. >>>>>>>> >>>>>>>> However I want now to assign different velocities in the x,y,z >>>>>>> directions. >>>>>>>> Which I thought it could only be done through the .gro file, >> but I >>>>>> don't >>>>>>>> know If I did that, should I change the value of the generate >>>>> velocity >>>>>> to >>>>>>>> be = NO in the .mdp files ? (otherwise I would have generated >> the >>>>>>>> velocities twice). >>>>>>>> >>>>>>> >>>>>>> That sounds logical. Set it to no if you provide your own initial >>>>>>> velocities. >>>>>>> >>>>>>>> >>>>>>>> Moreover, if I added the velocities in the .gro file how can I >>>>> generate >>>>>>> the >>>>>>>> velocities in the .gro file from a distribution (Maxwell) with a >>>>>> specific >>>>>>>> mean and standard deviation ? >>>>>>>> >>>>>>>> I have tried to search in different sources (the user list, >>> manual, >>>>>> user >>>>>>>> guide, research gate and other platforms) how to solve this >>> velocity >>>>>>>> problem but I didn't find a clear way to insert different >>>>> velocities in >>>>>>> the >>>>>>>> x,y,z directions using distribution rater than constant >>> velocities. >>>>>>>> >>>>>>>> There is a good section on this in the manual. For example, >>> section >>>>>>> 3.4.1 >>>>>>> in the Gromacs 5.1.2 manual. >>>>>>> >>>>>>> Also, you know that the generate velocities option assigns >>> velocities >>>>> to >>>>>>> atoms from an approximate MB distribution at whatever temperature >>> you >>>>>>> specify in the MDP file, right? If I understand you correctly, >> the >>>>>>> generate velocities options should do exactly what you want. With >>> no >>>>>> extra >>>>>>> work. >>>>>>> >>>>>>> >>>>>>>> Please guide me how to do it as I am a little bit confused in >> the >>>>>>> velocity >>>>>>>> generation mechanisms. >>>>>>>> >>>>>>>> Many thanks, >>>>>>>> Mohamed >>>>>>>> >>>>>>>> On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul >>>>> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: >>>>>>>>>> Hello everybody :) >>>>>>>>>> >>>>>>>>>> Can I use the gmx insert-molecules to insert molecules in my >>> box >>>>>> with >>>>>>>>>> velocities by adding the velocities in t >>>>> < >>> >> https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g >>>> he >>>>> .gro file and insert the >>>>>>>>>> molecules from this .gro file ? >>>>>>>>> >>>>>>>>> Have you tried it? >>>>>>>>> >>>>>>>>> -Justin >>>>>>>>> >>>>>>>>> -- >>>>>>>>> ================================================== >>>>>>>>> >>>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>>> Assistant Professor >>>>>>>>> Office: 301 Fralin Hall >>>>>>>>> Lab: 303 Engel Hall >>>>>>>>> >>>>>>>>> Virginia Tech Department of Biochemistry >>>>>>>>> 340 West Campus Dr. >>>>>>>>> Blacksburg, VA 24061 >>>>>>>>> >>>>>>>>> jalemkul at vt.edu | (540) 231-3129 >>>>>>>>> http://www.thelemkullab.com >>>>>>>>> >>>>>>>>> ================================================== >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Gromacs Users mailing list >>>>>>>>> >>>>>>>>> * Please search the archive at >>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>>>> before >>>>>>>>> posting! >>>>>>>>> >>>>>>>>> * Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>> >>>>>>>>> * For (un)subscribe requests visit >>>>>>>>> >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>> or >>>>>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>>>>> >>>>>>>> -- >>>>>>>> Gromacs Users mailing list >>>>>>>> >>>>>>>> * Please search the archive at >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>> before >>>>>>>> posting! >>>>>>>> >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>> >>>>>>>> * For (un)subscribe requests visit >>>>>>>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>> or >>>>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>>>> >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>> or >>>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >>>>>> send a mail to gmx-users-request at gromacs.org. >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-request at gromacs.org. >>>> >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From pganguly at chem.ucsb.edu Wed Apr 15 02:37:06 2020 From: pganguly at chem.ucsb.edu (Pritam Ganguly) Date: Wed, 15 Apr 2020 00:37:06 -0000 Subject: [gmx-users] Replica exchange probabilities beyond version 2016 In-Reply-To: References: <19587795-4e28-887c-ead3-e06c7ee41e38@chem.ucsb.edu> Message-ID: <16eb81e4-1d9e-eebd-3990-e9b21595ba7c@chem.ucsb.edu> Hi G?l, You are absolutely correct! I just checked this with tau_t=10, and it brought back the old behavior! Thank you so much for your suggestion! Probabilities with tau_t=10, NH thermostat: Repl???? 0??? 1??? 2??? 3??? 4??? 5??? 6??? 7??? 8??? 9?? 10 11?? 12?? 13?? 14?? 15?? 16?? 17?? 18?? 19?? 20?? 21?? 22?? 23 24?? 25?? 26?? 27?? 28?? 29?? 30?? 31?? 32?? 33?? 34?? 35?? 36 37?? 38?? 39?? 40?? 41?? 42?? 43?? 44?? 45?? 46?? 47?? 48?? 49 50?? 51?? 52?? 53?? 54?? 55?? 56?? 57?? 58?? 59?? 60?? 61?? 62 63 Repl????? .29? .29? .30? .29? .30? .28? .31? .30? .29? .28? .29 .26? .28? .29? .28? .27? .29? .26? .27? .28? .26? .26? .28? .27 .26? .27? .26? .27? .26? .25? .26? .26? .23? .27? .26? .23? .24 .27? .23? .24? .28? .27? .26? .25? .27? .24? .28? .24? .27? .27 .27? .27? .28? .25? .27? .27? .26? .28? .26? .28? .27? .28? .30 Thanks again! Regards, Pritam On 4/13/20 7:55 PM, G?l Zerze wrote: > Hi Pritam, > > Did you check your energy fluctuations? Looks like you are using NH > thermostat, you might?be suffering from the interaction of NH > thermostat oscillations with resonance modes in the system, which > makes energy fluctuations substantially larger (compared to > fluctuations with NH in older versions of Gromacs). As a result of > amplified fluctuations, you have higher exchange probability. See here > for a previous relevant exchange: > https://redmine.gromacs.org/issues/2904?For my system, making tau_t=10 > helped to recover the old behavior. > > Best, > G?l > *--* > *G?l H. Zerze* > Postdoctoral Research Associate > > Chemical and Biological Engineering > Princeton University > http://pablonet.princeton.edu/ > > > > On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly > wrote: > > Hello, > > I have noticed that the average exchange probability for a replica > exchange run increases significantly if I use Gromacs versions > 2018, as > compared to versions 2016 or earlier. I have tested that by > simulating > the same system with versions 2016.4 and 2018.3 and the average > probabilities I find are: > > Version 2016.4: > > Replica exchange statistics > Repl? 1666 attempts, 833 odd, 833 even > Repl? average probabilities: > Repl???? 0??? 1??? 2??? 3??? 4??? 5??? 6??? 7??? 8??? 9?? 10 11 12 > 13?? 14?? 15?? 16?? 17?? 18?? 19?? 20?? 21?? 22?? 23 24 25 26?? 27 > 28?? 29?? 30?? 31?? 32?? 33?? 34?? 35?? 36 37 38?? 39?? 40 41?? 42 > 43?? 44?? 45?? 46?? 47?? 48?? 49 50 51?? 52?? 53?? 54?? 55 56?? 57 > 58?? 59?? 60?? 61?? 62 63 > Repl????? .29? .33? .29? .30? .28? .30? .30? .29? .29? .29 .30 .26 > .29? .30? .28? .29? .26? .26? .29? .28? .26? .27? .27? .27 .27? .28 > .26? .27? .26? .25? .27? .25? .26? .27? .25? .24? .25 .26 .27? .25 > .27? .26? .26? .26? .25? .26? .26? .24? .25? .27 .26? .27 .26? .25 > .27? .27? .28? .26? .27? .26? .27? .27? .28 > > > Version 2018.3: > > Replica exchange statistics > Repl? 1666 attempts, 833 odd, 833 even > Repl? average probabilities: > Repl???? 0??? 1??? 2??? 3??? 4??? 5??? 6??? 7??? 8??? 9?? 10 11 12 > 13?? 14?? 15?? 16?? 17?? 18?? 19?? 20?? 21?? 22?? 23 24 25 26?? 27 > 28?? 29?? 30?? 31?? 32?? 33?? 34?? 35?? 36 37 38?? 39?? 40 41?? 42 > 43?? 44?? 45?? 46?? 47?? 48?? 49 50 51?? 52?? 53?? 54?? 55 56?? 57 > 58?? 59?? 60?? 61?? 62 63 > Repl????? .39? .39? .37? .42? .38? .38? .39? .36? .36? .38 .40 .39 > .40? .39? .37? .35? .40? .39? .35? .38? .40? .35? .38? .35 .36? .35 > .36? .36? .38? .36? .37? .36? .35? .36? .36? .37? .35 .35 .35? .37 > .37? .35? .37? .36? .37? .34? .36? .38? .38? .38 .35? .37 .36? .39 > .36? .40? .38? .38? .40? .36? .37? .36? .33 > > These are test runs for 5 ns with exchange frequencies of 3 ps. I > have > used the same input parameters for both of these runs (mdp is > attached). > I actually observed this with many other systems and I was looking > for > any relevant gromacs release note for versions 2018 or beyond > related to > the replica exchange algorithm or the way the energies are > calculated, > but I could not figure it out. > > Regards, > > Pritam > > -- > Pritam Ganguly > Department of Chemistry and Biochemistry > University of California at Santa Barbara > Santa Barbara, CA, USA 93106 > > Office: PSBN 3606 > Phone: +1-805-893-2767 > http://people.chem.ucsb.edu/ganguly/pritam > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-request at gromacs.org > . > -- Pritam Ganguly Department of Chemistry and Biochemistry University of California at Santa Barbara Santa Barbara, CA, USA 93106 Office: PSBN 3606 Phone: +1-805-893-2767 http://people.chem.ucsb.edu/ganguly/pritam From miro.astore at gmail.com Wed Apr 15 04:12:57 2020 From: miro.astore at gmail.com (Miro Astore) Date: Wed, 15 Apr 2020 02:12:57 -0000 Subject: [gmx-users] semiisotropic pressure coupling. Message-ID: Hello all, I am working with a rather large membrane bound protein. I was getting an issue awhile ago where if the protein moved to the edge of the box the box would elongate in the z direction. I fixed this in the short term by setting my xy compressibility to 0 in my production mdp file pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 compressibility = 0 4.5e-5 ref_p = 1.0 1.0 I have a few questions, why was it blowing up in the first place? I would guess its to do with how the pressure is being calculated when this large 'vacuum' is being created in the solvent when the protein wraps around since my tc_grps is Protein non-Protein. The fact the problem only occurs when the protein wraps seems to indicate this sort of artifact, I can get into the hundreds of nano seconds before the protein drifts if I'm lucky, this is all after a well equilibrated system. I could fix the protein in the center of the box but I fear that might produce artifacts and I suspect there is a better way. I want to start studying how this protein interacts with the lipids and fixing the xy box size is not conducive to this so I'm wondering how I can let the lipids fluctuate while still maintaining sensible system behavior. Thank you for your time, Best, Miro mdp file can be found at https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From dallas.warren at monash.edu Wed Apr 15 04:59:48 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Wed, 15 Apr 2020 02:59:48 -0000 Subject: [gmx-users] energy minimization In-Reply-To: <1267325081.3286158.1586793572943@mail.yahoo.com> References: <1267325081.3286158.1586793572943.ref@mail.yahoo.com> <1267325081.3286158.1586793572943@mail.yahoo.com> Message-ID: Gas phase simulations the inter-molecular interactions are smaller, and intra-molecular interactions dominate. Therefore total energy will be positive. If it was filled with a solvent i.e. liquid phase, then inter-molecular inteactions dominate and the total energy will be negative. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.warren at monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 14 Apr 2020 at 01:59, Afsane Farhadi wrote: > hi friends I generated a box of mixed gas with gmx insert-molecules....I > ran an energy minimizing. the potential energy is 4.05e+07 and maximum > force is 1.25e+03.I used different algorithm likes cg and steep for > minimization. what do I have to do untill my system potential energy has > negative value??I need a information about energy minimizing and potential > energy. I know that positive value of potential energy means the > intermolecular interaction is weaker than intramolecular interaction but I > don't know how I can control this matter. please help > > Sent from Yahoo Mail on Android > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Wed Apr 15 12:46:29 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 15 Apr 2020 10:46:29 -0000 Subject: [gmx-users] semiisotropic pressure coupling. In-Reply-To: References: Message-ID: <7b25fd96-32d2-e69a-b97d-ae907bd885d6@vt.edu> On 4/14/20 10:12 PM, Miro Astore wrote: > Hello all, > > I am working with a rather large membrane bound protein. I was getting > an issue awhile ago where if the protein moved to the edge of the box > the box would elongate in the z direction. I fixed this in the short > term by setting my xy compressibility to 0 in my production mdp file > pcoupl = Parrinello-Rahman > pcoupltype = semiisotropic > tau_p = 5.0 > > compressibility = 0 4.5e-5 > ref_p = 1.0 1.0 > compressibility = 0 4.5e-5 > ref_p = 1.0 1.0 > > I have a few questions, why was it blowing up in the first place? I This was due to a CHARMM-specific bug in which CMAP forces were not correctly calculated when two atoms were in different periodic images: http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary It was fixed in version 2019.4. Update your GROMACS version and you don't have to try playing any tricks like zero compressibility. -Justin > would guess its to do with how the pressure is being calculated when > this large 'vacuum' is being created in the solvent when the protein > wraps around since my tc_grps is Protein non-Protein. The fact the > problem only occurs when the protein wraps seems to indicate this sort > of artifact, I can get into the hundreds of nano seconds before the > protein drifts if I'm lucky, this is all after a well equilibrated > system. > > I could fix the protein in the center of the box but I fear that might > produce artifacts and I suspect there is a better way. > > I want to start studying how this protein interacts with the lipids > and fixing the xy box size is not conducive to this so I'm wondering > how I can let the lipids fluctuate while still maintaining sensible > system behavior. > > Thank you for your time, > > Best, Miro > > mdp file can be found at > https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From tahsin-ashraf.khan at students.mq.edu.au Wed Apr 15 13:30:19 2020 From: tahsin-ashraf.khan at students.mq.edu.au (Tahsin Ashraf Khan) Date: Wed, 15 Apr 2020 11:30:19 -0000 Subject: [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system Message-ID: Hi All Hope everyone is doing well. I'm Tahsin, currently doing a Master of Engineering in Electronics at Macquarie University, Sydney, Australia. I would like to request everyone here to shed some light regarding a research I'm currently involved in. We are trying to develop a method of determining the Complex Dielectric property of solid sate systems through MD simulations. We've chosen the GROMACS software package to do that. Similar works have been done before but all of them involved solution-based systems. To be honest, It's been just 2 months that I'm trying to learn MD simulations so I'm not at all well versed in the capabilities of GROMACS. Have a nice day. Best Regards Tahsin From miro.astore at gmail.com Wed Apr 15 13:34:12 2020 From: miro.astore at gmail.com (Miro Astore) Date: Wed, 15 Apr 2020 11:34:12 -0000 Subject: [gmx-users] semiisotropic pressure coupling. In-Reply-To: <7b25fd96-32d2-e69a-b97d-ae907bd885d6@vt.edu> References: <7b25fd96-32d2-e69a-b97d-ae907bd885d6@vt.edu> Message-ID: Incredible thank you. On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, wrote: > > > On 4/14/20 10:12 PM, Miro Astore wrote: > > Hello all, > > > > I am working with a rather large membrane bound protein. I was getting > > an issue awhile ago where if the protein moved to the edge of the box > > the box would elongate in the z direction. I fixed this in the short > > term by setting my xy compressibility to 0 in my production mdp file > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 5.0 > > > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > compressibility = 0 4.5e-5 > > ref_p = 1.0 1.0 > > > > I have a few questions, why was it blowing up in the first place? I > > This was due to a CHARMM-specific bug in which CMAP forces were not > correctly calculated when two atoms were in different periodic images: > > http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary > > It was fixed in version 2019.4. > > Update your GROMACS version and you don't have to try playing any tricks > like zero compressibility. > > -Justin > > > would guess its to do with how the pressure is being calculated when > > this large 'vacuum' is being created in the solvent when the protein > > wraps around since my tc_grps is Protein non-Protein. The fact the > > problem only occurs when the protein wraps seems to indicate this sort > > of artifact, I can get into the hundreds of nano seconds before the > > protein drifts if I'm lucky, this is all after a well equilibrated > > system. > > > > I could fix the protein in the center of the box but I fear that might > > produce artifacts and I suspect there is a better way. > > > > I want to start studying how this protein interacts with the lipids > > and fixing the xy box size is not conducive to this so I'm wondering > > how I can let the lipids fluctuate while still maintaining sensible > > system behavior. > > > > Thank you for your time, > > > > Best, Miro > > > > mdp file can be found at > > > https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From 14.navneet at gmail.com Wed Apr 15 14:15:52 2020 From: 14.navneet at gmail.com (Chaturvedi Navneet) Date: Wed, 15 Apr 2020 12:15:52 -0000 Subject: [gmx-users] Can we implement NMR restraint data in Gromacs? Message-ID: Dear GMX user, I am working on NEF (NMR Exchange Format). I need to use NMR restraint data in gromacs (in force field) for simulation. Does Gromacs support either reading or writing NEF format at the moment? If yes, then how can we implement NMR restrain data like dihedral, angle, chemical shifts, NOE restrains with Gromacs associated force field? If not, which machine can I go for simulation using these data? Many thanks -- ------------------------------------------------------------ *Navaneet Chaturvedi* University of Leicester, UK Email: nc303 at leicester.ac.uk From olayiwolateslim9 at gmail.com Wed Apr 15 14:24:46 2020 From: olayiwolateslim9 at gmail.com (Teslim Olayiwola) Date: Wed, 15 Apr 2020 12:24:46 -0000 Subject: [gmx-users] Error with Output from GMX cluster analysis Message-ID: Dear GMX users, I am currently trying to use GMX to perform cluster analysis on a polymer. Inside the top file, I have two polymer molecules. After using the GMX cluster size, I got the following error. Kindly help with possible correction (if any) for this anomaly. Thank you Regards, Teslim Command line: gmx_mpi clustsize -f ../HPAM50_16%G_20%H_agg.nojump.mol.xtc -n polymer.ndx -s polymer.tpr -mol yes -cut 0.35 -pbc yes Reading frame 0 time 200.000 Reading file polymer.tpr, VERSION 2018.1 (single precision) Reading file polymer.tpr, VERSION 2018.1 (single precision) Using molecules rather than atoms. Not reading index file polymer.ndx Last frame 20000 time 200200.000 Total number of atoms in clusters = 1 cmid: 1, cmax: 2, max_size: 2 cmid: 2, cmax: 2, max_size: 2 ------------------------------------------------------- Program: gmx clustsize, version 2018.1 Source file: src/gromacs/fileio/matio.cpp (line 681) Fatal error: Lo: 0.000000, Mid: 2.000000, Hi: 2.000000 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor From spoel at xray.bmc.uu.se Wed Apr 15 17:33:11 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 15 Apr 2020 15:33:11 -0000 Subject: [gmx-users] Can we implement NMR restraint data in Gromacs? In-Reply-To: References: Message-ID: <5915bc62-7443-9917-548c-74aaa444e547@xray.bmc.uu.se> Den 2020-04-15 kl. 14:15, skrev Chaturvedi Navneet: > Dear GMX user, > I am working on NEF (NMR Exchange Format). I need to use NMR restraint data > in gromacs (in force field) for simulation. Does Gromacs support either > reading or writing NEF format at the moment? If yes, then how can we > implement NMR restrain data like dihedral, angle, chemical shifts, NOE > restrains with Gromacs associated force field? > If not, which machine can I go for simulation using these data? > Many thanks > We are working on an importer for NMR star files. Would that help? Please contact me off the mailing list in that case. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From spoel at xray.bmc.uu.se Wed Apr 15 17:36:49 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 15 Apr 2020 15:36:49 -0000 Subject: [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system In-Reply-To: References: Message-ID: <8639446d-a8b9-772e-1cc9-557cb0f87243@xray.bmc.uu.se> Den 2020-04-15 kl. 13:30, skrev Tahsin Ashraf Khan: > Hi All > Hope everyone is doing well. I'm Tahsin, currently doing a Master of > Engineering in Electronics at Macquarie University, Sydney, Australia. I > would like to request everyone here to shed some light regarding a research > I'm currently involved in. We are trying to develop a method of determining > the Complex Dielectric property of solid sate systems through MD > simulations. We've chosen the GROMACS software package to do that. > Similar works have been done before but all of them involved solution-based > systems. To be honest, It's been just 2 months that I'm trying to learn MD > simulations so I'm not at all well versed in the capabilities of GROMACS. > Have a nice day. > Best Regards > Tahsin > Have you done your simulations and run gmx dipoles to analyze? And then gmx dielectric on the output of that? Please report back when you have, this is a bit tricky business though. You may check my old paper, however it is not entirely correct since trying to extract the dielectric constant at infinite frequency from a non-polarizable ff is not possible. https://aip.scitation.org/doi/abs/10.1063/1.476482 -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From paolo.costa85 at gmail.com Wed Apr 15 23:48:26 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Wed, 15 Apr 2020 21:48:26 -0000 Subject: [gmx-users] Problem force constant bond stretc. Message-ID: Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From spoel at xray.bmc.uu.se Thu Apr 16 07:55:23 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 16 Apr 2020 05:55:23 -0000 Subject: [gmx-users] Problem force constant bond stretc. In-Reply-To: References: Message-ID: Den 2020-04-15 kl. 23:48, skrev Paolo Costa: > Dear Gromacs users, > > I have a problem regarding force constant for bond stretching. By employing > VFFDT software, I got C-C bond stretching force constant (for Benzene, > B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to > 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of > Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It > seems that the value I got from VFFDT is somehow half than the one reported > in Amber force field. > Can somebody help me to figure out such issue? > > Thanks a lot in advance for your help. > Vbond = (k/2) (r - r0)^2 Some methods do not use the division by two, so it can be a matter of definition. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From marko at kth.se Thu Apr 16 08:57:18 2020 From: marko at kth.se (Marko Petrovic) Date: Thu, 16 Apr 2020 06:57:18 -0000 Subject: [gmx-users] Trouble with restrained dihedrals Message-ID: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. The error message: ERROR 1 [file cv_restraints.itp, line 3]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). The .itp file contents: [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 7 9 15 1 1 -67.652 0 1 2 7 9 15 17 1 1 59.806 0 1 2 Other possibly relevant file snippets: .mdp file define row (1st row): define = -DPOSRES_CV topol.top ifdef statement (last in file): #ifdef POSRES_CV #include "cv_restraints.itp" #endif I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology From marko at kth.se Thu Apr 16 08:58:36 2020 From: marko at kth.se (Marko Petrovic) Date: Thu, 16 Apr 2020 06:58:36 -0000 Subject: [gmx-users] Trouble with restrained dihedrals In-Reply-To: References: Message-ID: Bottom post: On 16 Apr 2020, at 08:56, Marko Petrovic > wrote: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. The error message: ERROR 1 [file cv_restraints.itp, line 3]: Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. (after the function type). The .itp file contents: [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 5 7 9 15 1 1 -67.652 0 1 2 7 9 15 17 1 1 59.806 0 1 2 Other possibly relevant file snippets: .mdp file define row (1st row): define = -DPOSRES_CV topol.top ifdef statement (last in file): #ifdef POSRES_CV #include "cv_restraints.itp" #endif I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Also, the most up to date documentation on dihedral restraints I easily found was: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints Is this still relevant? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology From spoel at xray.bmc.uu.se Thu Apr 16 09:44:49 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 16 Apr 2020 07:44:49 -0000 Subject: [gmx-users] Trouble with restrained dihedrals In-Reply-To: References: Message-ID: <3be6767b-6944-265f-8711-2ea79332a5a5@xray.bmc.uu.se> Den 2020-04-16 kl. 08:56, skrev Marko Petrovic: > Hello > > I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs. > > The error message: > ERROR 1 [file cv_restraints.itp, line 3]: > Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest. > (after the function type). > > The .itp file contents: > [ dihedral_restraints ] > ; ai aj ak al type label phi dphi kfac power > 5 7 9 15 1 1 -67.652 0 1 2 > 7 9 15 17 1 1 59.806 0 1 2 Not sure where you have this format from but it should be ; ai aj ak al type phi dphi kfac > > Other possibly relevant file snippets: > .mdp file define row (1st row): > define = -DPOSRES_CV > > topol.top ifdef statement (last in file): > #ifdef POSRES_CV > #include "cv_restraints.itp" > #endif > > I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file) > > With Regards > Marko Petrovic > Educator > Computational Science and Technology > School of Electrical Engineering and Computer Science > KTH Royal Institute of Technology > -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org From paolo.costa85 at gmail.com Thu Apr 16 14:32:24 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Thu, 16 Apr 2020 12:32:24 -0000 Subject: [gmx-users] Problem force constant bond stretc. In-Reply-To: References: Message-ID: Thanks a lot. Best regards, Paolo Il giorno gio 16 apr 2020 alle ore 07:57 David van der Spoel < spoel at xray.bmc.uu.se> ha scritto: > Den 2020-04-15 kl. 23:48, skrev Paolo Costa: > > Dear Gromacs users, > > > > I have a problem regarding force constant for bond stretching. By > employing > > VFFDT software, I got C-C bond stretching force constant (for Benzene, > > B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to > > 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of > > Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It > > seems that the value I got from VFFDT is somehow half than the one > reported > > in Amber force field. > > Can somebody help me to figure out such issue? > > > > Thanks a lot in advance for your help. > > > Vbond = (k/2) (r - r0)^2 > > Some methods do not use the division by two, so it can be a matter of > definition. > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.org > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From lourenco.tuanan at gmail.com Thu Apr 16 15:34:54 2020 From: lourenco.tuanan at gmail.com (=?UTF-8?Q?Tuanan_Louren=C3=A7o?=) Date: Thu, 16 Apr 2020 13:34:54 -0000 Subject: [gmx-users] GROMACS PBS GPU JOB submission Message-ID: Hi everyone I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue system is PBS. I am having some issues with the GPU selection, what I want is to use 1 GPU per job but GROMACS is always using all the four GPUs. My submission script is the following: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod.tpr -deffnm TEST -ntomp 1 However, looking to the gromacs log file I see "On host gn01 4 GPUs auto-selected for this run". I know if I use the flag -gpu_id I can tell for GROMACS what GPU I want to use and in this case, everything is ok, GROMACS does what I say. But this can be a problem if I submit more than one job to the node, because the jobs will use the same GPU card. My question is; there is any way to say for GROMACS or PBS to use the GPU that is available at that moment? I have 4 GPU in the server, thus, I want to submit 4 jobs each one using one GPU. Thank you very much. -- __________________________________________________ Dr. Tuanan C. Louren?o From alang at nvidia.com Thu Apr 16 15:35:29 2020 From: alang at nvidia.com (Alan Gray) Date: Thu, 16 Apr 2020 13:35:29 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" Message-ID: Hi Leandro, I see from your command line that you are using an external MPI library and running gmx_mpi via mpirun. The new GPU communication features are currently only supported with use of thread MPI (see http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI), and this therefore means only within a single compute node. (It looks like we need better reporting on this.) We have removed this limitation in a branch of the development repository at https://gitlab.com/gromacs/gromacs/-/merge_requests/37, but this still needs some more work before it is merged into the master branch. I also see that you are using 16 MPI tasks - I suspect that (regardless of the new GPU features) your case might not scale this high since it will be limited by the single PME MPI task, but it is best to experiment and tune these options (similarly for -nstlist and -ntomp, as Szilard already mentioned). Best regards, Alan ----------------------------------------------------------------------------------- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. ----------------------------------------------------------------------------------- From byunjy0614 at gmail.com Thu Apr 16 15:42:18 2020 From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=) Date: Thu, 16 Apr 2020 13:42:18 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> Message-ID: <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> Thank you for reply Du, You You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology? Du you mean that I modify my topology file manually?? > 2020. 4. 14. ?? 5:08, Yu Du ??: > > Hi Jinyoung, > > I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring. > > After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology. > > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? > Sent: Tuesday, April 14, 2020 14:32 > To: gmx-users at gromacs.org > Subject: [gmx-users] How to solve the "LINCS WARNING" problem > > Dear GROMACS users, > > Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below > > Step 231785, time 463.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3035 3036 34.0 0.1090 0.1087 0.1090 > > ?. > > Step 231825, time 463.65 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3024 3025 90.0 0.1090 0.1236 0.1090 > 3026 3027 100.8 0.1090 6.6242 0.1090 > 3028 3029 162.5 1.7683 5245.4102 0.1090 > 3033 3034 106.7 0.1090 426.5654 0.1090 > 3035 3037 90.0 0.3851 0.7991 0.1090 > 3038 3039 90.0 0.6045 0.4497 0.1090 > 3038 3040 90.0 0.1123 0.2833 0.1090 > 3041 3042 59.0 0.1020 0.1020 0.1020 > Wrote pdb files with previous and current coordinates > > Step 231826, time 463.652 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1423 1424 140.4 0.1000 503.9983 0.1000 > 3024 3025 61.1 0.1236 223337872.0000 0.1090 > 3026 3027 168.8 6.6242 149263.5000 0.1090 > 3028 3029 165.8 5245.4102 263929.4375 0.1090 > 3031 3032 116.2 0.1090 223428336.0000 0.1090 > 3033 3034 179.9 426.5654 446766720.0000 0.1090 > 3035 3036 35.3 29.6105 831.0708 0.1090 > 3035 3037 102.9 0.7991 775.3371 0.1090 > 3038 3039 90.0 0.4497 0.6355 0.1090 > 3038 3040 47.7 0.2833 0.1111 0.1090 > step 231826: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > Why does the LINCS warning occurs? and How I solve this problem? > > Many Thanks > > Jinyoung > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From ydu-sci at outlook.com Thu Apr 16 15:56:39 2020 From: ydu-sci at outlook.com (Yu Du) Date: Thu, 16 Apr 2020 13:56:39 -0000 Subject: [gmx-users] GROMACS PBS GPU JOB submission In-Reply-To: References: Message-ID: Hi Tuanan, I think your problem can be separated into several parts: First, use one PBS script contains 4 GMX commands, shown as follows, may solve your problems: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod1.tpr -deffnm TEST1 -ntomp 1 -gpu_id 0 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod2.tpr -deffnm TEST2 -ntomp 1 -gpu_id 1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod3.tpr -deffnm TEST3 -ntomp 1 -gpu_id 2 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod4.tpr -deffnm TEST4 -ntomp 1 -gpu_id 3 Then, you should optimize the number of CPU used by one GPU to get the best performance. Last, check mdrun in the GMX manual, use pin and related options to set the CPU range which each subjob uses to avoid the interference between them. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Tuanan Louren?o Sent: Thursday, April 16, 2020 21:34 To: gmx-users at gromacs.org Subject: [gmx-users] GROMACS PBS GPU JOB submission Hi everyone I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue system is PBS. I am having some issues with the GPU selection, what I want is to use 1 GPU per job but GROMACS is always using all the four GPUs. My submission script is the following: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod.tpr -deffnm TEST -ntomp 1 However, looking to the gromacs log file I see "On host gn01 4 GPUs auto-selected for this run". I know if I use the flag -gpu_id I can tell for GROMACS what GPU I want to use and in this case, everything is ok, GROMACS does what I say. But this can be a problem if I submit more than one job to the node, because the jobs will use the same GPU card. My question is; there is any way to say for GROMACS or PBS to use the GPU that is available at that moment? I have 4 GPU in the server, thus, I want to submit 4 jobs each one using one GPU. Thank you very much. -- __________________________________________________ Dr. Tuanan C. Louren?o -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From ydu-sci at outlook.com Thu Apr 16 16:01:58 2020 From: ydu-sci at outlook.com (Yu Du) Date: Thu, 16 Apr 2020 14:01:58 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> , <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> Message-ID: If you haven't solved your LINCS WARNING, you need to show more details of how you got that problem, including the generation of your ligand topology file. There are maybe some errors in your ligand topology that you didn't figure out. Cheers, Yu ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? Sent: Thursday, April 16, 2020 21:43 To: gmx-users at gromacs.org Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem Thank you for reply Du, You You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology? Du you mean that I modify my topology file manually?? > 2020. 4. 14. ?? 5:08, Yu Du ??: > > Hi Jinyoung, > > I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring. > > After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology. > > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? > Sent: Tuesday, April 14, 2020 14:32 > To: gmx-users at gromacs.org > Subject: [gmx-users] How to solve the "LINCS WARNING" problem > > Dear GROMACS users, > > Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below > > Step 231785, time 463.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3035 3036 34.0 0.1090 0.1087 0.1090 > > ?. > > Step 231825, time 463.65 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3024 3025 90.0 0.1090 0.1236 0.1090 > 3026 3027 100.8 0.1090 6.6242 0.1090 > 3028 3029 162.5 1.7683 5245.4102 0.1090 > 3033 3034 106.7 0.1090 426.5654 0.1090 > 3035 3037 90.0 0.3851 0.7991 0.1090 > 3038 3039 90.0 0.6045 0.4497 0.1090 > 3038 3040 90.0 0.1123 0.2833 0.1090 > 3041 3042 59.0 0.1020 0.1020 0.1020 > Wrote pdb files with previous and current coordinates > > Step 231826, time 463.652 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1423 1424 140.4 0.1000 503.9983 0.1000 > 3024 3025 61.1 0.1236 223337872.0000 0.1090 > 3026 3027 168.8 6.6242 149263.5000 0.1090 > 3028 3029 165.8 5245.4102 263929.4375 0.1090 > 3031 3032 116.2 0.1090 223428336.0000 0.1090 > 3033 3034 179.9 426.5654 446766720.0000 0.1090 > 3035 3036 35.3 29.6105 831.0708 0.1090 > 3035 3037 102.9 0.7991 775.3371 0.1090 > 3038 3039 90.0 0.4497 0.6355 0.1090 > 3038 3040 47.7 0.2833 0.1111 0.1090 > step 231826: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > Why does the LINCS warning occurs? and How I solve this problem? > > Many Thanks > > Jinyoung > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From adarsh_p130085bt at nitc.ac.in Thu Apr 16 16:27:13 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Thu, 16 Apr 2020 14:27:13 -0000 Subject: [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution Message-ID: Dear all, While performing a protein ligand simulation, I received the following 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or any other method? ------------------------------------------------------------------------------------------------------- gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr WARNING 1 [file topol.top, line 60334]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ------------------------------------------------------------------------------------------------------- From adarsh_p130085bt at nitc.ac.in Thu Apr 16 16:27:17 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Thu, 16 Apr 2020 14:27:17 -0000 Subject: [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution Message-ID: Dear all, While performing a protein ligand simulation, I received the following 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or any other method? ------------------------------------------------------------------------------------------------------- gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr WARNING 1 [file topol.top, line 60334]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ------------------------------------------------------------------------------------------------------- From jalemkul at vt.edu Thu Apr 16 16:35:28 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 16 Apr 2020 14:35:28 -0000 Subject: [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution In-Reply-To: References: Message-ID: <5b13ec1d-16a4-48ff-37ec-214e0b414d08@vt.edu> On 4/16/20 10:26 AM, Adarsh V. K. wrote: > Dear all, > > While performing a protein ligand simulation, I received the following > 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or > any other method? > > ------------------------------------------------------------------------------------------------------- > gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o > nvt.tpr > > WARNING 1 [file topol.top, line 60334]: > You are using Ewald electrostatics in a system with net charge. This can > lead to severe artifacts, such as ions moving into regions with low > dielectric, due to the uniform background charge. We suggest to > neutralize your system with counter ions, possibly in combination with a > physiological salt concentration. > ------------------------------------------------------------------------------------------------------- The warning suggests what you should do. Your system isn't neutral but with PME it should be to avoid potential artifacts. Don't use -maxwarn to override cases in which grompp tells you that you're doing something unphysical. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Thu Apr 16 17:49:00 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 16 Apr 2020 15:49:00 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation Message-ID: Dear Gromacs users, I have been trying to do the tutorial title: "Free Energy Calculations: Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have problems and I get the following error: Program: gmx mdrun, version 2020.1 Source file: src/gromacs/options/options.cpp (line 179) Function: void gmx::internal::OptionSectionImpl::finish() Error in user input: Invalid input values In option s Required option was not provided, and the default file 'topol' does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr My path for the .mdp files would be: "/home/Lazaro/tutorial_gromacs" for example. Any help? Kindly, Lazaro From jalemkul at vt.edu Thu Apr 16 18:01:00 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 16 Apr 2020 16:01:00 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: References: Message-ID: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> On 4/16/20 11:48 AM, lazaro monteserin wrote: > Dear Gromacs users, > > I have been trying to do the tutorial title: "Free Energy Calculations: > Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my > paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have > problems and I get the following error: > > Program: gmx mdrun, version 2020.1 > Source file: src/gromacs/options/options.cpp (line 179) > Function: void gmx::internal::OptionSectionImpl::finish() > Error in user input: > Invalid input values > In option s > Required option was not provided, and the default file 'topol' does not > exist or is not accessible. > The following extensions were tried to complete the file name: > .tpr > > My path for the .mdp files would be: "/home/Lazaro/tutorial_gromacs" for > example. > > Any help? grompp is failing and not creating the .tpr files you need, so mdrun tries to rely on default file names, which also don't exist. Run the commands interactively, one by one, to find the error. When you've resolved that, you can use the script's automated approach. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From robert.cordina at strath.ac.uk Thu Apr 16 19:37:28 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Thu, 16 Apr 2020 17:37:28 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals Message-ID: Hi, I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories. I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them. I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart. I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees. This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms. What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads. Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS? Thanks, Robert From lamonteserincastanedo at gmail.com Thu Apr 16 19:47:23 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 16 Apr 2020 17:47:23 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> Message-ID: Dear Lemkul Thank you very much for the recommendation. I tried each step but separate and you were right I was missing the .gro in my directory. Now the script should work. But I am still unsure of how to declare the location of my file in the environmental variable $FREE_ENERGY and $MDP. Do you have any suggestions. The location of my file is /home/Lazaro/tutorial_gromacs Kindly, Lazaro El jue., 16 de abr. de 2020 a la(s) 13:01, Justin Lemkul (jalemkul at vt.edu) escribi?: > > > On 4/16/20 11:48 AM, lazaro monteserin wrote: > > Dear Gromacs users, > > > > I have been trying to do the tutorial title: "Free Energy Calculations: > > Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my > > paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I > have > > problems and I get the following error: > > > > Program: gmx mdrun, version 2020.1 > > Source file: src/gromacs/options/options.cpp (line 179) > > Function: void gmx::internal::OptionSectionImpl::finish() > > Error in user input: > > Invalid input values > > In option s > > Required option was not provided, and the default file 'topol' does > not > > exist or is not accessible. > > The following extensions were tried to complete the file name: > > .tpr > > > > My path for the .mdp files would be: "/home/Lazaro/tutorial_gromacs" for > > example. > > > > Any help? > > grompp is failing and not creating the .tpr files you need, so mdrun > tries to rely on default file names, which also don't exist. Run the > commands interactively, one by one, to find the error. When you've > resolved that, you can use the script's automated approach. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Thu Apr 16 21:00:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 16 Apr 2020 19:00:35 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> Message-ID: <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> On 4/16/20 1:47 PM, lazaro monteserin wrote: > Dear Lemkul > > Thank you very much for the recommendation. > > I tried each step but separate and you were right I was missing the .gro in > my directory. > > Now the script should work. But I am still unsure of how to declare the > location of my file in the environmental variable $FREE_ENERGY and $MDP. Do > you have any suggestions. $FREE_ENERGY is the top-level directory where you are executing the script: > The location of my file is /home/Lazaro/tutorial_gromacs $MDP is where you have all the .mdp files stored. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Thu Apr 16 21:20:31 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 16 Apr 2020 19:20:31 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> Message-ID: But how do I declare this in the script? I have try for example: FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then MPD="/$FREE_ENERGY/mpd" Using the " " But stills it doesn't work. I have all my .mdp files stored in a directory called "mdp" inside the directory "tutorial_gromacs". Am I making a syntax mistake here? Kindly, Lazaro El jue., 16 de abr. de 2020 a la(s) 16:02, Justin Lemkul (jalemkul at vt.edu) escribi?: > > > On 4/16/20 1:47 PM, lazaro monteserin wrote: > > Dear Lemkul > > > > Thank you very much for the recommendation. > > > > I tried each step but separate and you were right I was missing the .gro > in > > my directory. > > > > Now the script should work. But I am still unsure of how to declare the > > location of my file in the environmental variable $FREE_ENERGY and $MDP. > Do > > you have any suggestions. > > $FREE_ENERGY is the top-level directory where you are executing the script: > > The location of my file is /home/Lazaro/tutorial_gromacs > > $MDP is where you have all the .mdp files stored. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Thu Apr 16 21:23:31 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 16 Apr 2020 19:23:31 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> Message-ID: <15efcabf-2123-cd9a-6e2e-07145a06478b@vt.edu> On 4/16/20 3:20 PM, lazaro monteserin wrote: > But how do I declare this in the script? > > I have try for example: > > FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then > MPD="/$FREE_ENERGY/mpd" > > Using the " " > > But stills it doesn't work. I have all my .mdp files stored in a directory > called "mdp" inside the directory "tutorial_gromacs". > > Am I making a syntax mistake here? No, but you've got a typo of "MPD" and "mpd" in place of "MDP" and "mdp" that is probably your issue. And you don't need the leading slash before $FREE_ENERGY in the definition of $MDP. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From leandro.obt at gmail.com Thu Apr 16 23:09:32 2020 From: leandro.obt at gmail.com (Leandro Bortot) Date: Thu, 16 Apr 2020 21:09:32 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" In-Reply-To: References: Message-ID: Thank you for your reply, Alan. I didn't realize that I need to use thread-MPI in order to use the GPU communication features. Best regards, Leandro ------- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational Biology Brazilian Biosciences National Laboratory (LNBio) Brazilian Center for Research in Energy and Materials (CNPEM) Zip Code 13083-970, Campinas, S?o Paulo, Brazil. On Thu, Apr 16, 2020 at 10:37 AM Alan Gray wrote: > Hi Leandro, > > I see from your command line that you are using an external MPI library > and running gmx_mpi via mpirun. The new GPU communication features are > currently only supported with use of thread MPI (see > http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI), > and this therefore means only within a single compute node. (It looks like > we need better reporting on this.) We have removed this limitation in a > branch of the development repository at > https://gitlab.com/gromacs/gromacs/-/merge_requests/37, but this still > needs some more work before it is merged into the master branch. > > I also see that you are using 16 MPI tasks - I suspect that (regardless of > the new GPU features) your case might not scale this high since it will be > limited by the single PME MPI task, but it is best to experiment and tune > these options (similarly for -nstlist and -ntomp, as Szilard already > mentioned). > > Best regards, > > Alan > > > ----------------------------------------------------------------------------------- > This email message is for the sole use of the intended recipient(s) and > may contain > confidential information. Any unauthorized review, use, disclosure or > distribution > is prohibited. If you are not the intended recipient, please contact the > sender by > reply email and destroy all copies of the original message. > > ----------------------------------------------------------------------------------- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From leandro.obt at gmail.com Thu Apr 16 23:09:33 2020 From: leandro.obt at gmail.com (Leandro Bortot) Date: Thu, 16 Apr 2020 21:09:33 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" In-Reply-To: References: Message-ID: Thank you for your reply, Alan. I didn't realize that I need to use thread-MPI in order to use the GPU communication features. Best regards, Leandro ------- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational Biology Brazilian Biosciences National Laboratory (LNBio) Brazilian Center for Research in Energy and Materials (CNPEM) Zip Code 13083-970, Campinas, S?o Paulo, Brazil. On Thu, Apr 16, 2020 at 10:37 AM Alan Gray wrote: > Hi Leandro, > > I see from your command line that you are using an external MPI library > and running gmx_mpi via mpirun. The new GPU communication features are > currently only supported with use of thread MPI (see > http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI), > and this therefore means only within a single compute node. (It looks like > we need better reporting on this.) We have removed this limitation in a > branch of the development repository at > https://gitlab.com/gromacs/gromacs/-/merge_requests/37, but this still > needs some more work before it is merged into the master branch. > > I also see that you are using 16 MPI tasks - I suspect that (regardless of > the new GPU features) your case might not scale this high since it will be > limited by the single PME MPI task, but it is best to experiment and tune > these options (similarly for -nstlist and -ntomp, as Szilard already > mentioned). > > Best regards, > > Alan > > > ----------------------------------------------------------------------------------- > This email message is for the sole use of the intended recipient(s) and > may contain > confidential information. Any unauthorized review, use, disclosure or > distribution > is prohibited. If you are not the intended recipient, please contact the > sender by > reply email and destroy all copies of the original message. > > ----------------------------------------------------------------------------------- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From lamonteserincastanedo at gmail.com Fri Apr 17 00:49:06 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 16 Apr 2020 22:49:06 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: <15efcabf-2123-cd9a-6e2e-07145a06478b@vt.edu> References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> <15efcabf-2123-cd9a-6e2e-07145a06478b@vt.edu> Message-ID: Ah let me fix that and try again. I will let you know how it goes. Thank you very much for all the help On Thu, Apr 16, 2020 at 4:23 PM Justin Lemkul wrote: > > > On 4/16/20 3:20 PM, lazaro monteserin wrote: > > But how do I declare this in the script? > > > > I have try for example: > > > > FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then > > MPD="/$FREE_ENERGY/mpd" > > > > Using the " " > > > > But stills it doesn't work. I have all my .mdp files stored in a > directory > > called "mdp" inside the directory "tutorial_gromacs". > > > > Am I making a syntax mistake here? > > No, but you've got a typo of "MPD" and "mpd" in place of "MDP" and "mdp" > that is probably your issue. And you don't need the leading slash before > $FREE_ENERGY in the definition of $MDP. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From tuk04130 at temple.edu Fri Apr 17 02:12:25 2020 From: tuk04130 at temple.edu (Lei Qian) Date: Fri, 17 Apr 2020 00:12:25 -0000 Subject: [gmx-users] Question on running gmx trjconv without 2 prompts Message-ID: Dear users, Could I ask: how to run gmx trjconv without 2 prompts? I select 'Protein' to center, and 'System' to output. I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the selection automatically and asked me to choose from 'Protein' or 'System'. Thanks! Lei From jalemkul at vt.edu Fri Apr 17 02:17:44 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 00:17:44 -0000 Subject: [gmx-users] Question on running gmx trjconv without 2 prompts In-Reply-To: References: Message-ID: <6bc615a7-46fa-d58a-1408-e03203b7f0c5@vt.edu> On 4/16/20 8:12 PM, Lei Qian wrote: > Dear users, > > Could I ask: how to run gmx trjconv without 2 prompts? > I select 'Protein' to center, and 'System' to output. > > I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n > Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the > selection automatically and asked me to choose from 'Protein' or 'System'. http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ydu-sci at outlook.com Fri Apr 17 03:19:22 2020 From: ydu-sci at outlook.com (Yu Du) Date: Fri, 17 Apr 2020 01:19:22 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: Message-ID: Hi Robert, I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system, but it deserves the efforts and time. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Robert Cordina Sent: Friday, April 17, 2020 01:37 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals Hi, I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories. I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them. I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart. I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees. This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms. What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads. Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS? Thanks, Robert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From b.mijiddorj at gmail.com Fri Apr 17 04:15:19 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Fri, 17 Apr 2020 02:15:19 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header Message-ID: Dear GMX users, Hello, I performed MD simulation using gromacs 2018.7v. During this simulation, the calculation was stopped because of the electric cut. Then, I continued the simulation using "gmx mdrun with -noappend" in order to get separate trajectory for the safety of data. After that, I would like to concatenate the trr files. However, I received following error message. How, can I concatenate these trajectories. ********************************************** Program: gmx trjcat, version 2018.7 Source file: src/gromacs/fileio/trrio.cpp (line 114) Fatal error: Failed to find GROMACS magic number in trr frame header, so this is not a trr file! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ************************************************ Best regards, Mijiddorj From tuk04130 at temple.edu Fri Apr 17 04:32:27 2020 From: tuk04130 at temple.edu (Lei Qian) Date: Fri, 17 Apr 2020 02:32:27 -0000 Subject: [gmx-users] Question on running gmx trjconv without 2 prompts In-Reply-To: <6bc615a7-46fa-d58a-1408-e03203b7f0c5@vt.edu> References: <6bc615a7-46fa-d58a-1408-e03203b7f0c5@vt.edu> Message-ID: Thank you Dr. Lemkul, these two websites are very helpful. Thanks! On Thu, Apr 16, 2020 at 8:17 PM Justin Lemkul wrote: > > > On 4/16/20 8:12 PM, Lei Qian wrote: > > Dear users, > > > > Could I ask: how to run gmx trjconv without 2 prompts? > > I select 'Protein' to center, and 'System' to output. > > > > I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n > > Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the > > selection automatically and asked me to choose from 'Protein' or > 'System'. > > http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From m.b.abdelaal at gmail.com Fri Apr 17 05:00:50 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Fri, 17 Apr 2020 03:00:50 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: <276CD4BE-ECF1-411E-9B03-3D250763450A@gmail.com> References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> <276CD4BE-ECF1-411E-9B03-3D250763450A@gmail.com> Message-ID: I have one more question please regarding the velocity. What is the mean value for the velocity being generated by GROMACS ? Is it zero ? I have also understood fr om the below paragraph which is written in the manual section 3.4.1, that the values generated are selected from the range between 0 and 1, However I have opened my nvt.gro file and I have found negative values for the generated velocity. How come that I have negative values for the velocity if the generated velocity is within the range from 0-1 as written in the manual ? Am I missing something? "If velocities are not available, the program can generate initial atomic velocities at a given absolute temperature T : where k is Boltzmann?s constant (see chapter 2). To accomplish this, normally distributed random numbers are generated by adding twelve random numbers R k in the range 0 ? R k < 1 and subtracting 6.0 from their sum. The result is then multiplied by the standard deviation of the velocity distribution kT /m i . Since the resulting total energy will not correspond exactly to the required temperature T , a correction is made: first the center-of-mass motion is removed and then all velocities are scaled so that the total energy corresponds exactly to T (see eqn. 3.18)." Many thanks, Mohamed On Wed, Apr 15, 2020 at 12:26 AM Eric Smoll wrote: > My knowledge is a bit old. > > Tpr files are binary so you cannot read them without a special tool. In > gromacs 2018, there was a tool that would spit out the contents of a tpr > file in a readable format. Execute > ?gmx dump -h? to learn more. > > Justin is correct. There is no tool or file that will allow you to add a > constant velocity in the z direction to a set of atoms. I would suggest > writing a program to build a custom gro file from the start that has > everything you want. If that is not possible for you, you could use > gen-vel and attempt to export a gro with the resulting velocities at some > point afterward (e.g., use gen-vel tpr for a 1 step simulation writing > coordinates and velocities to the trr at every step and then extract gro > with velocities from the trr). Then go through the gro file and add a > constant z-velocity to all the atoms that need it. Then read the edited > gro file in again and proceed. > > -Eric > > Sent from my iPhone > > > On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal > wrote: > > > > Many thanks Dr. Erik for your reply :) > > > > > >> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll > wrote: > >> > >> No problem. > >> > >> Now it is clear what you are trying to do. The previous description of > >> your goals did not make much physical sense. The initial velocities are > >> such that all three dimensions are sampled from the same 3D velocity > >> distribution (gaussian with the same width). The difference is that > there > >> is a constant velocity added in the z-direction so there is net motion > in > >> the z-direction. > > > > > > > >> One way to do this is to use gen-vel as usual and just add the constant > to > >> the z-coordinate. > >> > > > > *Can you please tell me more details how to add the constant to the > > z-coordinate ? If I will generate the velocity from the .mdp file, in > which > > file should I add the constant to the z-coordinate ? * > > > >> > > > > The velocities were probably read in. By default, the velocities may not > >> be printed in the gro. What matters is that they were loaded in the > tpr. > >> Try a simulation to see if the molecule is moving as expected. > >> > > > > I will complete the simulation to the end to check whether or not the > > velocity was added from my .gro file. > > > > > >> Alternatively, dump the contents of the tpr and make sure the velocities > >> you created were read in. > >> > >> Do you mean that I should manually edit the .tpr file ? I have tried to > > open it with text editor but it can't be open. > > > > > >> -Eric > >> > >> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal < > m.b.abdelaal at gmail.com> > >> wrote: > >> > >>> Sorry for writing again in the same topic but I couldn't solve > >>> the velocity problem. > >>> > >>> I am trying to reproduce a paper written by: Claire Tonnel + , Martin > >>> Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, > >> Alpeshkumar > >>> K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > >>> Powell > >>> Title: Elucidating the Spatial Arrangement of Emitter Molecules in > >> Organic > >>> Light-Emitting Diode Films > >>> > >>> It was mentioned in the paper that " The molecule was inserted into the > >>> system such that the x and y coordinates of the centre of mass were > >> sampled > >>> from a uniform distribution covering the entire box while the z > >> coordinate > >>> of the centre of mass was set to 2.0 nm above the current surface. The > >>> initial orientation of the molecule was randomised. *The velocities of > >> each > >>> atom within the inserted molecule in x and y were sampled from a > Gaussian > >>> distribution with a mean of 0.0 nm/ps and a standard deviation > >> appropriate > >>> for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s > , T > >>> is the temperature and m is the mass of the atom). The velocities in z > >> were > >>> sampled from the distribution with the same standard deviation as x > and y > >>> but with a mean of 0.05 nmps -1 , negative z velocities (molecule > moving > >> in > >>> the direction opposite to the surface) were rectified by taking the > >>> absolute value. This ensured all molecules moved toward the surface.* > >>> > >>> I have read the section 3.4.1 of the manual version 5.1.2 as > recommended > >>> above and I have also read all the velocity related topics in the > manual > >>> and user guide. > >>> > >>> (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro > file > >>> and then I inserted the molecule in a box using insert-molecules, > However > >>> after the insertion process is completed I opened the output .gro file > >> but > >>> the velocity was not read. This means that I can only generate the > >> velocity > >>> through the .mdp file. > >>> > >>> If I am going to generate the velocity using my .mdp file, is it > possible > >>> to change the standard deviation and the mean ? if yes, how can I > modify > >>> them ? (I can't find any way to modify the parameters of the Maxwell > >>> distribution) > >>> > >>> I want to have velocity distributions with means equal to 0,0,0.5 nmps > in > >>> the x,y,z directions respectively. > >>> > >>> You wrote in your last email that, "A 3D Maxwell Boltzmann velocity > >>> distribution corresponds to three identical gaussian speed > distributions > >> in > >>> vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). > >> Just > >>> change the standard deviation of the velocity distribution sqrt(kT/m) > for > >>> each velocity component if you want them to be different. If you don't > >>> want the mean to be zero for whatever reason, add a constant." > >>> > >>> If the velocity will not be read from the .gro file where should I add > >> the > >>> constant to change the mean? > >>> > >>> Many thanks, > >>> Mohamed > >>> > >>> > >>> On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal < > m.b.abdelaal at gmail.com> > >>> wrote: > >>> > >>>> Many thanks for your reply :) > >>>> > >>>> All your language assumptions are true and that is exactly what I > >> wanted > >>>> to communicate, next time I will try to be more precise and sorry for > >> the > >>>> confusion ? > >>>> > >>>> I will read section 3.4.1 again carefully. > >>>> > >>>> Thanks again and sorry for the inconvenience. > >>>> > >>>> Mohamed > >>>> > >>>>> On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: > >>>>> > >>>>> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal < > >> m.b.abdelaal at gmail.com > >>>> > >>>>> wrote: > >>>>> > >>>>>> Many thanks for your reply ? > >>>>>> > >>>>>> The limitation in the generate velocity using the .mdp file, is that > >>>>> while > >>>>>> I can generate the velocity from Maxwell distribution, I will have > >>> the > >>>>>> same velocities in the x, y and z directions. > >>>>>> > >>>>> > >>>>> I think you mean "same velocity *distributions* in the x, y, and z > >>>>> directions." The distributions will be approximately the same but > >> each > >>>>> atom will have a different velocity. > >>>>> > >>>>>> > >>>>>> On the other hand, generating the velocity from the .gro file will > >> let > >>>>> me > >>>>>> specify different velocities in the x,y and z directions but they > >> will > >>>>> be > >>>>>> the same velocities for all the atoms (will not be taken from a > >>> maxwell > >>>>>> distribution with variation in the atoms velocities). > >>>>>> > >>>>> > >>>>> I think you mean "specify different velocity *distributions* in the > x, > >>> y, > >>>>> and z directions" > >>>>> > >>>>>> > >>>>>> Is it possible to generate different velocities in the x,y and z > >>>>> directions > >>>>>> > >>>>> > >>>>> I think you mean "generate different velocity *distributions* in the > >> x, > >>> y, > >>>>> and z directions." If so, the answer is obviously yes. Because you > >> can > >>>>> type in each individual vxi, vyi, and vzi for every atom i, you can > >>>>> generate different velocity distributions in the x, y, and z > >> directions. > >>>>> > >>>>> > >>>>>> from a maxwell distribution ? > >>>>> > >>>>> > >>>>> I am not sure what this part of the sentence means. If you do what > >> you > >>>>> are > >>>>> suggesting, you will not be working with a maxwell distribution > >> because > >>>>> all > >>>>> three directions should have identical distributions. See comment > >>> below. > >>>>> If there is another misunderstanding, you need to spend more time > >>> crafting > >>>>> precise sentences to communicate what you are after. > >>>>> > >>>>> > >>>>>> (for example the velocities to be taken from > >>>>>> a maxwell distribution with a mean of 0.1 in the x direction and > >> with > >>> a > >>>>>> mean of 0.2 in the y direction and with mean of 0.3 in the z > >>> direction?) > >>>>>> > >>>>> > >>>>> In my last email I suggested reading section 3.4.1 of the manual > >> version > >>>>> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity > >>>>> distribution > >>>>> corresponds to three identical gaussian speed distributions in vx, > vy, > >>> and > >>>>> vz centered at zero (mean should be zero for vx, vy, vz). Just > change > >>> the > >>>>> standard deviation of the velocity distribution sqrt(kT/m) for each > >>>>> velocity component if you want them to be different. If you don't > >> want > >>>>> the > >>>>> mean to be zero for whatever reason, add a constant. However, a > >>> non-zero > >>>>> mean for any of the velocity components will generate center of mass > >>>>> motion. If you want center of mass motion, turn off center of mass > >>> motion > >>>>> removal in the mdp file. > >>>>> > >>>>> > >>>>>> Thanks for your help :) > >>>>>> Mohamed > >>>>>> > >>>>>> On Wed, Apr 8, 2020 at 05:48 Eric Smoll > >> wrote: > >>>>>> > >>>>>>> On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < > >>>>> m.b.abdelaal at gmail.com> > >>>>>>> wrote: > >>>>>>> > >>>>>>>> No, I use the generate velocity option in the .mdp files. > >>>>>>>> > >>>>>>>> However I want now to assign different velocities in the x,y,z > >>>>>>> directions. > >>>>>>>> Which I thought it could only be done through the .gro file, > >> but I > >>>>>> don't > >>>>>>>> know If I did that, should I change the value of the generate > >>>>> velocity > >>>>>> to > >>>>>>>> be = NO in the .mdp files ? (otherwise I would have generated > >> the > >>>>>>>> velocities twice). > >>>>>>>> > >>>>>>> > >>>>>>> That sounds logical. Set it to no if you provide your own initial > >>>>>>> velocities. > >>>>>>> > >>>>>>>> > >>>>>>>> Moreover, if I added the velocities in the .gro file how can I > >>>>> generate > >>>>>>> the > >>>>>>>> velocities in the .gro file from a distribution (Maxwell) with a > >>>>>> specific > >>>>>>>> mean and standard deviation ? > >>>>>>>> > >>>>>>>> I have tried to search in different sources (the user list, > >>> manual, > >>>>>> user > >>>>>>>> guide, research gate and other platforms) how to solve this > >>> velocity > >>>>>>>> problem but I didn't find a clear way to insert different > >>>>> velocities in > >>>>>>> the > >>>>>>>> x,y,z directions using distribution rater than constant > >>> velocities. > >>>>>>>> > >>>>>>>> There is a good section on this in the manual. For example, > >>> section > >>>>>>> 3.4.1 > >>>>>>> in the Gromacs 5.1.2 manual. > >>>>>>> > >>>>>>> Also, you know that the generate velocities option assigns > >>> velocities > >>>>> to > >>>>>>> atoms from an approximate MB distribution at whatever temperature > >>> you > >>>>>>> specify in the MDP file, right? If I understand you correctly, > >> the > >>>>>>> generate velocities options should do exactly what you want. With > >>> no > >>>>>> extra > >>>>>>> work. > >>>>>>> > >>>>>>> > >>>>>>>> Please guide me how to do it as I am a little bit confused in > >> the > >>>>>>> velocity > >>>>>>>> generation mechanisms. > >>>>>>>> > >>>>>>>> Many thanks, > >>>>>>>> Mohamed > >>>>>>>> > >>>>>>>> On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul > >>>>> wrote: > >>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>>> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > >>>>>>>>>> Hello everybody :) > >>>>>>>>>> > >>>>>>>>>> Can I use the gmx insert-molecules to insert molecules in my > >>> box > >>>>>> with > >>>>>>>>>> velocities by adding the velocities in t > >>>>> < > >>> > >> > https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g > >>>> he > >>>>> .gro file and insert the > >>>>>>>>>> molecules from this .gro file ? > >>>>>>>>> > >>>>>>>>> Have you tried it? > >>>>>>>>> > >>>>>>>>> -Justin > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> ================================================== > >>>>>>>>> > >>>>>>>>> Justin A. Lemkul, Ph.D. > >>>>>>>>> Assistant Professor > >>>>>>>>> Office: 301 Fralin Hall > >>>>>>>>> Lab: 303 Engel Hall > >>>>>>>>> > >>>>>>>>> Virginia Tech Department of Biochemistry > >>>>>>>>> 340 West Campus Dr. > >>>>>>>>> Blacksburg, VA 24061 > >>>>>>>>> > >>>>>>>>> jalemkul at vt.edu | (540) 231-3129 > >>>>>>>>> http://www.thelemkullab.com > >>>>>>>>> > >>>>>>>>> ================================================== > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> Gromacs Users mailing list > >>>>>>>>> > >>>>>>>>> * Please search the archive at > >>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >>>>> before > >>>>>>>>> posting! > >>>>>>>>> > >>>>>>>>> * Can't post? Read > >> http://www.gromacs.org/Support/Mailing_Lists > >>>>>>>>> > >>>>>>>>> * For (un)subscribe requests visit > >>>>>>>>> > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >>>>>> or > >>>>>>>>> send a mail to gmx-users-request at gromacs.org. > >>>>>>>>> > >>>>>>>> -- > >>>>>>>> Gromacs Users mailing list > >>>>>>>> > >>>>>>>> * Please search the archive at > >>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >>> before > >>>>>>>> posting! > >>>>>>>> > >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>>>> > >>>>>>>> * For (un)subscribe requests visit > >>>>>>>> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >>>>> or > >>>>>>>> send a mail to gmx-users-request at gromacs.org. > >>>>>>>> > >>>>>>> -- > >>>>>>> Gromacs Users mailing list > >>>>>>> > >>>>>>> * Please search the archive at > >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > >> before > >>>>>>> posting! > >>>>>>> > >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>>> > >>>>>>> * For (un)subscribe requests visit > >>>>>>> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >>> or > >>>>>>> send a mail to gmx-users-request at gromacs.org. > >>>>>>> > >>>>>> -- > >>>>>> Gromacs Users mailing list > >>>>>> > >>>>>> * Please search the archive at > >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>>>> posting! > >>>>>> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>> > >>>>>> * For (un)subscribe requests visit > >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > >>>>>> send a mail to gmx-users-request at gromacs.org. > >>>>> -- > >>>>> Gromacs Users mailing list > >>>>> > >>>>> * Please search the archive at > >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>>> posting! > >>>>> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> * For (un)subscribe requests visit > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >>>> > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-request at gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From adarsh_p130085bt at nitc.ac.in Fri Apr 17 06:16:13 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Fri, 17 Apr 2020 04:16:13 -0000 Subject: [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation Message-ID: Dear all, A ligand molecule (lig) contains a Chlorine atom in it. While attempting to performing a protein-ligand simulation, the Gromacs returns an error message. It is observed that the *CGenFF server * Generate two additional lines, as shown below, in lig.str file ATOM LP1 LPH 0.050 ! on Cl1 LONEPAIR COLI LP1 Cl1 C18 DIST 1.6400 SCAL 0.0 Which later add an additional line in ' lig.gro ' file generated using python cgenff_charmm2gmx.py LIG lig_fix.mol2 lig.str charmm36-mar2019.ff gmx editconf -f lig_ini.pdb -o lig.gro at the later stages of simulation, the above 'LP1 lines' gives the following error message ----------------------------------------------------------------------------------------------------- WARNING 1 [file topol.top, line 60334]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ------------------------------------------------------------------------------------------------------- How to over come this problem while performing a simulation with a ligand containing halogens like Chlorine? 1) Delete Chlorine atom form the ligand molecule after an optimization with Avogadro and before uploading to CGenFF Server ? or 2) Delete (ATOM LP1 LPH 0.050 ! on Cl1 and LONEPAIR COLI LP1 Cl1 C18 DIST 1.6400 SCAL 0.0) lines from ' lig.str ' file before further processing to ' lig.gro ' and later part of simulation can manage with -maxwarn 1 ? or 3) just delete LP1 line from lig,gro and in later part of the simulation manage the lig.prm and lig.itp file? or 4) Gromacs 2020.1 can effectively handle this ' LP1 ' ? or 5) Any other methods to overcome the problem with Halogens / lone pair From adarsh_p130085bt at nitc.ac.in Fri Apr 17 06:16:14 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Fri, 17 Apr 2020 04:16:14 -0000 Subject: [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation Message-ID: Dear all, A ligand molecule (lig) contains a Chlorine atom in it. While attempting to performing a protein-ligand simulation, the Gromacs returns an error message. It is observed that the *CGenFF server * Generate two additional lines, as shown below, in lig.str file ATOM LP1 LPH 0.050 ! on Cl1 LONEPAIR COLI LP1 Cl1 C18 DIST 1.6400 SCAL 0.0 Which later add an additional line in ' lig.gro ' file generated using python cgenff_charmm2gmx.py LIG lig_fix.mol2 lig.str charmm36-mar2019.ff gmx editconf -f lig_ini.pdb -o lig.gro at the later stages of simulation, the above 'LP1 lines' gives the following error message ----------------------------------------------------------------------------------------------------- WARNING 1 [file topol.top, line 60334]: You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration. ------------------------------------------------------------------------------------------------------- How to over come this problem while performing a simulation with a ligand containing halogens like Chlorine? 1) Delete Chlorine atom form the ligand molecule after an optimization with Avogadro and before uploading to CGenFF Server ? or 2) Delete (ATOM LP1 LPH 0.050 ! on Cl1 and LONEPAIR COLI LP1 Cl1 C18 DIST 1.6400 SCAL 0.0) lines from ' lig.str ' file before further processing to ' lig.gro ' and later part of simulation can manage with -maxwarn 1 ? or 3) just delete LP1 line from lig,gro and in later part of the simulation manage the lig.prm and lig.itp file? or 4) Gromacs 2020.1 can effectively handle this ' LP1 ' ? or 5) Any other methods to overcome the problem with Halogens / lone pair From ericsmoll at gmail.com Fri Apr 17 06:21:03 2020 From: ericsmoll at gmail.com (Eric Smoll) Date: Fri, 17 Apr 2020 04:21:03 -0000 Subject: [gmx-users] Velocities from the .gro file In-Reply-To: References: <9bab0f05-9f78-3f93-ae50-ffb8587dc7b4@vt.edu> <276CD4BE-ECF1-411E-9B03-3D250763450A@gmail.com> Message-ID: Sent from my iPhone > On Apr 16, 2020, at 7:53 PM, Mohamed Abdelaal wrote: > > I have one more question please regarding the velocity. No problem. > > What is the mean value for the velocity being generated by GROMACS ? Is it > zero ? Yes. > > I have also understood fr om the below paragraph which is written in the > manual section 3.4.1, that the values generated are selected from the range > between 0 and 1, However I have opened my nvt.gro file and I have found > negative values for the generated velocity. How come that I have negative > values for the velocity if the generated velocity is within the range from > 0-1 as written in the manual ? Am I missing something? Yes you are missing something. Read again. Each random number is generated between 0 and 1 but 12 of these are added together before subtracting 6 from the sum. If, by chance, all twelve numbers are 0.1, the sum is 1.2. 1.2 - 6 is -4.8. This is why negative numbers are possible. > > "If velocities are not available, the program can generate initial atomic > velocities at a given absolute temperature T : > where k is Boltzmann?s constant (see chapter 2). To accomplish this, normally > distributed random > numbers are generated by adding twelve random numbers R k in the range 0 ? > R k < 1 and > subtracting 6.0 from their sum. The result is then multiplied by the > standard deviation of the > velocity distribution kT /m i . Since the resulting total energy will not > correspond exactly to the > required temperature T , a correction is made: first the center-of-mass > motion is removed and then > all velocities are scaled so that the total energy corresponds exactly to T > (see eqn. 3.18)." > > Many thanks, > Mohamed > >> On Wed, Apr 15, 2020 at 12:26 AM Eric Smoll wrote: >> >> My knowledge is a bit old. >> >> Tpr files are binary so you cannot read them without a special tool. In >> gromacs 2018, there was a tool that would spit out the contents of a tpr >> file in a readable format. Execute >> ?gmx dump -h? to learn more. >> >> Justin is correct. There is no tool or file that will allow you to add a >> constant velocity in the z direction to a set of atoms. I would suggest >> writing a program to build a custom gro file from the start that has >> everything you want. If that is not possible for you, you could use >> gen-vel and attempt to export a gro with the resulting velocities at some >> point afterward (e.g., use gen-vel tpr for a 1 step simulation writing >> coordinates and velocities to the trr at every step and then extract gro >> with velocities from the trr). Then go through the gro file and add a >> constant z-velocity to all the atoms that need it. Then read the edited >> gro file in again and proceed. >> >> -Eric >> >> Sent from my iPhone >> >>> On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal >> wrote: >>> >>> Many thanks Dr. Erik for your reply :) >>> >>> >>>> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll >> wrote: >>>> >>>> No problem. >>>> >>>> Now it is clear what you are trying to do. The previous description of >>>> your goals did not make much physical sense. The initial velocities are >>>> such that all three dimensions are sampled from the same 3D velocity >>>> distribution (gaussian with the same width). The difference is that >> there >>>> is a constant velocity added in the z-direction so there is net motion >> in >>>> the z-direction. >>> >>> >>> >>>> One way to do this is to use gen-vel as usual and just add the constant >> to >>>> the z-coordinate. >>>> >>> >>> *Can you please tell me more details how to add the constant to the >>> z-coordinate ? If I will generate the velocity from the .mdp file, in >> which >>> file should I add the constant to the z-coordinate ? * >>> >>>> >>> >>> The velocities were probably read in. By default, the velocities may not >>>> be printed in the gro. What matters is that they were loaded in the >> tpr. >>>> Try a simulation to see if the molecule is moving as expected. >>>> >>> >>> I will complete the simulation to the end to check whether or not the >>> velocity was added from my .gro file. >>> >>> >>>> Alternatively, dump the contents of the tpr and make sure the velocities >>>> you created were read in. >>>> >>>> Do you mean that I should manually edit the .tpr file ? I have tried to >>> open it with text editor but it can't be open. >>> >>> >>>> -Eric >>>> >>>> On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal < >> m.b.abdelaal at gmail.com> >>>> wrote: >>>> >>>>> Sorry for writing again in the same topic but I couldn't solve >>>>> the velocity problem. >>>>> >>>>> I am trying to reproduce a paper written by: Claire Tonnel + , Martin >>>>> Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, >>>> Alpeshkumar >>>>> K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. >>>>> Powell >>>>> Title: Elucidating the Spatial Arrangement of Emitter Molecules in >>>> Organic >>>>> Light-Emitting Diode Films >>>>> >>>>> It was mentioned in the paper that " The molecule was inserted into the >>>>> system such that the x and y coordinates of the centre of mass were >>>> sampled >>>>> from a uniform distribution covering the entire box while the z >>>> coordinate >>>>> of the centre of mass was set to 2.0 nm above the current surface. The >>>>> initial orientation of the molecule was randomised. *The velocities of >>>> each >>>>> atom within the inserted molecule in x and y were sampled from a >> Gaussian >>>>> distribution with a mean of 0.0 nm/ps and a standard deviation >>>> appropriate >>>>> for the temperature constant (? = sqrt(kT/m), where k B is Botzmann?s >> , T >>>>> is the temperature and m is the mass of the atom). The velocities in z >>>> were >>>>> sampled from the distribution with the same standard deviation as x >> and y >>>>> but with a mean of 0.05 nmps -1 , negative z velocities (molecule >> moving >>>> in >>>>> the direction opposite to the surface) were rectified by taking the >>>>> absolute value. This ensured all molecules moved toward the surface.* >>>>> >>>>> I have read the section 3.4.1 of the manual version 5.1.2 as >> recommended >>>>> above and I have also read all the velocity related topics in the >> manual >>>>> and user guide. >>>>> >>>>> (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro >> file >>>>> and then I inserted the molecule in a box using insert-molecules, >> However >>>>> after the insertion process is completed I opened the output .gro file >>>> but >>>>> the velocity was not read. This means that I can only generate the >>>> velocity >>>>> through the .mdp file. >>>>> >>>>> If I am going to generate the velocity using my .mdp file, is it >> possible >>>>> to change the standard deviation and the mean ? if yes, how can I >> modify >>>>> them ? (I can't find any way to modify the parameters of the Maxwell >>>>> distribution) >>>>> >>>>> I want to have velocity distributions with means equal to 0,0,0.5 nmps >> in >>>>> the x,y,z directions respectively. >>>>> >>>>> You wrote in your last email that, "A 3D Maxwell Boltzmann velocity >>>>> distribution corresponds to three identical gaussian speed >> distributions >>>> in >>>>> vx, vy, andvz centered at zero (mean should be zero for vx, vy, vz). >>>> Just >>>>> change the standard deviation of the velocity distribution sqrt(kT/m) >> for >>>>> each velocity component if you want them to be different. If you don't >>>>> want the mean to be zero for whatever reason, add a constant." >>>>> >>>>> If the velocity will not be read from the .gro file where should I add >>>> the >>>>> constant to change the mean? >>>>> >>>>> Many thanks, >>>>> Mohamed >>>>> >>>>> >>>>> On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal < >> m.b.abdelaal at gmail.com> >>>>> wrote: >>>>> >>>>>> Many thanks for your reply :) >>>>>> >>>>>> All your language assumptions are true and that is exactly what I >>>> wanted >>>>>> to communicate, next time I will try to be more precise and sorry for >>>> the >>>>>> confusion ? >>>>>> >>>>>> I will read section 3.4.1 again carefully. >>>>>> >>>>>> Thanks again and sorry for the inconvenience. >>>>>> >>>>>> Mohamed >>>>>> >>>>>>> On Thu, Apr 9, 2020 at 04:33 Eric Smoll wrote: >>>>>>> >>>>>>> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal < >>>> m.b.abdelaal at gmail.com >>>>>> >>>>>>> wrote: >>>>>>> >>>>>>>> Many thanks for your reply ? >>>>>>>> >>>>>>>> The limitation in the generate velocity using the .mdp file, is that >>>>>>> while >>>>>>>> I can generate the velocity from Maxwell distribution, I will have >>>>> the >>>>>>>> same velocities in the x, y and z directions. >>>>>>>> >>>>>>> >>>>>>> I think you mean "same velocity *distributions* in the x, y, and z >>>>>>> directions." The distributions will be approximately the same but >>>> each >>>>>>> atom will have a different velocity. >>>>>>> >>>>>>>> >>>>>>>> On the other hand, generating the velocity from the .gro file will >>>> let >>>>>>> me >>>>>>>> specify different velocities in the x,y and z directions but they >>>> will >>>>>>> be >>>>>>>> the same velocities for all the atoms (will not be taken from a >>>>> maxwell >>>>>>>> distribution with variation in the atoms velocities). >>>>>>>> >>>>>>> >>>>>>> I think you mean "specify different velocity *distributions* in the >> x, >>>>> y, >>>>>>> and z directions" >>>>>>> >>>>>>>> >>>>>>>> Is it possible to generate different velocities in the x,y and z >>>>>>> directions >>>>>>>> >>>>>>> >>>>>>> I think you mean "generate different velocity *distributions* in the >>>> x, >>>>> y, >>>>>>> and z directions." If so, the answer is obviously yes. Because you >>>> can >>>>>>> type in each individual vxi, vyi, and vzi for every atom i, you can >>>>>>> generate different velocity distributions in the x, y, and z >>>> directions. >>>>>>> >>>>>>> >>>>>>>> from a maxwell distribution ? >>>>>>> >>>>>>> >>>>>>> I am not sure what this part of the sentence means. If you do what >>>> you >>>>>>> are >>>>>>> suggesting, you will not be working with a maxwell distribution >>>> because >>>>>>> all >>>>>>> three directions should have identical distributions. See comment >>>>> below. >>>>>>> If there is another misunderstanding, you need to spend more time >>>>> crafting >>>>>>> precise sentences to communicate what you are after. >>>>>>> >>>>>>> >>>>>>>> (for example the velocities to be taken from >>>>>>>> a maxwell distribution with a mean of 0.1 in the x direction and >>>> with >>>>> a >>>>>>>> mean of 0.2 in the y direction and with mean of 0.3 in the z >>>>> direction?) >>>>>>>> >>>>>>> >>>>>>> In my last email I suggested reading section 3.4.1 of the manual >>>> version >>>>>>> 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity >>>>>>> distribution >>>>>>> corresponds to three identical gaussian speed distributions in vx, >> vy, >>>>> and >>>>>>> vz centered at zero (mean should be zero for vx, vy, vz). Just >> change >>>>> the >>>>>>> standard deviation of the velocity distribution sqrt(kT/m) for each >>>>>>> velocity component if you want them to be different. If you don't >>>> want >>>>>>> the >>>>>>> mean to be zero for whatever reason, add a constant. However, a >>>>> non-zero >>>>>>> mean for any of the velocity components will generate center of mass >>>>>>> motion. If you want center of mass motion, turn off center of mass >>>>> motion >>>>>>> removal in the mdp file. >>>>>>> >>>>>>> >>>>>>>> Thanks for your help :) >>>>>>>> Mohamed >>>>>>>> >>>>>>>> On Wed, Apr 8, 2020 at 05:48 Eric Smoll >>>> wrote: >>>>>>>> >>>>>>>>> On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal < >>>>>>> m.b.abdelaal at gmail.com> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> No, I use the generate velocity option in the .mdp files. >>>>>>>>>> >>>>>>>>>> However I want now to assign different velocities in the x,y,z >>>>>>>>> directions. >>>>>>>>>> Which I thought it could only be done through the .gro file, >>>> but I >>>>>>>> don't >>>>>>>>>> know If I did that, should I change the value of the generate >>>>>>> velocity >>>>>>>> to >>>>>>>>>> be = NO in the .mdp files ? (otherwise I would have generated >>>> the >>>>>>>>>> velocities twice). >>>>>>>>>> >>>>>>>>> >>>>>>>>> That sounds logical. Set it to no if you provide your own initial >>>>>>>>> velocities. >>>>>>>>> >>>>>>>>>> >>>>>>>>>> Moreover, if I added the velocities in the .gro file how can I >>>>>>> generate >>>>>>>>> the >>>>>>>>>> velocities in the .gro file from a distribution (Maxwell) with a >>>>>>>> specific >>>>>>>>>> mean and standard deviation ? >>>>>>>>>> >>>>>>>>>> I have tried to search in different sources (the user list, >>>>> manual, >>>>>>>> user >>>>>>>>>> guide, research gate and other platforms) how to solve this >>>>> velocity >>>>>>>>>> problem but I didn't find a clear way to insert different >>>>>>> velocities in >>>>>>>>> the >>>>>>>>>> x,y,z directions using distribution rater than constant >>>>> velocities. >>>>>>>>>> >>>>>>>>>> There is a good section on this in the manual. For example, >>>>> section >>>>>>>>> 3.4.1 >>>>>>>>> in the Gromacs 5.1.2 manual. >>>>>>>>> >>>>>>>>> Also, you know that the generate velocities option assigns >>>>> velocities >>>>>>> to >>>>>>>>> atoms from an approximate MB distribution at whatever temperature >>>>> you >>>>>>>>> specify in the MDP file, right? If I understand you correctly, >>>> the >>>>>>>>> generate velocities options should do exactly what you want. With >>>>> no >>>>>>>> extra >>>>>>>>> work. >>>>>>>>> >>>>>>>>> >>>>>>>>>> Please guide me how to do it as I am a little bit confused in >>>> the >>>>>>>>> velocity >>>>>>>>>> generation mechanisms. >>>>>>>>>> >>>>>>>>>> Many thanks, >>>>>>>>>> Mohamed >>>>>>>>>> >>>>>>>>>> On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul >>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: >>>>>>>>>>>> Hello everybody :) >>>>>>>>>>>> >>>>>>>>>>>> Can I use the gmx insert-molecules to insert molecules in my >>>>> box >>>>>>>> with >>>>>>>>>>>> velocities by adding the velocities in t >>>>>>> < >>>>> >>>> >> https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g >>>>>> he >>>>>>> .gro file and insert the >>>>>>>>>>>> molecules from this .gro file ? >>>>>>>>>>> >>>>>>>>>>> Have you tried it? >>>>>>>>>>> >>>>>>>>>>> -Justin >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> ================================================== >>>>>>>>>>> >>>>>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>>>>> Assistant Professor >>>>>>>>>>> Office: 301 Fralin Hall >>>>>>>>>>> Lab: 303 Engel Hall >>>>>>>>>>> >>>>>>>>>>> Virginia Tech Department of Biochemistry >>>>>>>>>>> 340 West Campus Dr. >>>>>>>>>>> Blacksburg, VA 24061 >>>>>>>>>>> >>>>>>>>>>> jalemkul at vt.edu | (540) 231-3129 >>>>>>>>>>> http://www.thelemkullab.com >>>>>>>>>>> >>>>>>>>>>> ================================================== >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Gromacs Users mailing list >>>>>>>>>>> >>>>>>>>>>> * Please search the archive at >>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>>>>>> before >>>>>>>>>>> posting! >>>>>>>>>>> >>>>>>>>>>> * Can't post? Read >>>> http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>>>> >>>>>>>>>>> * For (un)subscribe requests visit >>>>>>>>>>> >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>> or >>>>>>>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Gromacs Users mailing list >>>>>>>>>> >>>>>>>>>> * Please search the archive at >>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >>>>> before >>>>>>>>>> posting! >>>>>>>>>> >>>>>>>>>> * Can't post? 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Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From byunjy0614 at gmail.com Fri Apr 17 06:28:38 2020 From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=) Date: Fri, 17 Apr 2020 04:28:38 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> Message-ID: Thank you Yu Du I encountered the problem while I have tried to simulate the protein-ligand complex system. 1. I generated the all atom ligand topology file from the ATB website. And I make both ligand .gro file and protein .gro file by using pdb2gmx and editconf module. 2. Then I run solvation, adding ion, energy minimization step with no problem 3. The problem I mailed is from NVT or NPT equilibration step. During equilibration step, I met the problem mentioned. I attached my ligand topology file -------------- next part -------------- . Is the problem from the wrong ligand topology (parameter) file? Thank you. > 2020. 4. 16. ?? 11:01, Yu Du ??: > > If you haven't solved your LINCS WARNING, you need to show more details of how you got that problem, including the generation of your ligand topology file. There are maybe some errors in your ligand topology that you didn't figure out. > > Cheers, > > Yu > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? > Sent: Thursday, April 16, 2020 21:43 > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > > Thank you for reply Du, You > You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology? > Du you mean that I modify my topology file manually?? > > >> 2020. 4. 14. ?? 5:08, Yu Du ??: >> >> Hi Jinyoung, >> >> I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring. >> >> After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology. >> >> Du, Yu >> PhD Student, >> Shanghai Institute of Organic Chemistry >> 345 Ling Ling Rd., Shanghai, China. >> Zip: 200032, Tel: (86) 021 5492 5275 >> ________________________________ >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? >> Sent: Tuesday, April 14, 2020 14:32 >> To: gmx-users at gromacs.org >> Subject: [gmx-users] How to solve the "LINCS WARNING" problem >> >> Dear GROMACS users, >> >> Since I have run the nvt and npt processes for the protein-ligand interaction, I met the the warning messages below >> >> Step 231785, time 463.57 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.000176, max 0.003912 (between atoms 3035 and 3037) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 3035 3036 34.0 0.1090 0.1087 0.1090 >> >> ?. >> >> Step 231825, time 463.65 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 3024 3025 90.0 0.1090 0.1236 0.1090 >> 3026 3027 100.8 0.1090 6.6242 0.1090 >> 3028 3029 162.5 1.7683 5245.4102 0.1090 >> 3033 3034 106.7 0.1090 426.5654 0.1090 >> 3035 3037 90.0 0.3851 0.7991 0.1090 >> 3038 3039 90.0 0.6045 0.4497 0.1090 >> 3038 3040 90.0 0.1123 0.2833 0.1090 >> 3041 3042 59.0 0.1020 0.1020 0.1020 >> Wrote pdb files with previous and current coordinates >> >> Step 231826, time 463.652 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 1423 1424 140.4 0.1000 503.9983 0.1000 >> 3024 3025 61.1 0.1236 223337872.0000 0.1090 >> 3026 3027 168.8 6.6242 149263.5000 0.1090 >> 3028 3029 165.8 5245.4102 263929.4375 0.1090 >> 3031 3032 116.2 0.1090 223428336.0000 0.1090 >> 3033 3034 179.9 426.5654 446766720.0000 0.1090 >> 3035 3036 35.3 29.6105 831.0708 0.1090 >> 3035 3037 102.9 0.7991 775.3371 0.1090 >> 3038 3039 90.0 0.4497 0.6355 0.1090 >> 3038 3040 47.7 0.2833 0.1111 0.1090 >> step 231826: One or more water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. >> Why does the LINCS warning occurs? and How I solve this problem? >> >> Many Thanks >> >> Jinyoung >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From prasanthghanta at sssihl.edu.in Fri Apr 17 06:53:09 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Fri, 17 Apr 2020 04:53:09 -0000 Subject: [gmx-users] RIN (Residue interaction network) for protein ligand interactions Message-ID: Dear All, I am interested in viewing the Residue Interaction network during a protein - ligand simulation. Can someone suggest an easy way to go about it? I tried to use gRINN tool but I guess it doesn't work if ligands are present. Thanks in advance. -- Regards, Prasanth. From prasanthghanta at sssihl.edu.in Fri Apr 17 06:55:23 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Fri, 17 Apr 2020 04:55:23 -0000 Subject: [gmx-users] atomselection for index group of cyclic rings Message-ID: Dear all, I am interested in measuring the distance between two cyclic rings present in the residues and ligands over time. Can you kindly suggest how to go about this? Specially, if i am interested in measuring the distance between the center of the two rings over time. Thank you -- Regards, Prasanth. From ydu-sci at outlook.com Fri Apr 17 08:34:55 2020 From: ydu-sci at outlook.com (Yu Du) Date: Fri, 17 Apr 2020 06:34:55 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> , Message-ID: Hi Jinyoung, You made it clear. If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand. To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy. Could you run the following simulation to pinpoint the error? (1) Simulation only all-atom ligand in the system. (2) Simulation only protein in the system. (3) Simulation only united-atom ligand in the system if it's possible. In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation. PS: gmx-users mail list do not receive attachment. Cheers, Yu From Simone.Schirra at uibk.ac.at Fri Apr 17 10:45:33 2020 From: Simone.Schirra at uibk.ac.at (Schirra, Simone) Date: Fri, 17 Apr 2020 08:45:33 -0000 Subject: [gmx-users] atomtype "OE" in charmm36 Message-ID: <412999B95FB6894AAB9B6283E4C20DA126065042@XMBX3.uibk.ac.at> Dear Gromacs users, I want to simulate polyethylene glycol and I am using a script to build my .itp and .gro files. The script is designed to work with charmm35r, however I only found charmm36 available now (I read, that c35r was only temporary). I thought, it should work with this version as well. When I try energy minimization, the atomtype OE is not found. OE is used for the ether oxygen's in the itp file. I also found an ether toppar file at MacKerell Lab Hompage, however it seems to be designed for use with charmm rather than gromacs. Is there a way to convert it for use with gromacs? Or is there another definition I can use to work with my PEG? Or maybe c35r is still somewhere around? I would be very grateful if someone could help me! Simone From robert.cordina at strath.ac.uk Fri Apr 17 10:50:42 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Fri, 17 Apr 2020 08:50:42 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: Message-ID: Hi Yu, I'm not looking for parameter extraction, just bond distances and angles between atom cluster centroids. Do you know of a way to create an artificial centroid to then measure distances and angles? Thanks, Robert -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Yu Du Sent: 17 April 2020 02:19 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals Hi Robert, I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system, but it deserves the efforts and time. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Robert Cordina Sent: Friday, April 17, 2020 01:37 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals Hi, I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories. I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want them. I am using modelling quite small molecules, so I'm only measuring distances, angles and dihedrals a few atoms apart. I'm doing this to start parameterising a new coarse-grained force field, and for example I get a bond angle of 160 degrees, when really it should be 180 degrees. This is happening because I'm calculating the angle between specific atoms spaced only 3-4 atoms apart which might be on opposite sides of a straight chain of carbon atoms. What I'd like to get out is the angle between the centroid of the groups of atoms that would form the coarse-grained beads. Does anyone have any suggestions if this can be done in GROMACS, or in any Python library which works with GROMACS? Thanks, Robert -- Gromacs Users mailing list * Please search the archive at https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7Ca1d4c2dbc1464fbe0f3d08d7e26d737a%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637226832050398015&sdata=OXUQK7a5DIPLWaSOYViYfxKTB%2Beqcp2%2BS3jCOWgDuyM%3D&reserved=0 before posting! * Can't post? 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From ydu-sci at outlook.com Fri Apr 17 11:32:33 2020 From: ydu-sci at outlook.com (Yu Du) Date: Fri, 17 Apr 2020 09:32:33 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: , Message-ID: Hi Robert, Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. Cheers, Yu From johannes.hermann at tum.de Fri Apr 17 11:35:50 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Fri, 17 Apr 2020 09:35:50 -0000 Subject: [gmx-users] Appending crashed Replica Exchange Simulations: init_step/-replex is not equal for all subsystems Message-ID: <2163e31d-6726-197a-ed3f-b1b4890b007e@tum.de> Dear all, I am doing free energy hamiltonian replica exchange simulations and unfortunately my simulation crashed (not because of the MD system itself but because of a hardware failure). The Problem is, that the "first exchange step: init_step/-replex is not equal for all subsystems" (log-file): first exchange step: init_step/-replex is not equal for all subsystems ? subsystem 0: 10697 ? subsystem 1: 10697 ? subsystem 2: 10697 ? subsystem 3: 10763 ? subsystem 4: 10763 ..... Is there a way that I can manipulate (stripe?) my output files so that I can append my simulation? Which files would I have to adapt? Thank you very much in advance! All the best Johannes -- ______________________________________ *Technische Universit?t M?nchen* *Johannes Hermann, M.Sc.* Lehrstuhl f?r Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 89289 15730 Fax: +49 89289 15714 Email: johannes.hermann at tum.de http://www.biovt.mw.tum.de/ From prasanthghanta at sssihl.edu.in Fri Apr 17 13:00:48 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Fri, 17 Apr 2020 11:00:48 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem (???) In-Reply-To: References: Message-ID: Hi Jinyoung Can you please tell which forcefield you are using for these simulations As far as I remember atb server generates gromos compatible parameters, which is a United atom forcefield. Since you said you are interested in an all atom simulation, I'm slightly confused Regards. On Fri, 17 Apr, 2020, 2:17 PM , < gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: How to solve the "LINCS WARNING" problem (???) > 2. RIN (Residue interaction network) for protein ligand > interactions (Prasanth G, Research Scholar) > 3. atomselection for index group of cyclic rings > (Prasanth G, Research Scholar) > 4. Re: How to solve the "LINCS WARNING" problem (Yu Du) > 5. atomtype "OE" in charmm36 (Schirra, Simone) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Apr 2020 13:30:14 +0900 > From: ??? > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Thank you Yu Du > I encountered the problem while I have tried to simulate the > protein-ligand complex system. > 1. I generated the all atom ligand topology file from the ATB website. And > I make both ligand .gro file and protein .gro file by using pdb2gmx and > editconf module. > 2. Then I run solvation, adding ion, energy minimization step with no > problem > 3. The problem I mailed is from NVT or NPT equilibration step. During > equilibration step, I met the problem mentioned. > > I attached my ligand topology file > -------------- next part -------------- > . > Is the problem from the wrong ligand topology (parameter) file? > > Thank you. > > > 2020. 4. 16. ?? 11:01, Yu Du ??: > > > > If you haven't solved your LINCS WARNING, you need to show more details > of how you got that problem, including the generation of your ligand > topology file. There are maybe some errors in your ligand topology that you > didn't figure out. > > > > Cheers, > > > > Yu > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < > byunjy0614 at gmail.com> > > Sent: Thursday, April 16, 2020 21:43 > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > > > > Thank you for reply Du, You > > You said that "If you want more suggestion, you need to provide some > details of the generation of ligand's topology? > > Du you mean that I modify my topology file manually?? > > > > > >> 2020. 4. 14. ?? 5:08, Yu Du ??: > >> > >> Hi Jinyoung, > >> > >> I guess that the LINCS WARNING you encountered maybe came from hiden > errors in the configuration of either protein or ligand OR more directly > from the ligand's topology. You need to carefully check the configuration > of protein and ligand, e.g. side chain goes through benzene ring. > >> > >> After a careful check, If you want more suggestion, you need to provide > some details of the generation of ligand's topology. > >> > >> Du, Yu > >> PhD Student, > >> Shanghai Institute of Organic Chemistry > >> 345 Ling Ling Rd., Shanghai, China. > >> Zip: 200032, Tel: (86) 021 5492 5275 > >> ________________________________ > >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < > byunjy0614 at gmail.com> > >> Sent: Tuesday, April 14, 2020 14:32 > >> To: gmx-users at gromacs.org > >> Subject: [gmx-users] How to solve the "LINCS WARNING" problem > >> > >> Dear GROMACS users, > >> > >> Since I have run the nvt and npt processes for the protein-ligand > interaction, I met the the warning messages below > >> > >> Step 231785, time 463.57 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 3035 3036 34.0 0.1090 0.1087 0.1090 > >> > >> ?. > >> > >> Step 231825, time 463.65 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 3024 3025 90.0 0.1090 0.1236 0.1090 > >> 3026 3027 100.8 0.1090 6.6242 0.1090 > >> 3028 3029 162.5 1.7683 5245.4102 0.1090 > >> 3033 3034 106.7 0.1090 426.5654 0.1090 > >> 3035 3037 90.0 0.3851 0.7991 0.1090 > >> 3038 3039 90.0 0.6045 0.4497 0.1090 > >> 3038 3040 90.0 0.1123 0.2833 0.1090 > >> 3041 3042 59.0 0.1020 0.1020 0.1020 > >> Wrote pdb files with previous and current coordinates > >> > >> Step 231826, time 463.652 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and > 3034) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 1423 1424 140.4 0.1000 503.9983 0.1000 > >> 3024 3025 61.1 0.1236 223337872.0000 0.1090 > >> 3026 3027 168.8 6.6242 149263.5000 0.1090 > >> 3028 3029 165.8 5245.4102 263929.4375 0.1090 > >> 3031 3032 116.2 0.1090 223428336.0000 0.1090 > >> 3033 3034 179.9 426.5654 446766720.0000 0.1090 > >> 3035 3036 35.3 29.6105 831.0708 0.1090 > >> 3035 3037 102.9 0.7991 775.3371 0.1090 > >> 3038 3039 90.0 0.4497 0.6355 0.1090 > >> 3038 3040 47.7 0.2833 0.1111 0.1090 > >> step 231826: One or more water molecules can not be settled. > >> Check for bad contacts and/or reduce the timestep if appropriate. > >> > >> So I checked the my input configuration. the 3035, 3028, 3035 atoms are > ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > >> Why does the LINCS warning occurs? and How I solve this problem? > >> > >> Many Thanks > >> > >> Jinyoung > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Apr 2020 10:25:38 +0530 > From: "Prasanth G, Research Scholar" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] RIN (Residue interaction network) for protein > ligand interactions > Message-ID: > < > CAGpSbSR1UhXoXuxOeAh7h0F2UKzTgJ_rfXm7zfYKDezxSH3oVQ at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > > I am interested in viewing the Residue Interaction network during a protein > - ligand simulation. Can someone suggest an easy way to go about it? > > I tried to use gRINN tool but I guess it doesn't work if ligands are > present. > Thanks in advance. > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Apr 2020 10:27:52 +0530 > From: "Prasanth G, Research Scholar" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] atomselection for index group of cyclic rings > Message-ID: > < > CAGpSbSSQBMcpnSvm5nvWq9ZqbiSvUrc1FktAhgwOTyqw6kP60g at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > I am interested in measuring the distance between two cyclic rings present > in the residues and ligands over time. Can you kindly suggest how to go > about this? > Specially, if i am interested in measuring the distance between the center > of the two rings over time. Thank you > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 4 > Date: Fri, 17 Apr 2020 06:34:48 +0000 > From: Yu Du > To: "gmx-users at gromacs.org" > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > < > SL2PR04MB30335B7BE660077087DED2CEE0D90 at SL2PR04MB3033.apcprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you > can also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with > only protein and only ligand in the same process you followed in a divide > and conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly > follow the instruction in the ATB ff file folders for protein-ligand > simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > > > ------------------------------ > > Message: 5 > Date: Fri, 17 Apr 2020 08:45:26 +0000 > From: "Schirra, Simone" > To: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] atomtype "OE" in charmm36 > Message-ID: > <412999B95FB6894AAB9B6283E4C20DA126065042 at XMBX3.uibk.ac.at> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my > .itp and .gro files. The script is designed to work with charmm35r, however > I only found charmm36 available now (I read, that c35r was only temporary). > I thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used > for the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it > seems to be designed for use with charmm rather than gromacs. > Is there a way to convert it for use with gromacs? Or is there another > definition I can use to work with my PEG? Or maybe c35r is still somewhere > around? > > I would be very grateful if someone could help me! > Simone > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 57 > ****************************************************** > From prasanthghanta at sssihl.edu.in Fri Apr 17 13:05:49 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Fri, 17 Apr 2020 11:05:49 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem (???) In-Reply-To: References: Message-ID: Hi Jinyoung Can you please tell which forcefield you are using for these simulations As far as I remember atb server generates gromos compatible parameters, which is a United atom forcefield. Since you said you are interested in an all atom simulation, I'm slightly confused Regards. On Fri, 17 Apr, 2020, 2:17 PM , < gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: How to solve the "LINCS WARNING" problem (???) > 2. RIN (Residue interaction network) for protein ligand > interactions (Prasanth G, Research Scholar) > 3. atomselection for index group of cyclic rings > (Prasanth G, Research Scholar) > 4. Re: How to solve the "LINCS WARNING" problem (Yu Du) > 5. atomtype "OE" in charmm36 (Schirra, Simone) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Apr 2020 13:30:14 +0900 > From: ??? > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Thank you Yu Du > I encountered the problem while I have tried to simulate the > protein-ligand complex system. > 1. I generated the all atom ligand topology file from the ATB website. And > I make both ligand .gro file and protein .gro file by using pdb2gmx and > editconf module. > 2. Then I run solvation, adding ion, energy minimization step with no > problem > 3. The problem I mailed is from NVT or NPT equilibration step. During > equilibration step, I met the problem mentioned. > > I attached my ligand topology file > -------------- next part -------------- > . > Is the problem from the wrong ligand topology (parameter) file? > > Thank you. > > > 2020. 4. 16. ?? 11:01, Yu Du ??: > > > > If you haven't solved your LINCS WARNING, you need to show more details > of how you got that problem, including the generation of your ligand > topology file. There are maybe some errors in your ligand topology that you > didn't figure out. > > > > Cheers, > > > > Yu > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < > byunjy0614 at gmail.com> > > Sent: Thursday, April 16, 2020 21:43 > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > > > > Thank you for reply Du, You > > You said that "If you want more suggestion, you need to provide some > details of the generation of ligand's topology? > > Du you mean that I modify my topology file manually?? > > > > > >> 2020. 4. 14. ?? 5:08, Yu Du ??: > >> > >> Hi Jinyoung, > >> > >> I guess that the LINCS WARNING you encountered maybe came from hiden > errors in the configuration of either protein or ligand OR more directly > from the ligand's topology. You need to carefully check the configuration > of protein and ligand, e.g. side chain goes through benzene ring. > >> > >> After a careful check, If you want more suggestion, you need to provide > some details of the generation of ligand's topology. > >> > >> Du, Yu > >> PhD Student, > >> Shanghai Institute of Organic Chemistry > >> 345 Ling Ling Rd., Shanghai, China. > >> Zip: 200032, Tel: (86) 021 5492 5275 > >> ________________________________ > >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < > byunjy0614 at gmail.com> > >> Sent: Tuesday, April 14, 2020 14:32 > >> To: gmx-users at gromacs.org > >> Subject: [gmx-users] How to solve the "LINCS WARNING" problem > >> > >> Dear GROMACS users, > >> > >> Since I have run the nvt and npt processes for the protein-ligand > interaction, I met the the warning messages below > >> > >> Step 231785, time 463.57 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 0.000176, max 0.003912 (between atoms 3035 and 3037) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 3035 3036 34.0 0.1090 0.1087 0.1090 > >> > >> ?. > >> > >> Step 231825, time 463.65 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 3024 3025 90.0 0.1090 0.1236 0.1090 > >> 3026 3027 100.8 0.1090 6.6242 0.1090 > >> 3028 3029 162.5 1.7683 5245.4102 0.1090 > >> 3033 3034 106.7 0.1090 426.5654 0.1090 > >> 3035 3037 90.0 0.3851 0.7991 0.1090 > >> 3038 3039 90.0 0.6045 0.4497 0.1090 > >> 3038 3040 90.0 0.1123 0.2833 0.1090 > >> 3041 3042 59.0 0.1020 0.1020 0.1020 > >> Wrote pdb files with previous and current coordinates > >> > >> Step 231826, time 463.652 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and > 3034) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 1423 1424 140.4 0.1000 503.9983 0.1000 > >> 3024 3025 61.1 0.1236 223337872.0000 0.1090 > >> 3026 3027 168.8 6.6242 149263.5000 0.1090 > >> 3028 3029 165.8 5245.4102 263929.4375 0.1090 > >> 3031 3032 116.2 0.1090 223428336.0000 0.1090 > >> 3033 3034 179.9 426.5654 446766720.0000 0.1090 > >> 3035 3036 35.3 29.6105 831.0708 0.1090 > >> 3035 3037 102.9 0.7991 775.3371 0.1090 > >> 3038 3039 90.0 0.4497 0.6355 0.1090 > >> 3038 3040 47.7 0.2833 0.1111 0.1090 > >> step 231826: One or more water molecules can not be settled. > >> Check for bad contacts and/or reduce the timestep if appropriate. > >> > >> So I checked the my input configuration. the 3035, 3028, 3035 atoms are > ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. > >> Why does the LINCS warning occurs? and How I solve this problem? > >> > >> Many Thanks > >> > >> Jinyoung > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Apr 2020 10:25:38 +0530 > From: "Prasanth G, Research Scholar" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] RIN (Residue interaction network) for protein > ligand interactions > Message-ID: > < > CAGpSbSR1UhXoXuxOeAh7h0F2UKzTgJ_rfXm7zfYKDezxSH3oVQ at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > > I am interested in viewing the Residue Interaction network during a protein > - ligand simulation. Can someone suggest an easy way to go about it? > > I tried to use gRINN tool but I guess it doesn't work if ligands are > present. > Thanks in advance. > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Apr 2020 10:27:52 +0530 > From: "Prasanth G, Research Scholar" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] atomselection for index group of cyclic rings > Message-ID: > < > CAGpSbSSQBMcpnSvm5nvWq9ZqbiSvUrc1FktAhgwOTyqw6kP60g at mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > I am interested in measuring the distance between two cyclic rings present > in the residues and ligands over time. Can you kindly suggest how to go > about this? > Specially, if i am interested in measuring the distance between the center > of the two rings over time. Thank you > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 4 > Date: Fri, 17 Apr 2020 06:34:48 +0000 > From: Yu Du > To: "gmx-users at gromacs.org" > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > < > SL2PR04MB30335B7BE660077087DED2CEE0D90 at SL2PR04MB3033.apcprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you > can also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with > only protein and only ligand in the same process you followed in a divide > and conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly > follow the instruction in the ATB ff file folders for protein-ligand > simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > > > ------------------------------ > > Message: 5 > Date: Fri, 17 Apr 2020 08:45:26 +0000 > From: "Schirra, Simone" > To: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] atomtype "OE" in charmm36 > Message-ID: > <412999B95FB6894AAB9B6283E4C20DA126065042 at XMBX3.uibk.ac.at> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my > .itp and .gro files. The script is designed to work with charmm35r, however > I only found charmm36 available now (I read, that c35r was only temporary). > I thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used > for the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it > seems to be designed for use with charmm rather than gromacs. > Is there a way to convert it for use with gromacs? Or is there another > definition I can use to work with my PEG? Or maybe c35r is still somewhere > around? > > I would be very grateful if someone could help me! > Simone > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 57 > ****************************************************** > From jalemkul at vt.edu Fri Apr 17 13:07:32 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 11:07:32 -0000 Subject: [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation In-Reply-To: References: Message-ID: <57a998f1-a14f-4c43-ea19-6782c1ec8946@vt.edu> On 4/17/20 12:15 AM, Adarsh V. K. wrote: > Dear all, > > A ligand molecule (lig) contains a Chlorine atom in it. While attempting to > performing a protein-ligand simulation, the Gromacs returns an error > message. It is observed that the > *CGenFF server * > Generate two additional lines, as shown below, in lig.str file > > ATOM LP1 LPH 0.050 ! on Cl1 > LONEPAIR COLI LP1 Cl1 C18 DIST 1.6400 SCAL 0.0 > > Which later add an additional line in ' lig.gro ' file generated using > > python cgenff_charmm2gmx.py LIG lig_fix.mol2 lig.str charmm36-mar2019.ff > gmx editconf -f lig_ini.pdb -o lig.gro > > at the later stages of simulation, the above 'LP1 lines' gives the > following error message > ----------------------------------------------------------------------------------------------------- > WARNING 1 [file topol.top, line 60334]: > You are using Ewald electrostatics in a system with net charge. This can > lead to severe artifacts, such as ions moving into regions with low > dielectric, due to the uniform background charge. We suggest to > neutralize your system with counter ions, possibly in combination with a > physiological salt concentration. > ------------------------------------------------------------------------------------------------------- > How to over come this problem while performing a simulation with a ligand > containing halogens like Chlorine? Do what the warning tells you and add neutralizing counterions. > 1) Delete Chlorine atom form the ligand molecule after an optimization with > Avogadro and before uploading to CGenFF Server ? Deleting atoms from the ligand is not a reasonable solution. It will only make your problem worse because it will leave you with an unphysical fractional charge. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 17 13:10:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 11:10:39 -0000 Subject: [gmx-users] atomtype "OE" in charmm36 In-Reply-To: <412999B95FB6894AAB9B6283E4C20DA126065042@XMBX3.uibk.ac.at> References: <412999B95FB6894AAB9B6283E4C20DA126065042@XMBX3.uibk.ac.at> Message-ID: <094e29ff-bfea-49d9-241f-99086ae84594@vt.edu> On 4/17/20 4:45 AM, Schirra, Simone wrote: > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my .itp and .gro files. The script is designed to work with charmm35r, however I only found charmm36 available now (I read, that c35r was only temporary). I thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used for the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it seems to be designed for use with charmm rather than gromacs. Which toppar file are you trying to use? > Is there a way to convert it for use with gromacs? Or is there another definition I can use to work with my PEG? Or maybe c35r is still somewhere around? C35r became C36 in official implementation. Likely the atom type just got renamed or assumed into an existing one, but without knowing which topology you're using, I can't comment. The PEO "toppar_ether" from Alex's site doesn't have anything called OE in it. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From Zuzana.Benkova at savba.sk Fri Apr 17 13:14:34 2020 From: Zuzana.Benkova at savba.sk (Zuzana Benkova) Date: Fri, 17 Apr 2020 11:14:34 -0000 Subject: [gmx-users] weird output from simultions of a protein between two sheets Message-ID: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> Dear Gromacs users, I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000. The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK. I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows 1GRA C1 1 0 0 0 1GRA C2 2 0 0 0 1GRA C3 3 0 0 0 1GRA C4 4 0 0 0 2GRA C1 5 0 0 0 2GRA C2 6 0 1 0 2GRA C3 7 0 1 0 2GRA C4 8 0 1 0 3GRA C1 9 0 1 0 3GRA C2 10 0 1 0 3GRA C3 11 0 1 0 3GRA C4 12 0 1 0 my mdp parameters are as follows integrator = md tinit = 0 dt = 0.001 nsteps = 100 comm-mode = None nstcomm = 0 comm-grps = freezegrps = Gra1 Gra2 freezedim = Y Y Y Y Y Y energygrps = Gra1 Gra2 Protein SOL NA ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy = 1 nstxout-compressed = 1 compressed-x-precision = 1 pbc = xyz periodic_molecules = yes cutoff-scheme = Verlet nstlist = 10 ns_type = grid verlet-buffer-tolerance = 0.005 rlist = 1.4 ;ignored with Verlet coulombtype = PME coulomb-modifier = None rcoulomb-switch = 1.1 rcoulomb = 1.3 vdw-type = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.3 DispCorr = EnerPres fourierspacing = 0.12 pme-order = 4 ewald-rtol = 1e-05 ewald-geometry = 3d Tcoupl = V-rescale nsttcouple = -1 tc-grps = Protein SOL_NA Gra1_Gra2 tau-t = 0.1 0.1 0.1 ref-t = 310 310 310 Pcoupl = no I have to note that I got the same output with no position restraints on protein. Do you have any idea what the problem is? Thank you in advance. Greetings Zuzana From dr_m_ganj at yahoo.com Fri Apr 17 13:45:23 2020 From: dr_m_ganj at yahoo.com (m g) Date: Fri, 17 Apr 2020 11:45:23 -0000 Subject: [gmx-users] position restrain of water References: <1601524880.1399838.1587123778973.ref@mail.yahoo.com> Message-ID: <1601524880.1399838.1587123778973@mail.yahoo.com> Dear All,?I want to restrain just my drug in product step in all of the simulation time. Hence, I used #define = -DPOSRES in the product.mdp file.In my topol.top file there is below lines: ; Include water topology#include "oplsaa.ff/spce.itp" #ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ];? i funct? ? ? ?fcx? ? ? ? fcy? ? ? ? fcz? ?1? ? 1? ? ? ?1000? ? ? ?1000? ? ? ?1000#endif In this case, are the water molecules also restrained? Must I delete the top lines? Thanks,Ganj From jalemkul at vt.edu Fri Apr 17 13:46:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 11:46:57 -0000 Subject: [gmx-users] position restrain of water In-Reply-To: <1601524880.1399838.1587123778973@mail.yahoo.com> References: <1601524880.1399838.1587123778973.ref@mail.yahoo.com> <1601524880.1399838.1587123778973@mail.yahoo.com> Message-ID: <54289e54-01ac-c143-6441-b0ae54841791@vt.edu> On 4/17/20 7:42 AM, m g wrote: > Dear All,?I want to restrain just my drug in product step in all of the simulation time. Hence, I used #define = -DPOSRES in the product.mdp file.In my topol.top file there is below lines: > ; Include water topology#include "oplsaa.ff/spce.itp" > #ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ];? i funct? ? ? ?fcx? ? ? ? fcy? ? ? ? fcz? ?1? ? 1? ? ? ?1000? ? ? ?1000? ? ? ?1000#endif > > In this case, are the water molecules also restrained? Must I delete the top lines? No, and no. Position restraints are conditional. You are not defining -DPOSRES_WATER, so those restraints are not employed. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 17 13:48:38 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 11:48:38 -0000 Subject: [gmx-users] weird output from simultions of a protein between two sheets In-Reply-To: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> Message-ID: <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> On 4/17/20 7:14 AM, Zuzana Benkova wrote: > Dear Gromacs users, > > I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000. > The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK. > I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows > > 1GRA C1 1 0 0 0 > 1GRA C2 2 0 0 0 > 1GRA C3 3 0 0 0 > 1GRA C4 4 0 0 0 > 2GRA C1 5 0 0 0 > 2GRA C2 6 0 1 0 > 2GRA C3 7 0 1 0 > 2GRA C4 8 0 1 0 > 3GRA C1 9 0 1 0 > 3GRA C2 10 0 1 0 > 3GRA C3 11 0 1 0 > 3GRA C4 12 0 1 0 Is this just in the final coordinate file? Are coordinates in the trajectory correct when visualized? > my mdp parameters are as follows > > integrator = md > tinit = 0 > dt = 0.001 > nsteps = 100 > comm-mode = None Are you sure you don't want to remove artificial contributions to COM motion? This is unusual for a periodic system. > nstcomm = 0 > comm-grps = > freezegrps = Gra1 Gra2 > freezedim = Y Y Y Y Y Y > energygrps = Gra1 Gra2 Protein SOL NA > ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1 > nstcalcenergy = 1 > nstenergy = 1 > nstxout-compressed = 1 > compressed-x-precision = 1 Saving output every step is unnecessary (because you will be skewing your statistics with completely correlated frames) and also will severely degrade the performance of your simulation. -Justin > pbc = xyz > periodic_molecules = yes > cutoff-scheme = Verlet > nstlist = 10 > ns_type = grid > verlet-buffer-tolerance = 0.005 > rlist = 1.4 ;ignored with Verlet > coulombtype = PME > coulomb-modifier = None > rcoulomb-switch = 1.1 > rcoulomb = 1.3 > vdw-type = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.3 > DispCorr = EnerPres > fourierspacing = 0.12 > pme-order = 4 > ewald-rtol = 1e-05 > ewald-geometry = 3d > Tcoupl = V-rescale > nsttcouple = -1 > tc-grps = Protein SOL_NA Gra1_Gra2 > tau-t = 0.1 0.1 0.1 > ref-t = 310 310 310 > Pcoupl = no > > > I have to note that I got the same output with no position restraints on protein. > > Do you have any idea what the problem is? > > Thank you in advance. > > Greetings > > Zuzana > > > > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From nt_mahmood at yahoo.com Fri Apr 17 14:07:08 2020 From: nt_mahmood at yahoo.com (Mahmood Naderan) Date: Fri, 17 Apr 2020 12:07:08 -0000 Subject: [gmx-users] Disabling MKL References: <1314707627.1382055.1587123896143.ref@mail.yahoo.com> Message-ID: <1314707627.1382055.1587123896143@mail.yahoo.com> Hi How can I disable MKL while building gromacs? With this configure command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on? -DGMX_FFT_LIBRARY=fftw3 I see -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2 -- Using external FFT library - FFTW3 build managed by GROMACS -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_thread.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.so;/opt/intel/lib/intel64/libguide.so;-lpthread;-lm;-ldl Then I get these errors [100%] Linking CXX executable ../../bin/gmx [100%] Linking CXX executable ../../bin/template /bin/ld: warning: libmkl_intel_lp64.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libmkl_intel_thread.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libmkl_core.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libguide.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) ../../lib/libgromacs.so.4.0.0: undefined reference to `ssteqr_' ../../lib/libgromacs.so.4.0.0: undefined reference to `dsteqr_' ../../lib/libgromacs.so.4.0.0: undefined reference to `sger_' Regards, Mahmood From nt_mahmood at yahoo.com Fri Apr 17 14:47:18 2020 From: nt_mahmood at yahoo.com (Mahmood Naderan) Date: Fri, 17 Apr 2020 12:47:18 -0000 Subject: [gmx-users] Disabling MKL References: <1314707627.1382055.1587123896143.ref@mail.yahoo.com> Message-ID: <1314707627.1382055.1587123896143@mail.yahoo.com> Hi How can I disable MKL while building gromacs? With this configure command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on? -DGMX_FFT_LIBRARY=fftw3 I see -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2 -- Using external FFT library - FFTW3 build managed by GROMACS -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_thread.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.so;/opt/intel/lib/intel64/libguide.so;-lpthread;-lm;-ldl Then I get these errors [100%] Linking CXX executable ../../bin/gmx [100%] Linking CXX executable ../../bin/template /bin/ld: warning: libmkl_intel_lp64.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libmkl_intel_thread.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libmkl_core.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) /bin/ld: warning: libguide.so, needed by ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) ../../lib/libgromacs.so.4.0.0: undefined reference to `ssteqr_' ../../lib/libgromacs.so.4.0.0: undefined reference to `dsteqr_' ../../lib/libgromacs.so.4.0.0: undefined reference to `sger_' Regards, Mahmood From Zuzana.Benkova at savba.sk Fri Apr 17 15:16:54 2020 From: Zuzana.Benkova at savba.sk (Zuzana Benkova) Date: Fri, 17 Apr 2020 13:16:54 -0000 Subject: [gmx-users] weird output from simultions of a protein between two sheets In-Reply-To: <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> Message-ID: <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> Dear Justin, thank you for your prompt response. I will answer your questions step by step. Is this just in the final coordinate file? Are coordinates in the trajectory correct when visualized? No, I converted all compressed trajectories to gro format and this outputs are identical in all trajectories. When I visualize the trajectory, I can see it as well. The atoms are placed in apices of boxes (1x1x1). Are you sure you don't want to remove artificial contributions to COM motion? This is unusual for a periodic system. I am not sure. If I leave the Linear option does the correction apply to all system even though I freeze the coordinates of graphene sheets? Anyway, I have just performed the same simulation with comm-mode = Linear and the problem persists. Saving output every step is unnecessary (because you will be skewing your statistics with completely correlated frames) and also will severely degrade the performance of your simulation. Thank you for this notification. I reduce the frequency when I do equilibration and production run. I do block averages. I have saved the data every step because I tried to trace the problem. Greetings Zuzana ----- Original Message ----- From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 17, 2020 1:48:28 PM Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets On 4/17/20 7:14 AM, Zuzana Benkova wrote: > Dear Gromacs users, > > I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000. > The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK. > I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows > > 1GRA C1 1 0 0 0 > 1GRA C2 2 0 0 0 > 1GRA C3 3 0 0 0 > 1GRA C4 4 0 0 0 > 2GRA C1 5 0 0 0 > 2GRA C2 6 0 1 0 > 2GRA C3 7 0 1 0 > 2GRA C4 8 0 1 0 > 3GRA C1 9 0 1 0 > 3GRA C2 10 0 1 0 > 3GRA C3 11 0 1 0 > 3GRA C4 12 0 1 0 Is this just in the final coordinate file? Are coordinates in the trajectory correct when visualized? > my mdp parameters are as follows > > integrator = md > tinit = 0 > dt = 0.001 > nsteps = 100 > comm-mode = None Are you sure you don't want to remove artificial contributions to COM motion? This is unusual for a periodic system. > nstcomm = 0 > comm-grps = > freezegrps = Gra1 Gra2 > freezedim = Y Y Y Y Y Y > energygrps = Gra1 Gra2 Protein SOL NA > ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1 > nstcalcenergy = 1 > nstenergy = 1 > nstxout-compressed = 1 > compressed-x-precision = 1 Saving output every step is unnecessary (because you will be skewing your statistics with completely correlated frames) and also will severely degrade the performance of your simulation. -Justin > pbc = xyz > periodic_molecules = yes > cutoff-scheme = Verlet > nstlist = 10 > ns_type = grid > verlet-buffer-tolerance = 0.005 > rlist = 1.4 ;ignored with Verlet > coulombtype = PME > coulomb-modifier = None > rcoulomb-switch = 1.1 > rcoulomb = 1.3 > vdw-type = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.3 > DispCorr = EnerPres > fourierspacing = 0.12 > pme-order = 4 > ewald-rtol = 1e-05 > ewald-geometry = 3d > Tcoupl = V-rescale > nsttcouple = -1 > tc-grps = Protein SOL_NA Gra1_Gra2 > tau-t = 0.1 0.1 0.1 > ref-t = 310 310 310 > Pcoupl = no > > > I have to note that I got the same output with no position restraints on protein. > > Do you have any idea what the problem is? > > Thank you in advance. > > Greetings > > Zuzana > > > > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From smithmd at ornl.gov Fri Apr 17 15:19:33 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Fri, 17 Apr 2020 13:19:33 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: , Message-ID: Gmx chi I believe gives the dihedral information. Distances can be obtained from gmx mindist -Micholas -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Yu Du Sent: Friday, April 17, 2020 5:32 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and dihedrals Hi Robert, Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. Cheers, Yu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Fri Apr 17 15:21:44 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 13:21:44 -0000 Subject: [gmx-users] weird output from simultions of a protein between two sheets In-Reply-To: <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> Message-ID: <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> On 4/17/20 9:16 AM, Zuzana Benkova wrote: > Dear Justin, > > thank you for your prompt response. I will answer your questions step by step. > > Is this just in the final coordinate file? Are coordinates in the > trajectory correct when visualized? > > No, I converted all compressed trajectories to gro format and this outputs are identical in all trajectories. When I visualize the trajectory, I can see it as well. The atoms are placed in apices of boxes (1x1x1). This is clearly a bug. Please report it on https://gitlab.com/groups/gromacs/-/issues and include a .tpr file. Freezing is, in any case, completely artificial and results in collisions that do not conserve energy. Try a stiff position restraint instead. > > Are you sure you don't want to remove artificial contributions to COM > motion? This is unusual for a periodic system. > > I am not sure. If I leave the Linear option does the correction apply to all system even though I freeze the coordinates of graphene sheets? Anyway, I have just performed the same simulation with comm-mode = Linear and the problem persists. The use of COM motion removal isn't directly related to your issue, but you should still treat it properly. -Justin > Saving output every step is unnecessary (because you will be skewing > your statistics with completely correlated frames) and also will > severely degrade the performance of your simulation. > > Thank you for this notification. I reduce the frequency when I do equilibration and production run. I do block averages. I have saved the data every step because I tried to trace the problem. > > Greetings > > Zuzana > > > > > ----- Original Message ----- > From: "Justin Lemkul" > To: "gmx-users" > Sent: Friday, April 17, 2020 1:48:28 PM > Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets > > On 4/17/20 7:14 AM, Zuzana Benkova wrote: >> Dear Gromacs users, >> >> I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000. >> The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK. >> I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows >> >> 1GRA C1 1 0 0 0 >> 1GRA C2 2 0 0 0 >> 1GRA C3 3 0 0 0 >> 1GRA C4 4 0 0 0 >> 2GRA C1 5 0 0 0 >> 2GRA C2 6 0 1 0 >> 2GRA C3 7 0 1 0 >> 2GRA C4 8 0 1 0 >> 3GRA C1 9 0 1 0 >> 3GRA C2 10 0 1 0 >> 3GRA C3 11 0 1 0 >> 3GRA C4 12 0 1 0 > Is this just in the final coordinate file? Are coordinates in the > trajectory correct when visualized? > >> my mdp parameters are as follows >> >> integrator = md >> tinit = 0 >> dt = 0.001 >> nsteps = 100 >> comm-mode = None > Are you sure you don't want to remove artificial contributions to COM > motion? This is unusual for a periodic system. > >> nstcomm = 0 >> comm-grps = >> freezegrps = Gra1 Gra2 >> freezedim = Y Y Y Y Y Y >> energygrps = Gra1 Gra2 Protein SOL NA >> ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2 >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1 >> nstcalcenergy = 1 >> nstenergy = 1 >> nstxout-compressed = 1 >> compressed-x-precision = 1 > Saving output every step is unnecessary (because you will be skewing > your statistics with completely correlated frames) and also will > severely degrade the performance of your simulation. > > -Justin > >> pbc = xyz >> periodic_molecules = yes >> cutoff-scheme = Verlet >> nstlist = 10 >> ns_type = grid >> verlet-buffer-tolerance = 0.005 >> rlist = 1.4 ;ignored with Verlet >> coulombtype = PME >> coulomb-modifier = None >> rcoulomb-switch = 1.1 >> rcoulomb = 1.3 >> vdw-type = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.3 >> DispCorr = EnerPres >> fourierspacing = 0.12 >> pme-order = 4 >> ewald-rtol = 1e-05 >> ewald-geometry = 3d >> Tcoupl = V-rescale >> nsttcouple = -1 >> tc-grps = Protein SOL_NA Gra1_Gra2 >> tau-t = 0.1 0.1 0.1 >> ref-t = 310 310 310 >> Pcoupl = no >> >> >> I have to note that I got the same output with no position restraints on protein. >> >> Do you have any idea what the problem is? >> >> Thank you in advance. >> >> Greetings >> >> Zuzana >> >> >> >> >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 17 15:23:27 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 13:23:27 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: Message-ID: On 4/17/20 9:19 AM, Smith, Micholas D. wrote: > Gmx chi I believe gives the dihedral information. Distances can be obtained from gmx mindist More generally, gmx angle or gangle are for angles and dihedrals (and gangle can calculate angles between planes and/or vectors as may be required here), gmx distance or gmx pairdist for bond lengths. -Justin > -Micholas > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Yu Du > Sent: Friday, April 17, 2020 5:32 AM > To: gmx-users at gromacs.org > Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and dihedrals > > Hi Robert, > > Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. > > Cheers, > Yu -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From robert.cordina at strath.ac.uk Fri Apr 17 15:26:50 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Fri, 17 Apr 2020 13:26:50 -0000 Subject: [gmx-users] Measuring bond distances, angles and dihedrals In-Reply-To: References: Message-ID: Thanks all, I'll investigate these options. Best regards, Robert -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: 17 April 2020 14:23 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Measuring bond distances, angles and dihedrals On 4/17/20 9:19 AM, Smith, Micholas D. wrote: > Gmx chi I believe gives the dihedral information. Distances can be > obtained from gmx mindist More generally, gmx angle or gangle are for angles and dihedrals (and gangle can calculate angles between planes and/or vectors as may be required here), gmx distance or gmx pairdist for bond lengths. -Justin > -Micholas > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of Yu Du > Sent: Friday, April 17, 2020 5:32 AM > To: gmx-users at gromacs.org > Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles > and dihedrals > > Hi Robert, > > Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. > > Cheers, > Yu -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com%2F&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C7945dc5276ec44866f4a08d7e2d29756%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637227266415604373&sdata=xLM1%2BrubIQgm2TkEU4awV0Zhv6IgKe19TcMKv%2F%2Fkqbc%3D&reserved=0 ================================================== -- Gromacs Users mailing list * Please search the archive at https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C7945dc5276ec44866f4a08d7e2d29756%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637227266415614368&sdata=YS7YeGoQtYBFOkM5gmp96F%2F8Hdd%2BfD1I%2BHhKmTthh9o%3D&reserved=0 before posting! * Can't post? Read https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C7945dc5276ec44866f4a08d7e2d29756%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637227266415614368&sdata=Xki6Ky%2B%2BpgySEnfyQutO2TmhNTBg1sIQP5wbEaIODLc%3D&reserved=0 * For (un)subscribe requests visit https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Crobert.cordina%40strath.ac.uk%7C7945dc5276ec44866f4a08d7e2d29756%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637227266415614368&sdata=VslM0lZ9scMLNnGqN9EpfSmn0Dz%2Bi9kZjqR7Gt0Oiow%3D&reserved=0 or send a mail to gmx-users-request at gromacs.org. From smithmd at ornl.gov Fri Apr 17 15:27:28 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Fri, 17 Apr 2020 13:27:28 -0000 Subject: [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals In-Reply-To: References: Message-ID: I had forgotten about gmx pairdist, thank you for the reminder Justin. Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology information, all of the bonds/angles/dihedral information is inferred, so make sure you are using your selections very carefully. -Micholas -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Friday, April 17, 2020 9:23 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and dihedrals On 4/17/20 9:19 AM, Smith, Micholas D. wrote: > Gmx chi I believe gives the dihedral information. Distances can be > obtained from gmx mindist More generally, gmx angle or gangle are for angles and dihedrals (and gangle can calculate angles between planes and/or vectors as may be required here), gmx distance or gmx pairdist for bond lengths. -Justin > -Micholas > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of Yu Du > Sent: Friday, April 17, 2020 5:32 AM > To: gmx-users at gromacs.org > Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles > and dihedrals > > Hi Robert, > > Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. The bond distances and angles between atom cluster centroids can definitely be extracted by VMD. But I don't know how to extract them using GROMACS. If your project is not so urgent, VMD is your choice. It is fairly flexible and can almost satisfy all your requirements. > > Cheers, > Yu -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From ydu-sci at outlook.com Fri Apr 17 16:01:42 2020 From: ydu-sci at outlook.com (Yu Du) Date: Fri, 17 Apr 2020 14:01:42 -0000 Subject: [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals In-Reply-To: References: , Message-ID: Hi Micholas, Also a word of warning for the original suggestion of using VMD. Two words of caution: 1) Be sure you unwrap your trajectories carefully before using vmd for the analysis (otherwise you may get odd 'spikes' in your distances due to the PBC), 2) Since vmd doesn't have any topology information, all of the bonds/angles/dihedral information is inferred, so make sure you are using your selections very carefully. Yes, I really omitted the versatile tools that GROMACS have provided and heavily relied on VMD. VMD indeed needs a careful preprocess of trajectories and selection of atom set for correct and reliable analysis. Thanks for your caveats. Yu From b.mijiddorj at gmail.com Fri Apr 17 16:21:26 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Fri, 17 Apr 2020 14:21:26 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: Dear GMX users, Hello, I performed MD simulation using gromacs 2018.7v. During this simulation, the calculation was stopped because of the electric cut. Then, I continued the simulation using "gmx mdrun with -noappend" in order to get separate trajectory for the safety of data. After that, I would like to concatenate the trr files. However, I received following error message. How, can I concatenate these trajectories. ********************************************** Program: gmx trjcat, version 2018.7 Source file: src/gromacs/fileio/trrio.cpp (line 114) Fatal error: Failed to find GROMACS magic number in trr frame header, so this is not a trr file! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ************************************************ Best regards, Mijiddorj From batdorj230 at yahoo.com Fri Apr 17 16:54:03 2020 From: batdorj230 at yahoo.com (Dorj Bat) Date: Fri, 17 Apr 2020 14:54:03 -0000 Subject: [gmx-users] Dramatic decrease NVE production References: <1124532024.2166424.1587133912492.ref@mail.yahoo.com> Message-ID: <1124532024.2166424.1587133912492@mail.yahoo.com> Dear users, I would like to perform MD simulations using NVE simulation and to check temperature increasing behavior while applying an E-field. However, I started a short 100 ps simulation. Initial velocity was generated around T=300K. However, the system temperature was rapidly decreased around at 230 K.? If you have any experience with this kind of situation, please advise me to handle the temperature without dramatic change during the simulation. Best regards, Bat From m.b.abdelaal at gmail.com Fri Apr 17 17:07:04 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Fri, 17 Apr 2020 15:07:04 -0000 Subject: [gmx-users] Does the energy minimization deals with velocity ? Message-ID: Hello everyone, If I will add the velocity manually to my system, should I add them before the energy minimization or after ? I will do the below steps: 1. insert molecules 2. energy minimization 3. NVT equilibiration 4. NPT equilibiration 5. production run. should I add the velocity before the NVT equilibiration step or before the energy minimization ? I am trying to reproduce the results of the below paper: Title: Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor Concentration Authors: Thomas Lee, ? Audrey Sanzogni, ? Ningxin Zhangzhou, ? Paul L. Burn,* ,?,? and Alan E. Mark* ,? Paragraph: All deposition simulations were performed using the GROMACS simulation package version 4.6. 27. During the deposition process, new molecules were inserted 2 nm from the top of the film every 10 ps with a random orientation and an initial velocity toward the surface to ensure they reach the growing film. The net velocity was randomly selected from a normal distribution with a mean of 0.05 nm ps ?1 and a standard deviation of square root ( k B T / m) where m is the mass of the molecule. Molecules that were more than 1 nm above the top of the film and moving away from the substrate (after having bounced on impact or sublimed from the surface) *were removed prior to the insertion of the next molecule.* The highlighted paragraph means that each inserted molecule had the time to move until it reaches the growing film before inserting the next molecule. I thought I can do that by doing energy minimization between single molecules insertion. But if the molecules will not move during the energy minimization then how can I allow each molecule to move to the growing molecule before inserting the next molecule ? Thanks, Mohamed From lamonteserincastanedo at gmail.com Fri Apr 17 17:49:13 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Fri, 17 Apr 2020 15:49:13 -0000 Subject: [gmx-users] about problem running script for Gibbs free energy simulation In-Reply-To: References: <9f792a76-7112-025a-b394-ced5c7580429@vt.edu> <476db20c-fbb7-9d15-4f89-3e10f4e45920@vt.edu> <15efcabf-2123-cd9a-6e2e-07145a06478b@vt.edu> Message-ID: Dear Dr. Lemkul I fix it. It works now. Thank you very much El jue., 16 de abr. de 2020 a la(s) 19:48, lazaro monteserin ( lamonteserincastanedo at gmail.com) escribi?: > Ah let me fix that and try again. I will let you know how it goes. Thank > you very much for all the help > > On Thu, Apr 16, 2020 at 4:23 PM Justin Lemkul wrote: > >> >> >> On 4/16/20 3:20 PM, lazaro monteserin wrote: >> > But how do I declare this in the script? >> > >> > I have try for example: >> > >> > FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then >> > MPD="/$FREE_ENERGY/mpd" >> > >> > Using the " " >> > >> > But stills it doesn't work. I have all my .mdp files stored in a >> directory >> > called "mdp" inside the directory "tutorial_gromacs". >> > >> > Am I making a syntax mistake here? >> >> No, but you've got a typo of "MPD" and "mpd" in place of "MDP" and "mdp" >> that is probably your issue. And you don't need the leading slash before >> $FREE_ENERGY in the definition of $MDP. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > From jalemkul at vt.edu Fri Apr 17 17:50:32 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 15:50:32 -0000 Subject: [gmx-users] Does the energy minimization deals with velocity ? In-Reply-To: References: Message-ID: <87429c9d-221c-4d5f-31d6-c1c85416eeab@vt.edu> On 4/17/20 11:06 AM, Mohamed Abdelaal wrote: > Hello everyone, > > If I will add the velocity manually to my system, should I add them before > the energy minimization or after ? > > I will do the below steps: > > 1. insert molecules > 2. energy minimization > 3. NVT equilibiration > 4. NPT equilibiration > 5. production run. > > should I add the velocity before the NVT equilibiration step or before the > energy minimization ? > > I am trying to reproduce the results of the below paper: > Title: Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor > Concentration > Authors: Thomas Lee, ? Audrey Sanzogni, ? Ningxin Zhangzhou, ? Paul L. > Burn,* ,?,? and Alan E. Mark* ,? > Paragraph: > All deposition simulations were performed using the GROMACS simulation > package version 4.6. 27. During the deposition process, new molecules were > inserted 2 nm from the top of the film every 10 ps with a random > orientation and an initial velocity toward the surface to ensure they reach > the growing film. The net velocity was randomly selected from a normal > distribution with a mean of 0.05 nm ps ?1 and a standard deviation of > square root ( k B T / m) where m is the mass of the molecule. Molecules > that were more than 1 nm above the top of the film and moving away from the > substrate (after having bounced on impact or sublimed from the surface) *were > removed prior to the insertion of the next molecule.* > > The highlighted paragraph means that each inserted molecule had the time to > move until it reaches the growing film before inserting the next molecule. > I thought I can do that by doing energy minimization between single > molecules insertion. But if the molecules will not move during the energy > minimization then how can I allow each molecule to move to the growing > molecule before inserting the next molecule ? Energy minimization is not a dynamical process. It is performed at 0 K and there are no velocities. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 17 17:51:10 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 15:51:10 -0000 Subject: [gmx-users] Dramatic decrease NVE production In-Reply-To: <1124532024.2166424.1587133912492@mail.yahoo.com> References: <1124532024.2166424.1587133912492.ref@mail.yahoo.com> <1124532024.2166424.1587133912492@mail.yahoo.com> Message-ID: <0c7dea8a-0602-2631-b9d3-65ecfb7c8d9c@vt.edu> On 4/17/20 10:31 AM, Dorj Bat wrote: > Dear users, > I would like to perform MD simulations using NVE simulation and to check temperature increasing behavior while applying an E-field. However, I started a short 100 ps simulation. Initial velocity was generated around T=300K. However, the system temperature was rapidly decreased around at 230 K. > If you have any experience with this kind of situation, please advise me to handle the temperature without dramatic change during the simulation. If you want to conserve temperature, that requires an NVT ensemble. Temperature can vary freely in an NVE simulation. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Fri Apr 17 17:51:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 15:51:35 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65@vt.edu> On 4/17/20 10:13 AM, Mijiddorj B wrote: > Dear GMX users, > > Hello, I performed MD simulation using gromacs 2018.7v. During this > simulation, the calculation was stopped because of the electric cut. Then, > I continued the simulation using "gmx mdrun with -noappend" in order to get > separate trajectory for the safety of data. After that, I would like to > concatenate the trr files. > However, I received following error message. > > How, can I concatenate these trajectories. > ********************************************** > Program: gmx trjcat, version 2018.7 > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > Fatal error: > Failed to find GROMACS magic number in trr frame header, so this is not a > trr > file! > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ************************************************ Your file is corrupted and you will have to run that portion of the simulation again. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Fri Apr 17 22:50:20 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Fri, 17 Apr 2020 20:50:20 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= Message-ID: Dear GROMACS user, I am aware that such error occurs frequently for new users as I am. I am learning how to add new residue in Gromacs; I tried first following a tutorial (https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) and later by creating a benzene, C6H6 molecule, using amber99.ff force field. Everything goes fine without any problems. For the next step I tried to create residue for a molecule, SnCl6, for which there are no parameters (just for training). Thus, within amber99.ff, I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ parameters for Sn (again for Cl there are already present). Finally I add in ffbonded.itp the parameters for bond stretch and angle (I calculated them by Gaussian and VFFDT software). I created *my .pdb file* as following: COMPND stannate REMARK 1 File created by GaussView 6.0.16 HETATM 1 Sn SnCl6 0 0.000 0.000 0.000 Sn HETATM 2 Cl1 SnCl6 0 -0.000 0.000 2.502 Cl HETATM 3 Cl2 SnCl6 0 -0.000 2.502 -0.000 Cl HETATM 4 Cl3 SnCl6 0 2.502 0.000 0.000 Cl HETATM 5 Cl4 SnCl6 0 -0.000 -2.502 0.000 Cl HETATM 6 Cl5 SnCl6 0 -2.502 0.000 -0.000 Cl HETATM 7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 Cl END CONECT 1 2 3 4 5 CONECT 1 6 7 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 CONECT 6 1 CONECT 7 1 and *the .rtp file* which I add in the amber99.ff folder: [ SnCl6 ] [ atoms ] Sn Sn 1.2468 1 Cl1 Cl -0.5411 2 Cl2 Cl -0.5411 3 Cl3 Cl -0.5411 4 Cl4 Cl -0.5411 5 Cl5 Cl -0.5411 6 Cl6 Cl -0.5411 7 [ bonds ] Sn Cl1 Sn Cl2 Sn Cl3 Sn Cl4 Sn Cl5 Sn Cl6 However, although to my eyes I did everything OK, I get such error. *Please, can somebody help me to figure out where I am doing wrong? * Thanks a lot in advance. Paolo Costa -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Fri Apr 17 22:54:11 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 17 Apr 2020 20:54:11 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: References: Message-ID: On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa wrote: > Dear GROMACS user, > > I am aware that such error occurs frequently for new users as I am. > I am learning how to add new residue in Gromacs; I tried first following a > tutorial ( > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) > and later by creating a benzene, C6H6 molecule, using amber99.ff force > field. Everything goes fine without any problems. > > For the next step I tried to create residue for a molecule, SnCl6, for > which there are no parameters (just for training). Thus, within amber99.ff, > I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ > parameters for Sn (again for Cl there are already present). Finally I add > in ffbonded.itp the parameters for bond stretch and angle (I calculated > them by Gaussian and VFFDT software). > > I created *my .pdb file* as following: > COMPND stannate > REMARK 1 File created by GaussView 6.0.16 > HETATM 1 Sn SnCl6 0 0.000 0.000 0.000 > Sn > HETATM 2 Cl1 SnCl6 0 -0.000 0.000 2.502 > Cl > HETATM 3 Cl2 SnCl6 0 -0.000 2.502 -0.000 > Cl > HETATM 4 Cl3 SnCl6 0 2.502 0.000 0.000 > Cl > HETATM 5 Cl4 SnCl6 0 -0.000 -2.502 0.000 > Cl > HETATM 6 Cl5 SnCl6 0 -2.502 0.000 -0.000 > Cl > HETATM 7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 > Cl > END > CONECT 1 2 3 4 5 > CONECT 1 6 7 > CONECT 2 1 > CONECT 3 1 > CONECT 4 1 > CONECT 5 1 > CONECT 6 1 > CONECT 7 1 > > > and *the .rtp file* which I add in the amber99.ff folder: > [ SnCl6 ] > [ atoms ] > Sn Sn 1.2468 1 > Cl1 Cl -0.5411 2 > Cl2 Cl -0.5411 3 > Cl3 Cl -0.5411 4 > Cl4 Cl -0.5411 5 > Cl5 Cl -0.5411 6 > Cl6 Cl -0.5411 7 > [ bonds ] > Sn Cl1 > Sn Cl2 > Sn Cl3 > Sn Cl4 > Sn Cl5 > Sn Cl6 > > However, although to my eyes I did everything OK, I get such error. > *Please, can somebody help me to figure out where I am doing wrong? * > PDB format only allows 4 characters in a residue name. Rename to something else (in the correct columns of the fixed format) and if that doesn?t fix it, please provide the full screen output from pdb2gmx. -Justin > Thanks a lot in advance. > > Paolo Costa > > -- > Paolo Costa, Ph.D. > Postdoctoral Researcher > Department of Chemistry and Biomolecular Sciences > University of Ottawa > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada > Room number: DRO 326 (D'Iorio Hall) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- ========================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ========================================== From ali.khodayari at student.kuleuven.be Fri Apr 17 23:14:49 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Fri, 17 Apr 2020 21:14:49 -0000 Subject: [gmx-users] Installation on iPad? Message-ID: <5459C9F3-47DA-4C90-8BDA-58A7E6ACF605@student.kuleuven.be> Dears, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you?ll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali From paolo.costa85 at gmail.com Fri Apr 17 23:25:52 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Fri, 17 Apr 2020 21:25:52 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: References: Message-ID: Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b Reading stannate.pdb... WARNING: all CONECT records are ignored Read 'stannate', 7 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp Atomtype 68 Reading residue database... (amber99) Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp Residue 94 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp Residue 127 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.19# Processing chain 1 (7 atoms, 1 residues) Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add SnC to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully ------------------------------------------------------- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) Fatal error: Residue 'SnC' not found in residue topology database *Thanks a lot for helping!* Paolo Il giorno ven 17 apr 2020 alle ore 22:55 Justin Lemkul ha scritto: > On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa > wrote: > > > Dear GROMACS user, > > > > I am aware that such error occurs frequently for new users as I am. > > I am learning how to add new residue in Gromacs; I tried first following > a > > tutorial ( > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) > > and later by creating a benzene, C6H6 molecule, using amber99.ff force > > field. Everything goes fine without any problems. > > > > For the next step I tried to create residue for a molecule, SnCl6, for > > which there are no parameters (just for training). Thus, within > amber99.ff, > > I add in the atomtypes.atp the atom Sn with the corresponding mass (the > Cl > > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ > > parameters for Sn (again for Cl there are already present). Finally I add > > in ffbonded.itp the parameters for bond stretch and angle (I calculated > > them by Gaussian and VFFDT software). > > > > I created *my .pdb file* as following: > > COMPND stannate > > REMARK 1 File created by GaussView 6.0.16 > > HETATM 1 Sn SnCl6 0 0.000 0.000 0.000 > > Sn > > HETATM 2 Cl1 SnCl6 0 -0.000 0.000 2.502 > > Cl > > HETATM 3 Cl2 SnCl6 0 -0.000 2.502 -0.000 > > Cl > > HETATM 4 Cl3 SnCl6 0 2.502 0.000 0.000 > > Cl > > HETATM 5 Cl4 SnCl6 0 -0.000 -2.502 0.000 > > Cl > > HETATM 6 Cl5 SnCl6 0 -2.502 0.000 -0.000 > > Cl > > HETATM 7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 > > Cl > > END > > CONECT 1 2 3 4 5 > > CONECT 1 6 7 > > CONECT 2 1 > > CONECT 3 1 > > CONECT 4 1 > > CONECT 5 1 > > CONECT 6 1 > > CONECT 7 1 > > > > > > and *the .rtp file* which I add in the amber99.ff folder: > > [ SnCl6 ] > > [ atoms ] > > Sn Sn 1.2468 1 > > Cl1 Cl -0.5411 2 > > Cl2 Cl -0.5411 3 > > Cl3 Cl -0.5411 4 > > Cl4 Cl -0.5411 5 > > Cl5 Cl -0.5411 6 > > Cl6 Cl -0.5411 7 > > [ bonds ] > > Sn Cl1 > > Sn Cl2 > > Sn Cl3 > > Sn Cl4 > > Sn Cl5 > > Sn Cl6 > > > > However, although to my eyes I did everything OK, I get such error. > > *Please, can somebody help me to figure out where I am doing wrong? * > > > > PDB format only allows 4 characters in a residue name. Rename to something > else (in the correct columns of the fixed format) and if that doesn?t fix > it, please provide the full screen output from pdb2gmx. > > -Justin > > > > Thanks a lot in advance. > > > > Paolo Costa > > > > -- > > Paolo Costa, Ph.D. > > Postdoctoral Researcher > > Department of Chemistry and Biomolecular Sciences > > University of Ottawa > > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada > > Room number: DRO 326 (D'Iorio Hall) > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > > ========================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From Zuzana.Benkova at savba.sk Sat Apr 18 00:04:23 2020 From: Zuzana.Benkova at savba.sk (Zuzana Benkova) Date: Fri, 17 Apr 2020 22:04:23 -0000 Subject: [gmx-users] weird output from simultions of a protein between two sheets In-Reply-To: <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> Message-ID: <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Dear Justin, thank you for your time. In fact, I checked the coordinates and energy values in more details. It seems that the simulation is running as it should according to the mdp parameters as the energy values indicates. The integer numbers are the rounds of real coordinates. Maybe, there is some wrong declaration of the corresponding variables in the source code. I will report it on https://gitlab.com/groups/gromacs/-/issues Greetings Zuzana ----- Original Message ----- From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 17, 2020 3:21:33 PM Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets On 4/17/20 9:16 AM, Zuzana Benkova wrote: > Dear Justin, > > thank you for your prompt response. I will answer your questions step by step. > > Is this just in the final coordinate file? Are coordinates in the > trajectory correct when visualized? > > No, I converted all compressed trajectories to gro format and this outputs are identical in all trajectories. When I visualize the trajectory, I can see it as well. The atoms are placed in apices of boxes (1x1x1). This is clearly a bug. Please report it on https://gitlab.com/groups/gromacs/-/issues and include a .tpr file. Freezing is, in any case, completely artificial and results in collisions that do not conserve energy. Try a stiff position restraint instead. > > Are you sure you don't want to remove artificial contributions to COM > motion? This is unusual for a periodic system. > > I am not sure. If I leave the Linear option does the correction apply to all system even though I freeze the coordinates of graphene sheets? Anyway, I have just performed the same simulation with comm-mode = Linear and the problem persists. The use of COM motion removal isn't directly related to your issue, but you should still treat it properly. -Justin > Saving output every step is unnecessary (because you will be skewing > your statistics with completely correlated frames) and also will > severely degrade the performance of your simulation. > > Thank you for this notification. I reduce the frequency when I do equilibration and production run. I do block averages. I have saved the data every step because I tried to trace the problem. > > Greetings > > Zuzana > > > > > ----- Original Message ----- > From: "Justin Lemkul" > To: "gmx-users" > Sent: Friday, April 17, 2020 1:48:28 PM > Subject: Re: [gmx-users] weird output from simultions of a protein between two sheets > > On 4/17/20 7:14 AM, Zuzana Benkova wrote: >> Dear Gromacs users, >> >> I want to simulate a protein between two graphene sheets separated by 21 nm. The system is solvated and placed in the cell of dimensions 17.09360 17.18200 25.00000. >> The energy minimzation of this system with position restrain applied to protein and frozen carbon atoms ran OK. >> I continued with short simulations in an NVT ensemble with position restrains applied to protein. My output coordinates for all atoms of the systems were integers. Small fragment of a selected frame of the output is as follows >> >> 1GRA C1 1 0 0 0 >> 1GRA C2 2 0 0 0 >> 1GRA C3 3 0 0 0 >> 1GRA C4 4 0 0 0 >> 2GRA C1 5 0 0 0 >> 2GRA C2 6 0 1 0 >> 2GRA C3 7 0 1 0 >> 2GRA C4 8 0 1 0 >> 3GRA C1 9 0 1 0 >> 3GRA C2 10 0 1 0 >> 3GRA C3 11 0 1 0 >> 3GRA C4 12 0 1 0 > Is this just in the final coordinate file? Are coordinates in the > trajectory correct when visualized? > >> my mdp parameters are as follows >> >> integrator = md >> tinit = 0 >> dt = 0.001 >> nsteps = 100 >> comm-mode = None > Are you sure you don't want to remove artificial contributions to COM > motion? This is unusual for a periodic system. > >> nstcomm = 0 >> comm-grps = >> freezegrps = Gra1 Gra2 >> freezedim = Y Y Y Y Y Y >> energygrps = Gra1 Gra2 Protein SOL NA >> ;energygrp-excl = Gra1 Gra1 Gra2 Gra2 Gra1 Gra2 >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1 >> nstcalcenergy = 1 >> nstenergy = 1 >> nstxout-compressed = 1 >> compressed-x-precision = 1 > Saving output every step is unnecessary (because you will be skewing > your statistics with completely correlated frames) and also will > severely degrade the performance of your simulation. > > -Justin > >> pbc = xyz >> periodic_molecules = yes >> cutoff-scheme = Verlet >> nstlist = 10 >> ns_type = grid >> verlet-buffer-tolerance = 0.005 >> rlist = 1.4 ;ignored with Verlet >> coulombtype = PME >> coulomb-modifier = None >> rcoulomb-switch = 1.1 >> rcoulomb = 1.3 >> vdw-type = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.3 >> DispCorr = EnerPres >> fourierspacing = 0.12 >> pme-order = 4 >> ewald-rtol = 1e-05 >> ewald-geometry = 3d >> Tcoupl = V-rescale >> nsttcouple = -1 >> tc-grps = Protein SOL_NA Gra1_Gra2 >> tau-t = 0.1 0.1 0.1 >> ref-t = 310 310 310 >> Pcoupl = no >> >> >> I have to note that I got the same output with no position restraints on protein. >> >> Do you have any idea what the problem is? >> >> Thank you in advance. >> >> Greetings >> >> Zuzana >> >> >> >> >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From nedomacho at gmail.com Sat Apr 18 00:16:13 2020 From: nedomacho at gmail.com (Alex) Date: Fri, 17 Apr 2020 22:16:13 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: Hello all, Hope you're staying safe & healthy! We are starting to spec new machines and our end goal is two machines, each featuring: 1. ~16-18 CPU cores w/hyperthreading 2. Four GPUs 3. ~256 gigs of RAM. A very approximate allocation of money is ~$15-20K per unit, but we could of course buy more if each machine turns out to be significantly cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are welcome. We are somewhat open to AMD-based solutions, but wonder what the situation is with GPU acceleration, as so far we've been entirely Intel-based. Will it work with NVIDIA cards? Will we have to install AMD GPUs? Does current Gromacs perform well on AMD-based rigs? Thank you! Alex From fnabi at myamu.ac.in Sat Apr 18 01:17:29 2020 From: fnabi at myamu.ac.in (FAISAL NABI) Date: Fri, 17 Apr 2020 23:17:29 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: Gromacs is totally compatible with nvidia based gpu. You need to install cuda drivers and you can build easily with cmake. For amd gpu you would be needing openCL alongwith the sdk for amd gpu. I would suggest you to use nvidia acceleration for better performance. On Sat, Apr 18, 2020, 4:42 AM Alex wrote: > Hello all, > > Hope you're staying safe & healthy! We are starting to spec new machines > and our end goal is two machines, each featuring: > > 1. ~16-18 CPU cores w/hyperthreading > > 2. Four GPUs > > 3. ~256 gigs of RAM. > > A very approximate allocation of money is ~$15-20K per unit, but we > could of course buy more if each machine turns out to be significantly > cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are > welcome. We are somewhat open to AMD-based solutions, but wonder what > the situation is with GPU acceleration, as so far we've been entirely > Intel-based. Will it work with NVIDIA cards? Will we have to install AMD > GPUs? Does current Gromacs perform well on AMD-based rigs? > > Thank you! > > Alex > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From kevin.boyd at uconn.edu Sat Apr 18 02:29:22 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 18 Apr 2020 00:29:22 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: Hi, AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base regardless of the GPUs you end up choosing. In my experience AMD CPUs have had great value. A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very much overkill, but perhaps you have other uses for the machine that need it. Have you seen the updated "More bang for your buck" paper that goes into optimizing compute nodes? See On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: > *Message sent from a system outside of UConn.* > > > Gromacs is totally compatible with nvidia based gpu. You need to install > cuda drivers and you can build easily with cmake. For amd gpu you would be > needing openCL alongwith the sdk for amd gpu. I would suggest you to use > nvidia acceleration for better performance. > > On Sat, Apr 18, 2020, 4:42 AM Alex wrote: > > > Hello all, > > > > Hope you're staying safe & healthy! We are starting to spec new machines > > and our end goal is two machines, each featuring: > > > > 1. ~16-18 CPU cores w/hyperthreading > > > > 2. Four GPUs > > > > 3. ~256 gigs of RAM. > > > > A very approximate allocation of money is ~$15-20K per unit, but we > > could of course buy more if each machine turns out to be significantly > > cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are > > welcome. We are somewhat open to AMD-based solutions, but wonder what > > the situation is with GPU acceleration, as so far we've been entirely > > Intel-based. Will it work with NVIDIA cards? Will we have to install AMD > > GPUs? Does current Gromacs perform well on AMD-based rigs? > > > > Thank you! > > > > Alex > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nedomacho at gmail.com Sat Apr 18 02:58:27 2020 From: nedomacho at gmail.com (Alex) Date: Sat, 18 Apr 2020 00:58:27 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: Hi Kevin, Thanks for responding! RAM is mentioned for completeness. This amount is not for gmx -- we do other, much more RAM-intensive calculations, in fact 256 gigs is very modest for that. I have no doubt that AMD CPUs would work with Nvidia GPUs, was mainly wondering if there would be any additional speed boost if we also used AMD GPUs. Nope, haven't seen the paper, but quite interested in checking it out. Is this the latest version? https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 Thank you, Alex On 4/17/2020 6:29 PM, Kevin Boyd wrote: > Hi, > > AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base > regardless of the GPUs you end up choosing. In my experience AMD CPUs have > had great value. > > A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very much > overkill, but perhaps you have other uses for the machine that need it. > > Have you seen the updated "More bang for your buck" paper that goes into > optimizing compute nodes? > > > See > > > > On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: > >> *Message sent from a system outside of UConn.* >> >> >> Gromacs is totally compatible with nvidia based gpu. You need to install >> cuda drivers and you can build easily with cmake. For amd gpu you would be >> needing openCL alongwith the sdk for amd gpu. I would suggest you to use >> nvidia acceleration for better performance. >> >> On Sat, Apr 18, 2020, 4:42 AM Alex wrote: >> >>> Hello all, >>> >>> Hope you're staying safe & healthy! We are starting to spec new machines >>> and our end goal is two machines, each featuring: >>> >>> 1. ~16-18 CPU cores w/hyperthreading >>> >>> 2. Four GPUs >>> >>> 3. ~256 gigs of RAM. >>> >>> A very approximate allocation of money is ~$15-20K per unit, but we >>> could of course buy more if each machine turns out to be significantly >>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are >>> welcome. We are somewhat open to AMD-based solutions, but wonder what >>> the situation is with GPU acceleration, as so far we've been entirely >>> Intel-based. Will it work with NVIDIA cards? Will we have to install AMD >>> GPUs? Does current Gromacs perform well on AMD-based rigs? >>> >>> Thank you! >>> >>> Alex >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From kevin.boyd at uconn.edu Sat Apr 18 04:58:58 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 18 Apr 2020 02:58:58 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: Yes, that's it. I think consumer-class Nvidia cards are still the best value, unless you have other applications that need the benefits of industrial cards. Cheers, Kevin On Fri, Apr 17, 2020 at 5:58 PM Alex wrote: > *Message sent from a system outside of UConn.* > > > Hi Kevin, > > Thanks for responding! RAM is mentioned for completeness. This amount is > not for gmx -- we do other, much more RAM-intensive calculations, in > fact 256 gigs is very modest for that. I have no doubt that AMD CPUs > would work with Nvidia GPUs, was mainly wondering if there would be any > additional speed boost if we also used AMD GPUs. > > Nope, haven't seen the paper, but quite interested in checking it out. > Is this the latest version? > https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 > > Thank you, > > Alex > > On 4/17/2020 6:29 PM, Kevin Boyd wrote: > > Hi, > > > > AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base > > regardless of the GPUs you end up choosing. In my experience AMD CPUs > have > > had great value. > > > > A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very > much > > overkill, but perhaps you have other uses for the machine that need it. > > > > Have you seen the updated "More bang for your buck" paper that goes into > > optimizing compute nodes? > > > > > > See > > > > > > > > On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: > > > >> *Message sent from a system outside of UConn.* > >> > >> > >> Gromacs is totally compatible with nvidia based gpu. You need to install > >> cuda drivers and you can build easily with cmake. For amd gpu you would > be > >> needing openCL alongwith the sdk for amd gpu. I would suggest you to use > >> nvidia acceleration for better performance. > >> > >> On Sat, Apr 18, 2020, 4:42 AM Alex wrote: > >> > >>> Hello all, > >>> > >>> Hope you're staying safe & healthy! We are starting to spec new > machines > >>> and our end goal is two machines, each featuring: > >>> > >>> 1. ~16-18 CPU cores w/hyperthreading > >>> > >>> 2. Four GPUs > >>> > >>> 3. ~256 gigs of RAM. > >>> > >>> A very approximate allocation of money is ~$15-20K per unit, but we > >>> could of course buy more if each machine turns out to be significantly > >>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are > >>> welcome. We are somewhat open to AMD-based solutions, but wonder what > >>> the situation is with GPU acceleration, as so far we've been entirely > >>> Intel-based. Will it work with NVIDIA cards? Will we have to install > AMD > >>> GPUs? Does current Gromacs perform well on AMD-based rigs? > >>> > >>> Thank you! > >>> > >>> Alex > >>> > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-request at gromacs.org. > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nedomacho at gmail.com Sat Apr 18 07:56:26 2020 From: nedomacho at gmail.com (Alex) Date: Sat, 18 Apr 2020 05:56:26 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> Message-ID: <9bc1b76d-5a4b-78f4-eff1-dfd2a4bbf73f@gmail.com> From what I am seeing in this paper, we should just go with something along the lines of Ryzen 1950x + 4 x 2080 or 2080Ti. There are indications that Ryzen also rips (pun intended) Xeons in DFT/CC calculations, so overall this combination sounds quite reasonable for our purposes. This also outlines a path towards upgrading our existing nodes. Thanks Kevin, this is very informative. Alex On 4/17/2020 8:52 PM, Kevin Boyd wrote: > Yes, that's it. I think consumer-class Nvidia cards are still the best > value, unless you have other applications that need the benefits of > industrial cards. > > Cheers, > > Kevin > > On Fri, Apr 17, 2020 at 5:58 PM Alex wrote: > >> *Message sent from a system outside of UConn.* >> >> >> Hi Kevin, >> >> Thanks for responding! RAM is mentioned for completeness. This amount is >> not for gmx -- we do other, much more RAM-intensive calculations, in >> fact 256 gigs is very modest for that. I have no doubt that AMD CPUs >> would work with Nvidia GPUs, was mainly wondering if there would be any >> additional speed boost if we also used AMD GPUs. >> >> Nope, haven't seen the paper, but quite interested in checking it out. >> Is this the latest version? >> https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 >> >> Thank you, >> >> Alex >> >> On 4/17/2020 6:29 PM, Kevin Boyd wrote: >>> Hi, >>> >>> AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base >>> regardless of the GPUs you end up choosing. In my experience AMD CPUs >> have >>> had great value. >>> >>> A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very >> much >>> overkill, but perhaps you have other uses for the machine that need it. >>> >>> Have you seen the updated "More bang for your buck" paper that goes into >>> optimizing compute nodes? >>> >>> >>> See >>> >>> >>> >>> On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: >>> >>>> *Message sent from a system outside of UConn.* >>>> >>>> >>>> Gromacs is totally compatible with nvidia based gpu. You need to install >>>> cuda drivers and you can build easily with cmake. For amd gpu you would >> be >>>> needing openCL alongwith the sdk for amd gpu. I would suggest you to use >>>> nvidia acceleration for better performance. >>>> >>>> On Sat, Apr 18, 2020, 4:42 AM Alex wrote: >>>> >>>>> Hello all, >>>>> >>>>> Hope you're staying safe & healthy! We are starting to spec new >> machines >>>>> and our end goal is two machines, each featuring: >>>>> >>>>> 1. ~16-18 CPU cores w/hyperthreading >>>>> >>>>> 2. Four GPUs >>>>> >>>>> 3. ~256 gigs of RAM. >>>>> >>>>> A very approximate allocation of money is ~$15-20K per unit, but we >>>>> could of course buy more if each machine turns out to be significantly >>>>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are >>>>> welcome. We are somewhat open to AMD-based solutions, but wonder what >>>>> the situation is with GPU acceleration, as so far we've been entirely >>>>> Intel-based. Will it work with NVIDIA cards? Will we have to install >> AMD >>>>> GPUs? Does current Gromacs perform well on AMD-based rigs? >>>>> >>>>> Thank you! >>>>> >>>>> Alex >>>>> >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-request at gromacs.org. >>>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From sranjan at iiserb.ac.in Sat Apr 18 10:43:44 2020 From: sranjan at iiserb.ac.in (Shashank Ranjan Srivastava) Date: Sat, 18 Apr 2020 08:43:44 -0000 Subject: [gmx-users] Regarding use of harmonic wall model Message-ID: Hello everyone, I want to create a gap between the first and last strand of a beta barrel so that I can put a new strand in between. So, I have generated an input file using charmm-gui and using its gromacs production file (production.mdp) to run the simulation. I want to use a harmonic wall model to disrupt the bonding between the first and last strand of the beta barrel but not getting how to do it . I have asked it before as well but I did not get any suggestion. Please kindly help me with this query if anybody has any idea regarding this. Thank you, -- Shashank Ranjan Srivastava Molecular Biophysics Laboratory Department of Biological Sciences, IISER-Bhopal, Madhya Pradesh From b.mijiddorj at gmail.com Sat Apr 18 11:46:00 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Sat, 18 Apr 2020 09:46:00 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: Dear Justin, Thank you very much for your reply. I see. However, I have one more question. Is it caused by usage of -noappend or other reasons? Best regards, Mijiddorj --------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Apr 2020 11:51:25 -0400 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > frame header > Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 4/17/20 10:13 AM, Mijiddorj B wrote: > > Dear GMX users, > > > > Hello, I performed MD simulation using gromacs 2018.7v. During this > > simulation, the calculation was stopped because of the electric cut. > Then, > > I continued the simulation using "gmx mdrun with -noappend" in order to > get > > separate trajectory for the safety of data. After that, I would like to > > concatenate the trr files. > > However, I received following error message. > > > > How, can I concatenate these trajectories. > > ********************************************** > > Program: gmx trjcat, version 2018.7 > > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > > > Fatal error: > > Failed to find GROMACS magic number in trr frame header, so this is not a > > trr > > file! > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ************************************************ > > Your file is corrupted and you will have to run that portion of the > simulation again. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > From mark.j.abraham at gmail.com Sat Apr 18 14:36:51 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 18 Apr 2020 12:36:51 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: Hi, No, some kind of breakage, e.g. a filesystem disappeared, or a file transfer was incomplete or the file was edited with some inappropriate tool. Mark On Sat, 18 Apr 2020 at 11:46, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. However, I have one more > question. Is it caused by usage of -noappend or other reasons? > > Best regards, > > Mijiddorj > > --------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 17 Apr 2020 11:51:25 -0400 > > From: Justin Lemkul > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > > frame header > > Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu> > > Content-Type: text/plain; charset=utf-8; format=flowed > > > > > > > > On 4/17/20 10:13 AM, Mijiddorj B wrote: > > > Dear GMX users, > > > > > > Hello, I performed MD simulation using gromacs 2018.7v. During this > > > simulation, the calculation was stopped because of the electric cut. > > Then, > > > I continued the simulation using "gmx mdrun with -noappend" in order to > > get > > > separate trajectory for the safety of data. After that, I would like to > > > concatenate the trr files. > > > However, I received following error message. > > > > > > How, can I concatenate these trajectories. > > > ********************************************** > > > Program: gmx trjcat, version 2018.7 > > > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > > > > > Fatal error: > > > Failed to find GROMACS magic number in trr frame header, so this is > not a > > > trr > > > file! > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > ************************************************ > > > > Your file is corrupted and you will have to run that portion of the > > simulation again. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From mark.j.abraham at gmail.com Sat Apr 18 14:36:51 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 18 Apr 2020 12:36:51 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: Hi, No, some kind of breakage, e.g. a filesystem disappeared, or a file transfer was incomplete or the file was edited with some inappropriate tool. Mark On Sat, 18 Apr 2020 at 11:46, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. However, I have one more > question. Is it caused by usage of -noappend or other reasons? > > Best regards, > > Mijiddorj > > --------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 17 Apr 2020 11:51:25 -0400 > > From: Justin Lemkul > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > > frame header > > Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu> > > Content-Type: text/plain; charset=utf-8; format=flowed > > > > > > > > On 4/17/20 10:13 AM, Mijiddorj B wrote: > > > Dear GMX users, > > > > > > Hello, I performed MD simulation using gromacs 2018.7v. During this > > > simulation, the calculation was stopped because of the electric cut. > > Then, > > > I continued the simulation using "gmx mdrun with -noappend" in order to > > get > > > separate trajectory for the safety of data. After that, I would like to > > > concatenate the trr files. > > > However, I received following error message. > > > > > > How, can I concatenate these trajectories. > > > ********************************************** > > > Program: gmx trjcat, version 2018.7 > > > Source file: src/gromacs/fileio/trrio.cpp (line 114) > > > > > > Fatal error: > > > Failed to find GROMACS magic number in trr frame header, so this is > not a > > > trr > > > file! > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > ************************************************ > > > > Your file is corrupted and you will have to run that portion of the > > simulation again. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From ali.khodayari at student.kuleuven.be Sat Apr 18 14:44:11 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Sat, 18 Apr 2020 12:44:11 -0000 Subject: [gmx-users] Installation on iPad Message-ID: <014a01d6157f$0762be70$16283b50$@student.kuleuven.be> Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali From alexanderwien2k at gmail.com Sat Apr 18 20:13:14 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sat, 18 Apr 2020 18:13:14 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com Message-ID: Dear all, To generate the initial configurations for umbrella sampling, I conducted a simple pulling simulation by which a single-small molecule (mol_A) is being dragged along -Z from water into the body of a thin film. Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and "pull-group1-pbcatom = -1"* which cause a net shifting of the system along the pulling direction as soon as the mol_A reach to the thin film, please find below the pulling flags movie and plot in below links. Centering the thin film and mol_A could solve the issue, (echo 1 0 | trjconv -center yes) to some extent but still COM changes in the early stage below 2ns. , COM: https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 Movie in which the water molecules are hidden: https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv - gmx version 2020.1 ----- pull = yes pull-print-com = no pull-print-ref-value = yes pull-print-components = Yes pull-nstxout = 1000 pull-nstfout = 1000 pull-pbc-ref-prev-step-com = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Thin-film pull-group1-pbcatom = -1 pull-group2-name = mol_A pull-group2-pbcatom = 0 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-groups = 1 2 pull-coord1-dim = N N Y pull-coord1-origin = 0.0 0.0 0.0 pull-coord1-vec = 0.0 0.0 -1.0 pull-coord1-start = yes pull-coord1-init = 0 pull-coord1-rate = 0.0005 pull-coord1-k = 5000 ----- I wonder if I could extract correct initial configuration from this trajectory? With correct initial configuration, I mean a set of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? Thank you Alex From sinaomrani96 at gmail.com Sat Apr 18 20:33:06 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Sat, 18 Apr 2020 18:33:06 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) Message-ID: Hi, I am trying to post-processing my results and calculate MSD (mean square displacement) but my answer is different from the MSD value that GROMACS calculated. I use trjconv command and use the output .gro file. I tried to understand the GROMACS code but I am not a good programmer. Is there any specific detail except the Einstein relation in the manual? sorry if here is not the right place to ask this question. Best regards. Sina Omrani. From askforarun at gmail.com Sat Apr 18 20:59:52 2020 From: askforarun at gmail.com (Arun Srikanth) Date: Sat, 18 Apr 2020 18:59:52 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: Unless you give you give details how you calculate the MSD it will not be possible to help. Are you using unwrapped co-ordinates in your calculations for MSD? Arun On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote: > Hi, > I am trying to post-processing my results and calculate MSD (mean square > displacement) but my answer is different from the MSD value that GROMACS > calculated. I use trjconv command and use the output .gro file. I tried to > understand the GROMACS code but I am not a good programmer. Is there any > specific detail except the Einstein relation in the manual? > > sorry if here is not the right place to ask this question. > Best regards. > > Sina Omrani. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sinaomrani96 at gmail.com Sat Apr 18 21:38:02 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Sat, 18 Apr 2020 19:38:02 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: I use a file that contains the position of each atom at every saved frame. For the first time lag, I distract all trajectories that are 1 timestep different and averaging the result and so on. I tried the various methods with different systems but none of them worked. PS: here is the .gro file. I hope the link works. https://gofile.io/?c=meQ1dJ On Sat, 18 Apr 2020 at 23:30, Arun Srikanth wrote: > Unless you give you give details how you calculate the MSD it will not be > possible to help. > Are you using unwrapped co-ordinates in your calculations for MSD? > > Arun > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > wrote: > > > Hi, > > I am trying to post-processing my results and calculate MSD (mean square > > displacement) but my answer is different from the MSD value that GROMACS > > calculated. I use trjconv command and use the output .gro file. I tried > to > > understand the GROMACS code but I am not a good programmer. Is there any > > specific detail except the Einstein relation in the manual? > > > > sorry if here is not the right place to ask this question. > > Best regards. > > > > Sina Omrani. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From kevin.boyd at uconn.edu Sat Apr 18 21:40:10 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 18 Apr 2020 19:40:10 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: Hi, Are you talking about the reported diffusion coefficient or the MSD vs lag plot? You should be very careful about where you fit. By default, Gromacs calculates MSDs at much longer lag times than you typically have good data for. Use the -beginfit and -endfit options to restrict the fit to the lag times where the MSD plot is linear. > I use trjconv command and use the output .gro file This doesn't make much sense, how many frames are you analyzing? On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth wrote: > *Message sent from a system outside of UConn.* > > > Unless you give you give details how you calculate the MSD it will not be > possible to help. > Are you using unwrapped co-ordinates in your calculations for MSD? > > Arun > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > wrote: > > > Hi, > > I am trying to post-processing my results and calculate MSD (mean square > > displacement) but my answer is different from the MSD value that GROMACS > > calculated. I use trjconv command and use the output .gro file. I tried > to > > understand the GROMACS code but I am not a good programmer. Is there any > > specific detail except the Einstein relation in the manual? > > > > sorry if here is not the right place to ask this question. > > Best regards. > > > > Sina Omrani. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sinaomrani96 at gmail.com Sat Apr 18 21:54:40 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Sat, 18 Apr 2020 19:54:40 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: Thanks, Kevin, I am looking for the MSD vs lag plot. I use the saved frames that specified in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 ps simulation. should I lower this or is there another way for using more trajectories? On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > Hi, > > Are you talking about the reported diffusion coefficient or the MSD vs lag > plot? You should be very careful about where you fit. By default, Gromacs > calculates MSDs at much longer lag times than you typically have good data > for. Use the -beginfit and -endfit options to restrict the fit to the lag > times where the MSD plot is linear. > > > I use trjconv command and use the output .gro file > > This doesn't make much sense, how many frames are you analyzing? > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Unless you give you give details how you calculate the MSD it will not be > > possible to help. > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > Arun > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > wrote: > > > > > Hi, > > > I am trying to post-processing my results and calculate MSD (mean > square > > > displacement) but my answer is different from the MSD value that > GROMACS > > > calculated. I use trjconv command and use the output .gro file. I tried > > to > > > understand the GROMACS code but I am not a good programmer. Is there > any > > > specific detail except the Einstein relation in the manual? > > > > > > sorry if here is not the right place to ask this question. > > > Best regards. > > > > > > Sina Omrani. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From kevin.boyd at uconn.edu Sun Apr 19 00:02:48 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 18 Apr 2020 22:02:48 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: What are you trying to calculate MSD for? I doubt that would be sufficient sampling to calculate the diffusion coefficient of anything except maybe water. For lipids, you don't start getting accurate readings until you reach a **lag** time of 10 ns, and you need 100s of ns of data to get a good reading even at that lag time. That's with many lipids in a bilayer. I don't have experience with calculating diffusion coefficients for proteins, but I'd imagine you need microseconds of sampling, since they're much slower tumblers and you usually only have one per simulation box. Your save rate is fine, and could be even more granular. On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > Thanks, Kevin, > I am looking for the MSD vs lag plot. I use the saved frames that specified > in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 > ps simulation. should I lower this or is there another way for using more > trajectories? > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > Hi, > > > > Are you talking about the reported diffusion coefficient or the MSD vs > lag > > plot? You should be very careful about where you fit. By default, Gromacs > > calculates MSDs at much longer lag times than you typically have good > data > > for. Use the -beginfit and -endfit options to restrict the fit to the lag > > times where the MSD plot is linear. > > > > > I use trjconv command and use the output .gro file > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Unless you give you give details how you calculate the MSD it will not > be > > > possible to help. > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > Arun > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > > wrote: > > > > > > > Hi, > > > > I am trying to post-processing my results and calculate MSD (mean > > square > > > > displacement) but my answer is different from the MSD value that > > GROMACS > > > > calculated. I use trjconv command and use the output .gro file. I > tried > > > to > > > > understand the GROMACS code but I am not a good programmer. Is there > > any > > > > specific detail except the Einstein relation in the manual? > > > > > > > > sorry if here is not the right place to ask this question. > > > > Best regards. > > > > > > > > Sina Omrani. > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From lamonteserincastanedo at gmail.com Sun Apr 19 01:40:03 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sat, 18 Apr 2020 23:40:03 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs Message-ID: Dear Gromacs users, As I have referred before I am simulating small molecules (nucleosides) (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the end I want to select the most stable structure from the trajectory for the next steps. What would be the best methodology to use to run a molecular dynamics for this?: 1) Run an anneling and collect the different frames for the trajectory and then at the end analyze the RSMD, free energy and maybe do clustering for the different frames to select the most stable structure? 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella sampling"?, the only problem here is that I want all dihedral angles to rotate and I do not know how to do this. 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in which I generate the free energy from different lambda values from consecutive simulations. Any suggestions? I am not sure how to proceed correctly here. Kindly, Lazaro From jun.zhou at monash.edu Sun Apr 19 04:15:34 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Sun, 19 Apr 2020 02:15:34 -0000 Subject: [gmx-users] Triclinic box is too skewed Message-ID: Hi all, I apply a deform at the xy direction of the box, the rate is 0.01 nm/ps but I met this error : Warning: Triclinic box is too skewed. Box (3x3): Box[ 0]={ 1.06717e+01, 0.00000e+00, 0.00000e+00} Box[ 1]={ 5.34312e+00, 1.06717e+01, 0.00000e+00} Box[ 2]={ 0.00000e+00, 0.00000e+00, 1.06717e+01} Can not fix pbc. Any suggestions about this? Thanks Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From sinaomrani96 at gmail.com Sun Apr 19 11:38:30 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Sun, 19 Apr 2020 09:38:30 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: Dear Kevin, Thanks for your suggestions but the problem is the difference between my answer and GROMACS in calculated MSD. I performed 6 ns simulation just for checking my MSD results and I'm not going to calculate the diffusion coefficient from it. On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > What are you trying to calculate MSD for? I doubt that would be sufficient > sampling to calculate the diffusion coefficient of anything except maybe > water. For lipids, you don't start getting accurate readings until you > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a > good reading even at that lag time. That's with many lipids in a bilayer. I > don't have experience with calculating diffusion coefficients for > proteins, but I'd imagine you need microseconds of sampling, since they're > much slower tumblers and you usually only have one per simulation box. > > Your save rate is fine, and could be even more granular. > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Thanks, Kevin, > > I am looking for the MSD vs lag plot. I use the saved frames that > specified > > in mdp file. Is that the problem? I saved positions every 10 ps for a > 6000 > > ps simulation. should I lower this or is there another way for using more > > trajectories? > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > > > Hi, > > > > > > Are you talking about the reported diffusion coefficient or the MSD vs > > lag > > > plot? You should be very careful about where you fit. By default, > Gromacs > > > calculates MSDs at much longer lag times than you typically have good > > data > > > for. Use the -beginfit and -endfit options to restrict the fit to the > lag > > > times where the MSD plot is linear. > > > > > > > I use trjconv command and use the output .gro file > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > > wrote: > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it will > not > > be > > > > possible to help. > > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > > > Arun > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > > > wrote: > > > > > > > > > Hi, > > > > > I am trying to post-processing my results and calculate MSD (mean > > > square > > > > > displacement) but my answer is different from the MSD value that > > > GROMACS > > > > > calculated. I use trjconv command and use the output .gro file. I > > tried > > > > to > > > > > understand the GROMACS code but I am not a good programmer. Is > there > > > any > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > Best regards. > > > > > > > > > > Sina Omrani. > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From Simone.Schirra at uibk.ac.at Sun Apr 19 15:56:13 2020 From: Simone.Schirra at uibk.ac.at (Schirra, Simone) Date: Sun, 19 Apr 2020 13:56:13 -0000 Subject: [gmx-users] atomtype "OE" in charmm36 In-Reply-To: <094e29ff-bfea-49d9-241f-99086ae84594@vt.edu> References: <412999B95FB6894AAB9B6283E4C20DA126065042@XMBX3.uibk.ac.at>, <094e29ff-bfea-49d9-241f-99086ae84594@vt.edu> Message-ID: <412999B95FB6894AAB9B6283E4C20DA126065197@XMBX3.uibk.ac.at> I figured it out myself. It seems like it's calles "OC30A" now. My energy minimization problems came from somewhere else and I have now been able to solve them. Excuse me for asking this, kind of obvious, question. Simone ________________________________________ Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se]" im Auftrag von "Justin Lemkul [jalemkul at vt.edu] Gesendet: Freitag, 17. April 2020 13:10 An: gmx-users at gromacs.org Betreff: Re: [gmx-users] atomtype "OE" in charmm36 On 4/17/20 4:45 AM, Schirra, Simone wrote: > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my .itp and .gro files. The script is designed to work with charmm35r, however I only found charmm36 available now (I read, that c35r was only temporary). I thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used for the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it seems to be designed for use with charmm rather than gromacs. Which toppar file are you trying to use? > Is there a way to convert it for use with gromacs? Or is there another definition I can use to work with my PEG? Or maybe c35r is still somewhere around? C35r became C36 in official implementation. Likely the atom type just got renamed or assumed into an existing one, but without knowing which topology you're using, I can't comment. The PEO "toppar_ether" from Alex's site doesn't have anything called OE in it. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From sadafrani6 at gmail.com Sun Apr 19 15:58:37 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 19 Apr 2020 13:58:37 -0000 Subject: [gmx-users] error in pdb2gmx Message-ID: Dear Gromacs users I am facing a strange problem while doing pdb2gmx:- When I use the command:- gmx pdb2gmx -f 74A-G.pdb -o 74A-G.gro It shows the following:- going to rename ./amber99sb-ildn.ff/aminoacids.r2b Opening force field file ./amber99sb-ildn.ff/aminoacids.r2b going to rename ./amber99sb-ildn.ff/dna.r2b Opening force field file ./amber99sb-ildn.ff/dna.r2b going to rename ./amber99sb-ildn.ff/rna.r2b Opening force field file ./amber99sb-ildn.ff/rna.r2b Reading 74A-G.pdb... Read '', 4082 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 492 residues with 4082 atoms chain #res #atoms 1 'A' 489 3970 2 'B' 3 112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp ------------------------------------------------------- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' However, when I use without gmx, as below:- pdb2gmx -f 74A-G.pdb -o 74A-G.gro It generates topology file successfully. What's wrong with the format in atomtypes.atp I am unable to understand. Could you please help me to find out? I have added a new residue to my forcefield file as mentioned in gromacs manual. Please correct me where I am wrong, I have added following in atomtypes.atp file:- ;[ atomtypes ] ; name bond_type mass charge ptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.00000 0.000 A 3.00001e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.00000 0.000 A 2.95992e-1 8.78640e-1 oh 16.00000 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.00000e+0 0.00000e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Thanks. Sadaf From kevin.boyd at uconn.edu Sun Apr 19 18:21:57 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sun, 19 Apr 2020 16:21:57 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: Can you send links to the results Gromacs gives you and the results you're getting, along with the code that you're using to calculate the MSD? On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > Dear Kevin, Thanks for your suggestions but the problem is the difference > between my answer and GROMACS in calculated MSD. I performed 6 ns > simulation just for checking my MSD results and I'm not going to calculate > the diffusion coefficient from it. > > On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > > > What are you trying to calculate MSD for? I doubt that would be > sufficient > > sampling to calculate the diffusion coefficient of anything except maybe > > water. For lipids, you don't start getting accurate readings until you > > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a > > good reading even at that lag time. That's with many lipids in a > bilayer. I > > don't have experience with calculating diffusion coefficients for > > proteins, but I'd imagine you need microseconds of sampling, since > they're > > much slower tumblers and you usually only have one per simulation box. > > > > Your save rate is fine, and could be even more granular. > > > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Thanks, Kevin, > > > I am looking for the MSD vs lag plot. I use the saved frames that > > specified > > > in mdp file. Is that the problem? I saved positions every 10 ps for a > > 6000 > > > ps simulation. should I lower this or is there another way for using > more > > > trajectories? > > > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > > > > > Hi, > > > > > > > > Are you talking about the reported diffusion coefficient or the MSD > vs > > > lag > > > > plot? You should be very careful about where you fit. By default, > > Gromacs > > > > calculates MSDs at much longer lag times than you typically have good > > > data > > > > for. Use the -beginfit and -endfit options to restrict the fit to the > > lag > > > > times where the MSD plot is linear. > > > > > > > > > I use trjconv command and use the output .gro file > > > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > > > > wrote: > > > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it will > > not > > > be > > > > > possible to help. > > > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > > > > > Arun > > > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani < > sinaomrani96 at gmail.com> > > > > > wrote: > > > > > > > > > > > Hi, > > > > > > I am trying to post-processing my results and calculate MSD (mean > > > > square > > > > > > displacement) but my answer is different from the MSD value that > > > > GROMACS > > > > > > calculated. I use trjconv command and use the output .gro file. I > > > tried > > > > > to > > > > > > understand the GROMACS code but I am not a good programmer. Is > > there > > > > any > > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > > Best regards. > > > > > > > > > > > > Sina Omrani. > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > > > > posting! > > > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sadafrani6 at gmail.com Sun Apr 19 18:48:32 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 19 Apr 2020 16:48:32 -0000 Subject: [gmx-users] error in pdb2gmx Message-ID: Dear Gromacs users I have tried to sort out this problem with gromacs 2020 and 2019 versions. I gromacs 2019, It gives:- All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp Atomtype 106 Invalid format: However, It generates a topology file. In gromacs 2020, it gives:- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' I have modified my atomtypes.atp file as below:- ;[ atomtypes ] ; name mass nh 14.01 dnh 14.01 hn 1.008 dhn 1.008 ca 12.01 dca 12.01 nb 14.01 dnb 14.01 h5 1.008 dh5 1.008 nc 14.01 dnc 14.01 cd 12.01 dcd 12.01 na 14.01 dna 14.01 c3 12.01 dc3 12.01 h2 1.008 dh2 1.008 os 16 dos 16 h1 1.008 dh1 1.008 p5 30.97 dp5 30.97 o 16 do 16 oh 16 doh 16 ho 1.008 dho 1.008 h4 1.008 dh4 1.008 c 12.01 dc 12.01 n 14.01 dn 14.01 ha 1.008 dha 1.008 Atomtype 106 is ha, I cant find any thing wrong with it. Could you please help me to fix this error? Thanks. Sadaf From marko at kth.se Sun Apr 19 19:08:33 2020 From: marko at kth.se (Marko Petrovic) Date: Sun, 19 Apr 2020 17:08:33 -0000 Subject: [gmx-users] Installation on iPad In-Reply-To: <014a01d6157f$0762be70$16283b50$@student.kuleuven.be> References: <014a01d6157f$0762be70$16283b50$@student.kuleuven.be> Message-ID: <660BD15C-F4E4-453A-B3D6-D6A2BE639E2D@kth.se> You can at least run SSH clients on iOS so you can technically edit text files and run commands from it even if the execution is not on the iPad. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 18 Apr 2020, at 14:43, Ali Khodayari > wrote: Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From sinaomrani96 at gmail.com Sun Apr 19 19:19:43 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Sun, 19 Apr 2020 17:19:43 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: I wrote the code in Matlab. Thank you in advance. Results Link: https://gofile.io/?c=CjUYpo Code Link: .m file: https://gofile.io/?c=O2MPKP , txt file: https://gofile.io/?c=QI46nd On Sun, 19 Apr 2020 at 20:52, Kevin Boyd wrote: > Can you send links to the results Gromacs gives you and the results you're > getting, along with the code that you're using to calculate the MSD? > > On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Dear Kevin, Thanks for your suggestions but the problem is the difference > > between my answer and GROMACS in calculated MSD. I performed 6 ns > > simulation just for checking my MSD results and I'm not going to > calculate > > the diffusion coefficient from it. > > > > On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > > > > > What are you trying to calculate MSD for? I doubt that would be > > sufficient > > > sampling to calculate the diffusion coefficient of anything except > maybe > > > water. For lipids, you don't start getting accurate readings until you > > > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a > > > good reading even at that lag time. That's with many lipids in a > > bilayer. I > > > don't have experience with calculating diffusion coefficients for > > > proteins, but I'd imagine you need microseconds of sampling, since > > they're > > > much slower tumblers and you usually only have one per simulation box. > > > > > > Your save rate is fine, and could be even more granular. > > > > > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > > > wrote: > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > Thanks, Kevin, > > > > I am looking for the MSD vs lag plot. I use the saved frames that > > > specified > > > > in mdp file. Is that the problem? I saved positions every 10 ps for a > > > 6000 > > > > ps simulation. should I lower this or is there another way for using > > more > > > > trajectories? > > > > > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd > wrote: > > > > > > > > > Hi, > > > > > > > > > > Are you talking about the reported diffusion coefficient or the MSD > > vs > > > > lag > > > > > plot? You should be very careful about where you fit. By default, > > > Gromacs > > > > > calculates MSDs at much longer lag times than you typically have > good > > > > data > > > > > for. Use the -beginfit and -endfit options to restrict the fit to > the > > > lag > > > > > times where the MSD plot is linear. > > > > > > > > > > > I use trjconv command and use the output .gro file > > > > > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth < > askforarun at gmail.com > > > > > > > > wrote: > > > > > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it > will > > > not > > > > be > > > > > > possible to help. > > > > > > Are you using unwrapped co-ordinates in your calculations for > MSD? > > > > > > > > > > > > Arun > > > > > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani < > > sinaomrani96 at gmail.com> > > > > > > wrote: > > > > > > > > > > > > > Hi, > > > > > > > I am trying to post-processing my results and calculate MSD > (mean > > > > > square > > > > > > > displacement) but my answer is different from the MSD value > that > > > > > GROMACS > > > > > > > calculated. I use trjconv command and use the output .gro > file. I > > > > tried > > > > > > to > > > > > > > understand the GROMACS code but I am not a good programmer. Is > > > there > > > > > any > > > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > > > Best regards. > > > > > > > > > > > > > > Sina Omrani. > > > > > > > -- > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > * Please search the archive at > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > > > > > > posting! > > > > > > > > > > > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or > > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > > > > posting! > > > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From ask.archana at gmail.com Sun Apr 19 20:30:58 2020 From: ask.archana at gmail.com (Archana Sonawani-Jagtap) Date: Sun, 19 Apr 2020 18:30:58 -0000 Subject: [gmx-users] atomselection for index group of cyclic rings In-Reply-To: References: Message-ID: Hi, First make index file of the atoms involved in rings and then use following command: gmx distance -f .xtc -s .tpr -n .ndx -select 'cog of group " group 1" plus cog of group "group2"' -oav .xvg Hope this helps Thanks Archana On Fri, Apr 17, 2020 at 10:25 AM Prasanth G, Research Scholar < prasanthghanta at sssihl.edu.in> wrote: > Dear all, > I am interested in measuring the distance between two cyclic rings present > in the residues and ligands over time. Can you kindly suggest how to go > about this? > Specially, if i am interested in measuring the distance between the center > of the two rings over time. Thank you > > -- > Regards, > Prasanth. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From elham802011 at yahoo.com Sun Apr 19 20:53:10 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sun, 19 Apr 2020 18:53:10 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization References: <1827925722.3087998.1587321780778.ref@mail.yahoo.com> Message-ID: <1827925722.3087998.1587321780778@mail.yahoo.com> Hi ?I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents: ?? Tolerance (Fmax)?? =? 1.00000e+03 ?? Number of steps??? =??????? 50000 Step=??? 0, Dmax= 1.0e-02 nm, Epot=? 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation fault (core dumped) and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr = no Can anyone suggest how to troubleshoot this error? The system is nuetralized.?Thank you in advance. From jalemkul at vt.edu Sun Apr 19 21:35:15 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 19:35:15 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: References: Message-ID: On 4/17/20 5:25 PM, Paolo Costa wrote: > Hi Justin, > > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > stannate.pdb and also to stannate.rtp. But still I get the error. > Here the output file of from pdb2gmx: > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > Reading stannate.pdb... > WARNING: all CONECT records are ignored > Read 'stannate', 7 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > > chain #res #atoms > 1 ' ' 1 7 > > All occupancy fields zero. This is probably not an X-Ray structure > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp > Atomtype 68 > Reading residue database... (amber99) > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > Residue 93 > Sorting it all out... > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > Residue 94 > Sorting it all out... > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > Residue 110 > Sorting it all out... > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > Residue 126 > Sorting it all out... > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > Residue 127 > Sorting it all out... > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > > Back Off! I just backed up topol.top to ./#topol.top.19# > Processing chain 1 (7 atoms, 1 residues) > > Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. > This chain lacks identifiers, which makes it impossible to do strict > classification of the start/end residues. Here we need to guess this residue > should not be part of the chain and instead introduce a break, but that will > be catastrophic if they should in fact be linked. Please check your > structure, > and add SnC to residuetypes.dat if this was not correct. > > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > ------------------------------------------------------- > Program: gmx pdb2gmx, version 2018.1 > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > > Fatal error: > Residue 'SnC' not found in residue topology database > > *Thanks a lot for helping!* Without seeing the contents of the PDB file and stannate.rtp, there's not much to go on here. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Sun Apr 19 21:35:56 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 19:35:56 -0000 Subject: [gmx-users] Regarding use of harmonic wall model In-Reply-To: References: Message-ID: <46892ea0-77bf-d5d4-aaa0-de568b905ba7@vt.edu> On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote: > Hello everyone, > I want to create a gap between the first and last strand of a beta barrel > so that I can put a new strand in between. > So, I have generated an input file using charmm-gui and using its gromacs > production file (production.mdp) to run the simulation. I want to use a > harmonic wall model to disrupt the bonding between the first and last > strand of the beta barrel but not getting how to do it . > I have asked it before as well but I did not get any suggestion. > Please kindly help me with this query if anybody has any idea regarding > this. I suggest using the pull code. The implementation of walls in GROMACS does not do what you're asking. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Sun Apr 19 21:38:48 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 19:38:48 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: References: Message-ID: On 4/18/20 7:39 PM, lazaro monteserin wrote: > Dear Gromacs users, > > As I have referred before I am simulating small molecules (nucleosides) > (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the > end I want to select the most stable structure from the trajectory for the > next steps. > > What would be the best methodology to use to run a molecular dynamics for > this?: > > 1) Run an anneling and collect the different frames for the trajectory and > then at the end analyze the RSMD, free energy and maybe do clustering for > the different frames to select the most stable structure? How do you propose to compute the conformational free energy? Note also that no biomolecular force field is validated for use in the gas phase, so the balance of conformational sampling has no guarantee of being physically meaningful. > 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella > sampling"?, the only problem here is that I want all dihedral angles to > rotate and I do not know how to do this. You can enforce dihedral rotation with the pull code, but the tutorial has little use here aside from general concepts. > 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in which > I generate the free energy from different lambda values from consecutive > simulations. The tutorial is for decoupling a solute from water. You have a molecule in vacuum. The only thing to decouple is the molecule itself, which will give you an annihilated, physically nonsensical structure. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Sun Apr 19 21:41:07 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 19:41:07 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization In-Reply-To: <1827925722.3087998.1587321780778@mail.yahoo.com> References: <1827925722.3087998.1587321780778.ref@mail.yahoo.com> <1827925722.3087998.1587321780778@mail.yahoo.com> Message-ID: <7b146381-27bb-8553-762b-7c387835dd5c@vt.edu> On 4/19/20 2:43 PM, Elham Taghikhani wrote: > Hi > ?I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. > Steepest Descents: > ?? Tolerance (Fmax)?? =? 1.00000e+03 > ?? Number of steps??? =??????? 50000 > Step=??? 0, Dmax= 1.0e-02 nm, Epot=? 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Look for bad contacts around atom 1996. > Segmentation fault (core dumped) > > and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol > emstep = 0.01 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) steps to perform > > ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long range forces > cutoff-scheme = Verlet > ns_type = grid ; Method to determine neighbor list (simple, grid) > rlist = 1.2 ; Cut-off for making neighbor list (short range forces) > coulombtype = PME ; Treatment of long range electrostatic interactions > rcoulomb = 1.2 ; long range electrostatic cut-off > vdwtype = cutoff > vdw-modifier = force-switch > rvdw-switch = 1.0 > rvdw = 1.2 ; long range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > DispCorr = no > Can anyone suggest how to troubleshoot this error? Your cutoffs are for the CHARMM force field, not OPLS. This isn't the source of the error, but you are using the force field incorrectly. Other than that, protein-ligand complexes are specifically addressed in the troubleshooting section of http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Sun Apr 19 21:44:16 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 19:44:16 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: On 4/18/20 5:38 AM, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. However, I have one more > question. Is it caused by usage of -noappend or other reasons? No, it's because of the power failure likely causing an issue on the filesystem or with your file directly. -Justin > Best regards, > > Mijiddorj > > --------------------------------------------------------- >> Message: 1 >> Date: Fri, 17 Apr 2020 11:51:25 -0400 >> From: Justin Lemkul >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr >> frame header >> Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> >> >> On 4/17/20 10:13 AM, Mijiddorj B wrote: >>> Dear GMX users, >>> >>> Hello, I performed MD simulation using gromacs 2018.7v. During this >>> simulation, the calculation was stopped because of the electric cut. >> Then, >>> I continued the simulation using "gmx mdrun with -noappend" in order to >> get >>> separate trajectory for the safety of data. After that, I would like to >>> concatenate the trr files. >>> However, I received following error message. >>> >>> How, can I concatenate these trajectories. >>> ********************************************** >>> Program: gmx trjcat, version 2018.7 >>> Source file: src/gromacs/fileio/trrio.cpp (line 114) >>> >>> Fatal error: >>> Failed to find GROMACS magic number in trr frame header, so this is not a >>> trr >>> file! >>> >>> For more information and tips for troubleshooting, please check the >> GROMACS >>> website at http://www.gromacs.org/Documentation/Errors >>> ************************************************ >> Your file is corrupted and you will have to run that portion of the >> simulation again. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ali.khodayari at student.kuleuven.be Sun Apr 19 21:44:21 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Sun, 19 Apr 2020 19:44:21 -0000 Subject: [gmx-users] Installation on iPad In-Reply-To: <660BD15C-F4E4-453A-B3D6-D6A2BE639E2D@kth.se> References: <014a01d6157f$0762be70$16283b50$@student.kuleuven.be> <660BD15C-F4E4-453A-B3D6-D6A2BE639E2D@kth.se> Message-ID: <001c01d61682$e29b5ac0$a7d21040$@student.kuleuven.be> Dear Marko, Thank you for your response. Indeed SSH would be already proper help. I am also interested to see whether I can run GROMACS on itself as well. I came through a shell for iPad, called Blink Shell, which seems to be able to cover some aspects of coding, but I am not sure if it would be able to host gmx too. It is paid btw. My best, Ali -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Marko Petrovic Sent: zondag 19 april 2020 19:09 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Installation on iPad You can at least run SSH clients on iOS so you can technically edit text files and run commands from it even if the execution is not on the iPad. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 18 Apr 2020, at 14:43, Ali Khodayari > wrote: Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. Kind regards, Ali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From paolo.costa85 at gmail.com Sun Apr 19 21:54:27 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 19 Apr 2020 19:54:27 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: References: Message-ID: Hi Justin, I could fix the issue. Thanks again for your help. Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul ha scritto: > > > On 4/17/20 5:25 PM, Paolo Costa wrote: > > Hi Justin, > > > > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > > stannate.pdb and also to stannate.rtp. But still I get the error. > > Here the output file of from pdb2gmx: > > > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > > Reading stannate.pdb... > > WARNING: all CONECT records are ignored > > Read 'stannate', 7 atoms > > Analyzing pdb file > > Splitting chemical chains based on TER records or chain id changing. > > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > > > > chain #res #atoms > > 1 ' ' 1 7 > > > > All occupancy fields zero. This is probably not an X-Ray structure > > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp > > Atomtype 68 > > Reading residue database... (amber99) > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > > Residue 93 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > > Residue 94 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > > Residue 110 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > > Residue 126 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > > Residue 127 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > > > > Back Off! I just backed up topol.top to ./#topol.top.19# > > Processing chain 1 (7 atoms, 1 residues) > > > > Warning: Starting residue SnC0 in chain not identified as > Protein/RNA/DNA. > > This chain lacks identifiers, which makes it impossible to do strict > > classification of the start/end residues. Here we need to guess this > residue > > should not be part of the chain and instead introduce a break, but that > will > > be catastrophic if they should in fact be linked. Please check your > > structure, > > and add SnC to residuetypes.dat if this was not correct. > > > > Problem with chain definition, or missing terminal residues. > > This chain does not appear to contain a recognized chain molecule. > > If this is incorrect, you can edit residuetypes.dat to modify the > behavior. > > 8 out of 8 lines of specbond.dat converted successfully > > > > ------------------------------------------------------- > > Program: gmx pdb2gmx, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > > > > Fatal error: > > Residue 'SnC' not found in residue topology database > > > > *Thanks a lot for helping!* > > Without seeing the contents of the PDB file and stannate.rtp, there's > not much to go on here. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Sun Apr 19 22:04:53 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 20:04:53 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: References: Message-ID: <4bf9dad7-4357-52e1-cd9f-cf1990cd4913@vt.edu> On 4/19/20 3:47 PM, Paolo Costa wrote: > Hi Justin, > > I could fix the issue. > > Thanks again for your help. And in the spirit of helping others that use this mailing list, what exactly was the problem and how did you solve it? -Justin > Paolo > > Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul ha > scritto: > >> >> On 4/17/20 5:25 PM, Paolo Costa wrote: >>> Hi Justin, >>> >>> thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my >>> stannate.pdb and also to stannate.rtp. But still I get the error. >>> Here the output file of from pdb2gmx: >>> >>> Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b >>> Reading stannate.pdb... >>> WARNING: all CONECT records are ignored >>> Read 'stannate', 7 atoms >>> Analyzing pdb file >>> Splitting chemical chains based on TER records or chain id changing. >>> There are 1 chains and 0 blocks of water and 1 residues with 7 atoms >>> >>> chain #res #atoms >>> 1 ' ' 1 7 >>> >>> All occupancy fields zero. This is probably not an X-Ray structure >>> Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp >>> Atomtype 68 >>> Reading residue database... (amber99) >>> Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp >>> Residue 93 >>> Sorting it all out... >>> Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp >>> Residue 94 >>> Sorting it all out... >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp >>> Residue 110 >>> Sorting it all out... >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp >>> Residue 126 >>> Sorting it all out... >>> Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp >>> Residue 127 >>> Sorting it all out... >>> Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb >>> Opening force field file >> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb >>> Opening force field file >> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb >>> Back Off! I just backed up topol.top to ./#topol.top.19# >>> Processing chain 1 (7 atoms, 1 residues) >>> >>> Warning: Starting residue SnC0 in chain not identified as >> Protein/RNA/DNA. >>> This chain lacks identifiers, which makes it impossible to do strict >>> classification of the start/end residues. Here we need to guess this >> residue >>> should not be part of the chain and instead introduce a break, but that >> will >>> be catastrophic if they should in fact be linked. Please check your >>> structure, >>> and add SnC to residuetypes.dat if this was not correct. >>> >>> Problem with chain definition, or missing terminal residues. >>> This chain does not appear to contain a recognized chain molecule. >>> If this is incorrect, you can edit residuetypes.dat to modify the >> behavior. >>> 8 out of 8 lines of specbond.dat converted successfully >>> >>> ------------------------------------------------------- >>> Program: gmx pdb2gmx, version 2018.1 >>> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) >>> >>> Fatal error: >>> Residue 'SnC' not found in residue topology database >>> >>> *Thanks a lot for helping!* >> Without seeing the contents of the PDB file and stannate.rtp, there's >> not much to go on here. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Sun Apr 19 22:10:37 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 19 Apr 2020 20:10:37 -0000 Subject: [gmx-users] =?utf-8?q?Residue_=E2=80=98XXX=E2=80=99_not_found_in_?= =?utf-8?q?residue_topology_database_-_SnCl6?= In-Reply-To: <4bf9dad7-4357-52e1-cd9f-cf1990cd4913@vt.edu> References: <4bf9dad7-4357-52e1-cd9f-cf1990cd4913@vt.edu> Message-ID: It was a typos. In the .pdb file I wrote SnC as residue name, while in .rtp file it was still written SnCl. That's why the error. Thanks a lot again. Paolo Il dom 19 apr 2020, 22:05 Justin Lemkul ha scritto: > > > On 4/19/20 3:47 PM, Paolo Costa wrote: > > Hi Justin, > > > > I could fix the issue. > > > > Thanks again for your help. > > And in the spirit of helping others that use this mailing list, what > exactly was the problem and how did you solve it? > > -Justin > > > Paolo > > > > Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/17/20 5:25 PM, Paolo Costa wrote: > >>> Hi Justin, > >>> > >>> thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > >>> stannate.pdb and also to stannate.rtp. But still I get the error. > >>> Here the output file of from pdb2gmx: > >>> > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > >>> Reading stannate.pdb... > >>> WARNING: all CONECT records are ignored > >>> Read 'stannate', 7 atoms > >>> Analyzing pdb file > >>> Splitting chemical chains based on TER records or chain id changing. > >>> There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > >>> > >>> chain #res #atoms > >>> 1 ' ' 1 7 > >>> > >>> All occupancy fields zero. This is probably not an X-Ray structure > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/atomtypes.atp > >>> Atomtype 68 > >>> Reading residue database... (amber99) > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > >>> Residue 93 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > >>> Residue 94 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > >>> Residue 110 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > >>> Residue 126 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > >>> Residue 127 > >>> Sorting it all out... > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > >>> Back Off! I just backed up topol.top to ./#topol.top.19# > >>> Processing chain 1 (7 atoms, 1 residues) > >>> > >>> Warning: Starting residue SnC0 in chain not identified as > >> Protein/RNA/DNA. > >>> This chain lacks identifiers, which makes it impossible to do strict > >>> classification of the start/end residues. Here we need to guess this > >> residue > >>> should not be part of the chain and instead introduce a break, but that > >> will > >>> be catastrophic if they should in fact be linked. Please check your > >>> structure, > >>> and add SnC to residuetypes.dat if this was not correct. > >>> > >>> Problem with chain definition, or missing terminal residues. > >>> This chain does not appear to contain a recognized chain molecule. > >>> If this is incorrect, you can edit residuetypes.dat to modify the > >> behavior. > >>> 8 out of 8 lines of specbond.dat converted successfully > >>> > >>> ------------------------------------------------------- > >>> Program: gmx pdb2gmx, version 2018.1 > >>> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > >>> > >>> Fatal error: > >>> Residue 'SnC' not found in residue topology database > >>> > >>> *Thanks a lot for helping!* > >> Without seeing the contents of the PDB file and stannate.rtp, there's > >> not much to go on here. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From lamonteserincastanedo at gmail.com Sun Apr 19 22:12:35 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 19 Apr 2020 20:12:35 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: References: Message-ID: Dear Dr. Lemkul you are completely right. But then how could I approach this problem to get an answer at the end that make sense? On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: > > > On 4/18/20 7:39 PM, lazaro monteserin wrote: > > Dear Gromacs users, > > > > As I have referred before I am simulating small molecules (nucleosides) > > (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the > > end I want to select the most stable structure from the trajectory for > the > > next steps. > > > > What would be the best methodology to use to run a molecular dynamics for > > this?: > > > > 1) Run an anneling and collect the different frames for the trajectory > and > > then at the end analyze the RSMD, free energy and maybe do clustering for > > the different frames to select the most stable structure? > > How do you propose to compute the conformational free energy? Note also > that no biomolecular force field is validated for use in the gas phase, > so the balance of conformational sampling has no guarantee of being > physically meaningful. > > > 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella > > sampling"?, the only problem here is that I want all dihedral angles to > > rotate and I do not know how to do this. > > You can enforce dihedral rotation with the pull code, but the tutorial > has little use here aside from general concepts. > > > 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in > which > > I generate the free energy from different lambda values from consecutive > > simulations. > > The tutorial is for decoupling a solute from water. You have a molecule > in vacuum. The only thing to decouple is the molecule itself, which will > give you an annihilated, physically nonsensical structure. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Sun Apr 19 22:16:56 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 20:16:56 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: References: Message-ID: <1a7379b9-a9ac-23de-3b50-67d9fb73f8ca@vt.edu> On 4/19/20 4:12 PM, lazaro monteserin wrote: > Dear Dr. Lemkul you are completely right. But then how could I approach > this problem to get an answer at the end that make sense? What is the purpose of requiring that the simulation start from the most stable vacuum conformation? There are very few rotatable bonds in a nucleoside and they are likely capable of fairly exhaustive sampling in water, anyway. The force field isn't designed for vacuum so anything you generate is likely to either be irrelevant in water or otherwise easily accessible in water in the first place. -Justin > On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: > >> >> On 4/18/20 7:39 PM, lazaro monteserin wrote: >>> Dear Gromacs users, >>> >>> As I have referred before I am simulating small molecules (nucleosides) >>> (around 33 atoms) in vacuum in Gromacs. When I do the simulations at the >>> end I want to select the most stable structure from the trajectory for >> the >>> next steps. >>> >>> What would be the best methodology to use to run a molecular dynamics for >>> this?: >>> >>> 1) Run an anneling and collect the different frames for the trajectory >> and >>> then at the end analyze the RSMD, free energy and maybe do clustering for >>> the different frames to select the most stable structure? >> How do you propose to compute the conformational free energy? Note also >> that no biomolecular force field is validated for use in the gas phase, >> so the balance of conformational sampling has no guarantee of being >> physically meaningful. >> >>> 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella >>> sampling"?, the only problem here is that I want all dihedral angles to >>> rotate and I do not know how to do this. >> You can enforce dihedral rotation with the pull code, but the tutorial >> has little use here aside from general concepts. >> >>> 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in >> which >>> I generate the free energy from different lambda values from consecutive >>> simulations. >> The tutorial is for decoupling a solute from water. You have a molecule >> in vacuum. The only thing to decouple is the molecule itself, which will >> give you an annihilated, physically nonsensical structure. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Sun Apr 19 22:25:39 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 19 Apr 2020 20:25:39 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: <1a7379b9-a9ac-23de-3b50-67d9fb73f8ca@vt.edu> References: <1a7379b9-a9ac-23de-3b50-67d9fb73f8ca@vt.edu> Message-ID: I thought this approach initially because I will refine the calculations later at DFT level. What do you think? On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul wrote: > > > On 4/19/20 4:12 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul you are completely right. But then how could I approach > > this problem to get an answer at the end that make sense? > > What is the purpose of requiring that the simulation start from the most > stable vacuum conformation? There are very few rotatable bonds in a > nucleoside and they are likely capable of fairly exhaustive sampling in > water, anyway. The force field isn't designed for vacuum so anything you > generate is likely to either be irrelevant in water or otherwise easily > accessible in water in the first place. > > -Justin > > > On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: > > > >> > >> On 4/18/20 7:39 PM, lazaro monteserin wrote: > >>> Dear Gromacs users, > >>> > >>> As I have referred before I am simulating small molecules (nucleosides) > >>> (around 33 atoms) in vacuum in Gromacs. When I do the simulations at > the > >>> end I want to select the most stable structure from the trajectory for > >> the > >>> next steps. > >>> > >>> What would be the best methodology to use to run a molecular dynamics > for > >>> this?: > >>> > >>> 1) Run an anneling and collect the different frames for the trajectory > >> and > >>> then at the end analyze the RSMD, free energy and maybe do clustering > for > >>> the different frames to select the most stable structure? > >> How do you propose to compute the conformational free energy? Note also > >> that no biomolecular force field is validated for use in the gas phase, > >> so the balance of conformational sampling has no guarantee of being > >> physically meaningful. > >> > >>> 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella > >>> sampling"?, the only problem here is that I want all dihedral angles to > >>> rotate and I do not know how to do this. > >> You can enforce dihedral rotation with the pull code, but the tutorial > >> has little use here aside from general concepts. > >> > >>> 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in > >> which > >>> I generate the free energy from different lambda values from > consecutive > >>> simulations. > >> The tutorial is for decoupling a solute from water. You have a molecule > >> in vacuum. The only thing to decouple is the molecule itself, which will > >> give you an annihilated, physically nonsensical structure. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Sun Apr 19 22:33:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 20:33:35 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: References: <1a7379b9-a9ac-23de-3b50-67d9fb73f8ca@vt.edu> Message-ID: <59725de6-a4b7-d6f0-ef93-959f9f842ac4@vt.edu> On 4/19/20 4:25 PM, lazaro monteserin wrote: > I thought this approach initially because I will refine the calculations > later at DFT level. What do you think? If you need a QM reference state for subsequent geometry refinement, just generate the QM-optimized geometry and start your calculations from that. You can then do an energy minimization with the force field to determine how well the molecular mechanics approximation agrees with QM (perhaps not very well as most nucleic acid force fields have not used DFT methods in their derivation). -Justin > On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul wrote: > >> >> On 4/19/20 4:12 PM, lazaro monteserin wrote: >>> Dear Dr. Lemkul you are completely right. But then how could I approach >>> this problem to get an answer at the end that make sense? >> What is the purpose of requiring that the simulation start from the most >> stable vacuum conformation? There are very few rotatable bonds in a >> nucleoside and they are likely capable of fairly exhaustive sampling in >> water, anyway. The force field isn't designed for vacuum so anything you >> generate is likely to either be irrelevant in water or otherwise easily >> accessible in water in the first place. >> >> -Justin >> >>> On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: >>> >>>> On 4/18/20 7:39 PM, lazaro monteserin wrote: >>>>> Dear Gromacs users, >>>>> >>>>> As I have referred before I am simulating small molecules (nucleosides) >>>>> (around 33 atoms) in vacuum in Gromacs. When I do the simulations at >> the >>>>> end I want to select the most stable structure from the trajectory for >>>> the >>>>> next steps. >>>>> >>>>> What would be the best methodology to use to run a molecular dynamics >> for >>>>> this?: >>>>> >>>>> 1) Run an anneling and collect the different frames for the trajectory >>>> and >>>>> then at the end analyze the RSMD, free energy and maybe do clustering >> for >>>>> the different frames to select the most stable structure? >>>> How do you propose to compute the conformational free energy? Note also >>>> that no biomolecular force field is validated for use in the gas phase, >>>> so the balance of conformational sampling has no guarantee of being >>>> physically meaningful. >>>> >>>>> 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella >>>>> sampling"?, the only problem here is that I want all dihedral angles to >>>>> rotate and I do not know how to do this. >>>> You can enforce dihedral rotation with the pull code, but the tutorial >>>> has little use here aside from general concepts. >>>> >>>>> 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in >>>> which >>>>> I generate the free energy from different lambda values from >> consecutive >>>>> simulations. >>>> The tutorial is for decoupling a solute from water. You have a molecule >>>> in vacuum. The only thing to decouple is the molecule itself, which will >>>> give you an annihilated, physically nonsensical structure. >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Assistant Professor >>>> Office: 301 Fralin Hall >>>> Lab: 303 Engel Hall >>>> >>>> Virginia Tech Department of Biochemistry >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> >>>> jalemkul at vt.edu | (540) 231-3129 >>>> http://www.thelemkullab.com >>>> >>>> ================================================== >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Sun Apr 19 22:35:29 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 19 Apr 2020 20:35:29 -0000 Subject: [gmx-users] about correct methodology to run MD of small molecule in gromacs In-Reply-To: <59725de6-a4b7-d6f0-ef93-959f9f842ac4@vt.edu> References: <1a7379b9-a9ac-23de-3b50-67d9fb73f8ca@vt.edu> <59725de6-a4b7-d6f0-ef93-959f9f842ac4@vt.edu> Message-ID: Thank you very much Dr. Lemkul for the advice On Sun, Apr 19, 2020 at 5:33 PM Justin Lemkul wrote: > > > On 4/19/20 4:25 PM, lazaro monteserin wrote: > > I thought this approach initially because I will refine the calculations > > later at DFT level. What do you think? > > If you need a QM reference state for subsequent geometry refinement, > just generate the QM-optimized geometry and start your calculations from > that. You can then do an energy minimization with the force field to > determine how well the molecular mechanics approximation agrees with QM > (perhaps not very well as most nucleic acid force fields have not used > DFT methods in their derivation). > > -Justin > > > On Sun, Apr 19, 2020 at 5:17 PM Justin Lemkul wrote: > > > >> > >> On 4/19/20 4:12 PM, lazaro monteserin wrote: > >>> Dear Dr. Lemkul you are completely right. But then how could I approach > >>> this problem to get an answer at the end that make sense? > >> What is the purpose of requiring that the simulation start from the most > >> stable vacuum conformation? There are very few rotatable bonds in a > >> nucleoside and they are likely capable of fairly exhaustive sampling in > >> water, anyway. The force field isn't designed for vacuum so anything you > >> generate is likely to either be irrelevant in water or otherwise easily > >> accessible in water in the first place. > >> > >> -Justin > >> > >>> On Sun, Apr 19, 2020 at 4:39 PM Justin Lemkul wrote: > >>> > >>>> On 4/18/20 7:39 PM, lazaro monteserin wrote: > >>>>> Dear Gromacs users, > >>>>> > >>>>> As I have referred before I am simulating small molecules > (nucleosides) > >>>>> (around 33 atoms) in vacuum in Gromacs. When I do the simulations at > >> the > >>>>> end I want to select the most stable structure from the trajectory > for > >>>> the > >>>>> next steps. > >>>>> > >>>>> What would be the best methodology to use to run a molecular dynamics > >> for > >>>>> this?: > >>>>> > >>>>> 1) Run an anneling and collect the different frames for the > trajectory > >>>> and > >>>>> then at the end analyze the RSMD, free energy and maybe do clustering > >> for > >>>>> the different frames to select the most stable structure? > >>>> How do you propose to compute the conformational free energy? Note > also > >>>> that no biomolecular force field is validated for use in the gas > phase, > >>>> so the balance of conformational sampling has no guarantee of being > >>>> physically meaningful. > >>>> > >>>>> 2) Do an umbrella anneling similar to the Gromacs tutorial 3"umbrella > >>>>> sampling"?, the only problem here is that I want all dihedral angles > to > >>>>> rotate and I do not know how to do this. > >>>> You can enforce dihedral rotation with the pull code, but the tutorial > >>>> has little use here aside from general concepts. > >>>> > >>>>> 3) Do a procedure similar to tutorial 6 "Free energy of solvation" in > >>>> which > >>>>> I generate the free energy from different lambda values from > >> consecutive > >>>>> simulations. > >>>> The tutorial is for decoupling a solute from water. You have a > molecule > >>>> in vacuum. The only thing to decouple is the molecule itself, which > will > >>>> give you an annihilated, physically nonsensical structure. > >>>> > >>>> -Justin > >>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalemkul at vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From elham802011 at yahoo.com Sun Apr 19 22:38:41 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Sun, 19 Apr 2020 20:38:41 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization In-Reply-To: <1827925722.3087998.1587321780778@mail.yahoo.com> References: <1827925722.3087998.1587321780778@mail.yahoo.com> Message-ID: <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? I even tried the different box size but it didn't work. Both ligand and protein are ok with minimization separately. > On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: > > ? > Hi > > I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 > Segmentation fault (core dumped) > > and this is my mpd file: > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol > emstep = 0.01 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) steps to perform > > ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long range forces > cutoff-scheme = Verlet > ns_type = grid ; Method to determine neighbor list (simple, grid) > rlist = 1.2 ; Cut-off for making neighbor list (short range forces) > coulombtype = PME ; Treatment of long range electrostatic interactions > rcoulomb = 1.2 ; long range electrostatic cut-off > vdwtype = cutoff > vdw-modifier = force-switch > rvdw-switch = 1.0 > rvdw = 1.2 ; long range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > DispCorr = no > Can anyone suggest how to troubleshoot this error? > The system is nuetralized. > > Thank you in advance. > From alexanderwien2k at gmail.com Sun Apr 19 22:38:59 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 19 Apr 2020 20:38:59 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: Message-ID: Any comment on this would be so appreciated! Regards, Alex On Sat, Apr 18, 2020 at 2:12 PM Alex wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I conducted > a simple pulling simulation by which a single-small molecule (mol_A) is > being dragged along -Z from water into the body of a thin film. > Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" > and "pull-group1-pbcatom = -1"* which cause a net shifting of the > system along the pulling direction as soon as the mol_A reach to the thin > film, please find below the pulling flags movie and plot in below links. > > Centering the thin film and mol_A could solve the issue, (echo 1 0 | > trjconv -center yes) to some extent but still COM changes in the early > stage below 2ns. , > COM: > https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > > Movie in which the water molecules are hidden: > https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > > - > gmx version 2020.1 > ----- > pull = yes > pull-print-com = no > pull-print-ref-value = yes > pull-print-components = Yes > pull-nstxout = 1000 > pull-nstfout = 1000 > pull-pbc-ref-prev-step-com = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Thin-film > pull-group1-pbcatom = -1 > pull-group2-name = mol_A > pull-group2-pbcatom = 0 > pull-coord1-type = umbrella > pull-coord1-geometry = direction > pull-coord1-groups = 1 2 > pull-coord1-dim = N N Y > pull-coord1-origin = 0.0 0.0 0.0 > pull-coord1-vec = 0.0 0.0 -1.0 > pull-coord1-start = yes > pull-coord1-init = 0 > pull-coord1-rate = 0.0005 > pull-coord1-k = 5000 > ----- > I wonder if I could extract correct initial configuration from this > trajectory? With correct initial configuration, I mean a set of gro file in > which change from one from to another is the distance between the COM of > the thin-film and mol_A? > > Thank you > Alex > From jalemkul at vt.edu Sun Apr 19 23:06:56 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 19 Apr 2020 21:06:56 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization In-Reply-To: <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> References: <1827925722.3087998.1587321780778@mail.yahoo.com> <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> Message-ID: <6cd25582-bfe2-016c-2cb2-0fd14d3beb0e@vt.edu> On 4/19/20 4:38 PM, Elham Taghikhani wrote: > Thank you > I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. > Could you explain how can I observe bad contacts in the structure? Calculate interatomic distances and look for anything very close to atom 1996, check the topology to make sure sensible interactions will occur between that atom and its surroundings. > I even tried the different box size but it didn't work. Box size is not relevant here. -Justin > Both ligand and protein are ok with minimization separately. > > >> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: >> >> ? >> Hi >> >> I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+03 >> Number of steps = 50000 >> Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 >> Segmentation fault (core dumped) >> >> and this is my mpd file: >> ; LINES STARTING WITH ';' ARE COMMENTS >> title = Minimization ; Title of run >> >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol >> emstep = 0.01 ; Energy step size >> nsteps = 50000 ; Maximum number of (minimization) steps to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor list (simple, grid) >> rlist = 1.2 ; Cut-off for making neighbor list (short range forces) >> coulombtype = PME ; Treatment of long range electrostatic interactions >> rcoulomb = 1.2 ; long range electrostatic cut-off >> vdwtype = cutoff >> vdw-modifier = force-switch >> rvdw-switch = 1.0 >> rvdw = 1.2 ; long range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions >> DispCorr = no >> Can anyone suggest how to troubleshoot this error? >> The system is nuetralized. >> >> Thank you in advance. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sadafrani6 at gmail.com Sun Apr 19 23:54:56 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 19 Apr 2020 21:54:56 -0000 Subject: [gmx-users] Error in pdb2gmx Message-ID: Dear Gromacs users I have tried to sort out this problem with gromacs 2020 and 2019 versions. I gromacs 2019, It gives:- All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp Atomtype 106 Invalid format: However, It generates a topology file. In gromacs 2020, it gives:- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: Invalid atomtype format: '' I have modified my atomtypes.atp file as below:- ;[ atomtypes ] ; name mass nh 14.01 dnh 14.01 hn 1.008 dhn 1.008 ca 12.01 dca 12.01 nb 14.01 dnb 14.01 h5 1.008 dh5 1.008 nc 14.01 dnc 14.01 cd 12.01 dcd 12.01 na 14.01 dna 14.01 c3 12.01 dc3 12.01 h2 1.008 dh2 1.008 os 16 dos 16 h1 1.008 dh1 1.008 p5 30.97 dp5 30.97 o 16 do 16 oh 16 doh 16 ho 1.008 dho 1.008 h4 1.008 dh4 1.008 c 12.01 dc 12.01 n 14.01 dn 14.01 ha 1.008 dha 1.008 Atomtype 106 is ha, I cant find any thing wrong with it. Could you please help me to fix this error? Thanks. Sadaf From kevin.boyd at uconn.edu Mon Apr 20 01:43:57 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sun, 19 Apr 2020 23:43:57 -0000 Subject: [gmx-users] Question about Mean Square Displacement (MSD) In-Reply-To: References: Message-ID: I'm getting a bit lost in the Matlab, and I don't have access to Matlab to play around with it. I suggest trying to simplify by making your calculation for just one particle for a single time point, then once you have that right expand to multiple time points, then expand to multiple particles. You may not get exact matches, it would probably be sufficient to have the trend lines roughly align. Note that for Gromacs not every frame is used as a starting point, it strides along in increments of "-trestart" Feel free to follow up directly to my email, unless there's anything else directly Gromacs related to discuss. Kevin On Sun, Apr 19, 2020 at 10:19 AM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > I wrote the code in Matlab. Thank you in advance. > > Results Link: https://gofile.io/?c=CjUYpo > Code Link: .m file: https://gofile.io/?c=O2MPKP , txt file: > https://gofile.io/?c=QI46nd > > On Sun, 19 Apr 2020 at 20:52, Kevin Boyd wrote: > > > Can you send links to the results Gromacs gives you and the results > you're > > getting, along with the code that you're using to calculate the MSD? > > > > On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Dear Kevin, Thanks for your suggestions but the problem is the > difference > > > between my answer and GROMACS in calculated MSD. I performed 6 ns > > > simulation just for checking my MSD results and I'm not going to > > calculate > > > the diffusion coefficient from it. > > > > > > On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > > > > > > > What are you trying to calculate MSD for? I doubt that would be > > > sufficient > > > > sampling to calculate the diffusion coefficient of anything except > > maybe > > > > water. For lipids, you don't start getting accurate readings until > you > > > > reach a **lag** time of 10 ns, and you need 100s of ns of data to > get a > > > > good reading even at that lag time. That's with many lipids in a > > > bilayer. I > > > > don't have experience with calculating diffusion coefficients for > > > > proteins, but I'd imagine you need microseconds of sampling, since > > > they're > > > > much slower tumblers and you usually only have one per simulation > box. > > > > > > > > Your save rate is fine, and could be even more granular. > > > > > > > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > > > > > wrote: > > > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > > > > Thanks, Kevin, > > > > > I am looking for the MSD vs lag plot. I use the saved frames that > > > > specified > > > > > in mdp file. Is that the problem? I saved positions every 10 ps > for a > > > > 6000 > > > > > ps simulation. should I lower this or is there another way for > using > > > more > > > > > trajectories? > > > > > > > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd > > wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > Are you talking about the reported diffusion coefficient or the > MSD > > > vs > > > > > lag > > > > > > plot? You should be very careful about where you fit. By default, > > > > Gromacs > > > > > > calculates MSDs at much longer lag times than you typically have > > good > > > > > data > > > > > > for. Use the -beginfit and -endfit options to restrict the fit to > > the > > > > lag > > > > > > times where the MSD plot is linear. > > > > > > > > > > > > > I use trjconv command and use the output .gro file > > > > > > > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth < > > askforarun at gmail.com > > > > > > > > > > wrote: > > > > > > > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it > > will > > > > not > > > > > be > > > > > > > possible to help. > > > > > > > Are you using unwrapped co-ordinates in your calculations for > > MSD? > > > > > > > > > > > > > > Arun > > > > > > > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani < > > > sinaomrani96 at gmail.com> > > > > > > > wrote: > > > > > > > > > > > > > > > Hi, > > > > > > > > I am trying to post-processing my results and calculate MSD > > (mean > > > > > > square > > > > > > > > displacement) but my answer is different from the MSD value > > that > > > > > > GROMACS > > > > > > > > calculated. I use trjconv command and use the output .gro > > file. I > > > > > tried > > > > > > > to > > > > > > > > understand the GROMACS code but I am not a good programmer. > Is > > > > there > > > > > > any > > > > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > > > > Best regards. > > > > > > > > > > > > > > > > Sina Omrani. > > > > > > > > -- > > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > before > > > > > > > > posting! > > > > > > > > > > > > > > > > * Can't post? Read > > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > > or > > > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > > > > > -- > > > > > > > Gromacs Users mailing list > > > > > > > > > > > > > > * Please search the archive at > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > > > > > > posting! > > > > > > > > > > > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or > > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > > > > posting! > > > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From magnus.lundborg at scilifelab.se Mon Apr 20 09:24:48 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 20 Apr 2020 07:24:48 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: Message-ID: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Hi Alex, I don't think this is related to using pull-pbc-ref-prev-step-com. Have you tried without it? However, it is risky using pbcatom -1, since you don't know what atom you are using as the initial reference. I would suggest picking an atom you know is located at the centre of the structure. I would think that the problem has to do with the comm removal. What are your parameters for comm-mode, nstcomm and comm-grps? It is possible that you need to lower your nstcomm. It is also possible, but not certain, the comm-mode Linear-acceleration-correction might help you. For some reason, it seems like I have sometimes avoided similar problems by using the sd integrator instead, but I haven't evaluated that properly - it might just have been coincidences. If you see a clear difference using the sd integrator it might be good if you'd file an issue about it on gitlab so that someone can look into if there is something wrong. Regards, Magnus On 2020-04-18 20:12, Alex wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I conducted a > simple pulling simulation by which a single-small molecule (mol_A) is being > dragged along -Z from water into the body of a thin film. > Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" and > "pull-group1-pbcatom = -1"* which cause a net shifting of the system > along the pulling direction as soon as the mol_A reach to the thin film, > please find below the pulling flags movie and plot in below links. > > Centering the thin film and mol_A could solve the issue, (echo 1 0 | > trjconv -center yes) to some extent but still COM changes in the early > stage below 2ns. , > COM: > https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > > Movie in which the water molecules are hidden: > https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > > - > gmx version 2020.1 > ----- > pull = yes > pull-print-com = no > pull-print-ref-value = yes > pull-print-components = Yes > pull-nstxout = 1000 > pull-nstfout = 1000 > pull-pbc-ref-prev-step-com = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Thin-film > pull-group1-pbcatom = -1 > pull-group2-name = mol_A > pull-group2-pbcatom = 0 > pull-coord1-type = umbrella > pull-coord1-geometry = direction > pull-coord1-groups = 1 2 > pull-coord1-dim = N N Y > pull-coord1-origin = 0.0 0.0 0.0 > pull-coord1-vec = 0.0 0.0 -1.0 > pull-coord1-start = yes > pull-coord1-init = 0 > pull-coord1-rate = 0.0005 > pull-coord1-k = 5000 > ----- > I wonder if I could extract correct initial configuration from this > trajectory? With correct initial configuration, I mean a set of gro file in > which change from one from to another is the distance between the COM of > the thin-film and mol_A? > > Thank you > Alex From byunjy0614 at gmail.com Mon Apr 20 09:25:37 2020 From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=) Date: Mon, 20 Apr 2020 07:25:37 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> Message-ID: <861C2E3D-574C-4334-9000-B905B5ED61A0@gmail.com> Hi Yu I simulated the both case (1), (2) for only all-atom ligand system and only protein system respectively you mentioned. I run the each case; the NVT and NPT equilibration with 200ps and 1ns respectively. And there are no problems during NVT and NPT equilibration. And while I wrote the ligand only topology file, I realized that there is specific order in writing topology file (before I don?t exactly know about the order.) Below is the last section of my topology file: ; Include Position restraint file #ifdef POSRES #include "../PROTEIN/posre.itp" #endif #include "../LIGAND/lig.itp" #ifdef POSRES_LIG #include "../LIGAND/lig_posre.itp" #endif ; Include water topology #include "gromos54a7_atb_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos54a7_atb_lipid.ff/ions.itp" [ system ] ; Name --- in water [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 SOL 30059 NA 4 ????????????????????????????????????? Is there any problem with my topology file and Is it the right order? Thank you very much b, You > 2020. 4. 17. ?? 3:34, Yu Du ??: > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From magnus.lundborg at scilifelab.se Mon Apr 20 09:27:30 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 20 Apr 2020 07:27:30 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Sorry, about the statement about pbcatom -1. I was thinking about 0. I don't know if pbcatom -1 is good or not in this case. Regards, Magnus On 2020-04-20 09:24, Magnus Lundborg wrote: > Hi Alex, > > I don't think this is related to using pull-pbc-ref-prev-step-com. > Have you tried without it? However, it is risky using pbcatom -1, > since you don't know what atom you are using as the initial reference. > I would suggest picking an atom you know is located at the centre of > the structure. > > I would think that the problem has to do with the comm removal. What > are your parameters for comm-mode, nstcomm and comm-grps? It is > possible that you need to lower your nstcomm. It is also possible, but > not certain, the comm-mode Linear-acceleration-correction might help > you. For some reason, it seems like I have sometimes avoided similar > problems by using the sd integrator instead, but I haven't evaluated > that properly - it might just have been coincidences. If you see a > clear difference using the sd integrator it might be good if you'd > file an issue about it on gitlab so that someone can look into if > there is something wrong. > > Regards, > Magnus > > On 2020-04-18 20:12, Alex wrote: >> Dear all, >> To generate the initial configurations for umbrella sampling, I >> conducted a >> simple pulling simulation by which a single-small molecule (mol_A) is >> being >> dragged along -Z from water into the body of a thin film. >> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = >> yes" and >> "pull-group1-pbcatom????? = -1"*? which cause a net shifting of the >> system >> along the pulling direction as soon as the mol_A reach to the thin film, >> please find below the pulling flags movie and? plot in below links. >> >> Centering the thin film and mol_A could solve the issue,? (echo 1 0 | >> trjconv -center yes) to some extent but still COM changes in the early >> stage below 2ns. , >> COM: >> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 >> >> Movie in which the water molecules are hidden: >> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv >> >> - >> gmx version 2020.1 >> ----- >> pull???????????????????? = yes >> pull-print-com?????????? = no >> pull-print-ref-value???? = yes >> pull-print-components??? = Yes >> pull-nstxout???????????? = 1000 >> pull-nstfout???????????? = 1000 >> pull-pbc-ref-prev-step-com = yes >> pull-ngroups???????????? = 2 >> pull-ncoords???????????? = 1 >> pull-group1-name???????? = Thin-film >> pull-group1-pbcatom????? = -1 >> pull-group2-name???????? = mol_A >> pull-group2-pbcatom????? = 0 >> pull-coord1-type???????? = umbrella >> pull-coord1-geometry???? = direction >> pull-coord1-groups?????? = 1 2 >> pull-coord1-dim????????? = N N Y >> pull-coord1-origin?????? = 0.0 0.0 0.0 >> pull-coord1-vec????????? = 0.0 0.0 -1.0 >> pull-coord1-start??????? = yes >> pull-coord1-init???????? = 0 >> pull-coord1-rate???????? = 0.0005 >> pull-coord1-k??????????? = 5000 >> ----- >> I wonder if I could extract correct initial configuration from this >> trajectory? With correct initial configuration, I mean a set of gro >> file in >> which change from one from to another is the distance between the COM of >> the thin-film and mol_A? >> >> Thank you >> Alex > > From byunjy0614 at gmail.com Mon Apr 20 09:50:08 2020 From: byunjy0614 at gmail.com (=?utf-8?B?67OA7KeE7JiB?=) Date: Mon, 20 Apr 2020 07:50:08 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem (???) In-Reply-To: References: Message-ID: Hi Prasanth Firstly Sorry for late reply? The force field I used is Gromacs 5.x.x 54a7 came from ATB. I downloaded and used the all-atom topology file(.itp) so I said that it is all-atom simulation. By any chance, is it wrong approach?? > 2020. 4. 17. ?? 7:58, Prasanth G, Research Scholar ??: > > Hi Jinyoung > > Can you please tell which forcefield you are using for these simulations > As far as I remember atb server generates gromos compatible parameters, > which is a United atom forcefield. Since you said you are interested in an > all atom simulation, I'm slightly confused > > Regards. > > On Fri, 17 Apr, 2020, 2:17 PM , < > gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > So >> Send gromacs.org_gmx-users mailing list submissions to >> gromacs.org_gmx-users at maillist.sys.kth.se >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or, via email, send a message with subject or body 'help' to >> gromacs.org_gmx-users-request at maillist.sys.kth.se >> >> You can reach the person managing the list at >> gromacs.org_gmx-users-owner at maillist.sys.kth.se >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gromacs.org_gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: How to solve the "LINCS WARNING" problem (???) >> 2. RIN (Residue interaction network) for protein ligand >> interactions (Prasanth G, Research Scholar) >> 3. atomselection for index group of cyclic rings >> (Prasanth G, Research Scholar) >> 4. Re: How to solve the "LINCS WARNING" problem (Yu Du) >> 5. atomtype "OE" in charmm36 (Schirra, Simone) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 17 Apr 2020 13:30:14 +0900 >> From: ??? >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >> Message-ID: >> Content-Type: text/plain; charset="us-ascii" >> >> Thank you Yu Du >> I encountered the problem while I have tried to simulate the >> protein-ligand complex system. >> 1. I generated the all atom ligand topology file from the ATB website. And >> I make both ligand .gro file and protein .gro file by using pdb2gmx and >> editconf module. >> 2. Then I run solvation, adding ion, energy minimization step with no >> problem >> 3. The problem I mailed is from NVT or NPT equilibration step. During >> equilibration step, I met the problem mentioned. >> >> I attached my ligand topology file >> -------------- next part -------------- >> . >> Is the problem from the wrong ligand topology (parameter) file? >> >> Thank you. >> >>> 2020. 4. 16. ?? 11:01, Yu Du ??: >>> >>> If you haven't solved your LINCS WARNING, you need to show more details >> of how you got that problem, including the generation of your ligand >> topology file. There are maybe some errors in your ligand topology that you >> didn't figure out. >>> >>> Cheers, >>> >>> Yu >>> ________________________________ >>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < >> byunjy0614 at gmail.com> >>> Sent: Thursday, April 16, 2020 21:43 >>> To: gmx-users at gromacs.org >>> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >>> >>> Thank you for reply Du, You >>> You said that "If you want more suggestion, you need to provide some >> details of the generation of ligand's topology? >>> Du you mean that I modify my topology file manually?? >>> >>> >>>> 2020. 4. 14. ?? 5:08, Yu Du ??: >>>> >>>> Hi Jinyoung, >>>> >>>> I guess that the LINCS WARNING you encountered maybe came from hiden >> errors in the configuration of either protein or ligand OR more directly >> from the ligand's topology. You need to carefully check the configuration >> of protein and ligand, e.g. side chain goes through benzene ring. >>>> >>>> After a careful check, If you want more suggestion, you need to provide >> some details of the generation of ligand's topology. >>>> >>>> Du, Yu >>>> PhD Student, >>>> Shanghai Institute of Organic Chemistry >>>> 345 Ling Ling Rd., Shanghai, China. >>>> Zip: 200032, Tel: (86) 021 5492 5275 >>>> ________________________________ >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < >> byunjy0614 at gmail.com> >>>> Sent: Tuesday, April 14, 2020 14:32 >>>> To: gmx-users at gromacs.org >>>> Subject: [gmx-users] How to solve the "LINCS WARNING" problem >>>> >>>> Dear GROMACS users, >>>> >>>> Since I have run the nvt and npt processes for the protein-ligand >> interaction, I met the the warning messages below >>>> >>>> Step 231785, time 463.57 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.000176, max 0.003912 (between atoms 3035 and 3037) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 3035 3036 34.0 0.1090 0.1087 0.1090 >>>> >>>> ?. >>>> >>>> Step 231825, time 463.65 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 3024 3025 90.0 0.1090 0.1236 0.1090 >>>> 3026 3027 100.8 0.1090 6.6242 0.1090 >>>> 3028 3029 162.5 1.7683 5245.4102 0.1090 >>>> 3033 3034 106.7 0.1090 426.5654 0.1090 >>>> 3035 3037 90.0 0.3851 0.7991 0.1090 >>>> 3038 3039 90.0 0.6045 0.4497 0.1090 >>>> 3038 3040 90.0 0.1123 0.2833 0.1090 >>>> 3041 3042 59.0 0.1020 0.1020 0.1020 >>>> Wrote pdb files with previous and current coordinates >>>> >>>> Step 231826, time 463.652 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and >> 3034) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1423 1424 140.4 0.1000 503.9983 0.1000 >>>> 3024 3025 61.1 0.1236 223337872.0000 0.1090 >>>> 3026 3027 168.8 6.6242 149263.5000 0.1090 >>>> 3028 3029 165.8 5245.4102 263929.4375 0.1090 >>>> 3031 3032 116.2 0.1090 223428336.0000 0.1090 >>>> 3033 3034 179.9 426.5654 446766720.0000 0.1090 >>>> 3035 3036 35.3 29.6105 831.0708 0.1090 >>>> 3035 3037 102.9 0.7991 775.3371 0.1090 >>>> 3038 3039 90.0 0.4497 0.6355 0.1090 >>>> 3038 3040 47.7 0.2833 0.1111 0.1090 >>>> step 231826: One or more water molecules can not be settled. >>>> Check for bad contacts and/or reduce the timestep if appropriate. >>>> >>>> So I checked the my input configuration. the 3035, 3028, 3035 atoms are >> ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. >>>> Why does the LINCS warning occurs? and How I solve this problem? >>>> >>>> Many Thanks >>>> >>>> Jinyoung >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 17 Apr 2020 10:25:38 +0530 >> From: "Prasanth G, Research Scholar" >> To: gromacs.org_gmx-users at maillist.sys.kth.se >> Subject: [gmx-users] RIN (Residue interaction network) for protein >> ligand interactions >> Message-ID: >> < >> CAGpSbSR1UhXoXuxOeAh7h0F2UKzTgJ_rfXm7zfYKDezxSH3oVQ at mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> Dear All, >> >> I am interested in viewing the Residue Interaction network during a protein >> - ligand simulation. Can someone suggest an easy way to go about it? >> >> I tried to use gRINN tool but I guess it doesn't work if ligands are >> present. >> Thanks in advance. >> >> -- >> Regards, >> Prasanth. >> >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 17 Apr 2020 10:27:52 +0530 >> From: "Prasanth G, Research Scholar" >> To: gromacs.org_gmx-users at maillist.sys.kth.se >> Subject: [gmx-users] atomselection for index group of cyclic rings >> Message-ID: >> < >> CAGpSbSSQBMcpnSvm5nvWq9ZqbiSvUrc1FktAhgwOTyqw6kP60g at mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> Dear all, >> I am interested in measuring the distance between two cyclic rings present >> in the residues and ligands over time. Can you kindly suggest how to go >> about this? >> Specially, if i am interested in measuring the distance between the center >> of the two rings over time. Thank you >> >> -- >> Regards, >> Prasanth. >> >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 17 Apr 2020 06:34:48 +0000 >> From: Yu Du >> To: "gmx-users at gromacs.org" >> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >> Message-ID: >> < >> SL2PR04MB30335B7BE660077087DED2CEE0D90 at SL2PR04MB3033.apcprd04.prod.outlook.com >>> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Jinyoung, >> >> You made it clear. >> >> If you do not have special needs in all-atom version of the ligand, you >> can also try the united-atom topology of the very same ligand. >> >> To check the origin of LINCS WARNING, I suggest running MD simulation with >> only protein and only ligand in the same process you followed in a divide >> and conquer strategy. >> >> Could you run the following simulation to pinpoint the error? >> >> (1) Simulation only all-atom ligand in the system. >> (2) Simulation only protein in the system. >> (3) Simulation only united-atom ligand in the system if it's possible. >> >> In the end, I noticed that you used ATB topology, so you need to strictly >> follow the instruction in the ATB ff file folders for protein-ligand >> simulation. >> >> PS: gmx-users mail list do not receive attachment. >> >> Cheers, >> Yu >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Fri, 17 Apr 2020 08:45:26 +0000 >> From: "Schirra, Simone" >> To: "gromacs.org_gmx-users at maillist.sys.kth.se" >> >> Subject: [gmx-users] atomtype "OE" in charmm36 >> Message-ID: >> <412999B95FB6894AAB9B6283E4C20DA126065042 at XMBX3.uibk.ac.at> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Gromacs users, >> >> I want to simulate polyethylene glycol and I am using a script to build my >> .itp and .gro files. The script is designed to work with charmm35r, however >> I only found charmm36 available now (I read, that c35r was only temporary). >> I thought, it should work with this version as well. >> When I try energy minimization, the atomtype OE is not found. OE is used >> for the ether oxygen's in the itp file. >> I also found an ether toppar file at MacKerell Lab Hompage, however it >> seems to be designed for use with charmm rather than gromacs. >> Is there a way to convert it for use with gromacs? Or is there another >> definition I can use to work with my PEG? Or maybe c35r is still somewhere >> around? >> >> I would be very grateful if someone could help me! >> Simone >> >> >> >> ------------------------------ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> >> End of gromacs.org_gmx-users Digest, Vol 192, Issue 57 >> ****************************************************** >> > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From ydu-sci at outlook.com Mon Apr 20 09:53:32 2020 From: ydu-sci at outlook.com (Yu Du) Date: Mon, 20 Apr 2020 07:53:32 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem In-Reply-To: <861C2E3D-574C-4334-9000-B905B5ED61A0@gmail.com> References: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2@gmail.com> <4BA3A707-D2CA-423D-89CA-3C18C1006CAB@gmail.com> , <861C2E3D-574C-4334-9000-B905B5ED61A0@gmail.com> Message-ID: Hi Jinyoung, I'm glad to hear that you have found the problem. You can always use grompp to check your topology of the whole system. If you want to understand the GROMACS topology, check Chapter 5. Topologies in GROMACS Manual. Words in the end: If you have mastered the basic process of protein-ligand simulation with GROMOS ff, you probably wander why we droped GROMOS ff and use others (https://redmine.gromacs.org/issues/2884). Bye, Yu ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of ??? Sent: Monday, April 20, 2020 15:27 To: gmx-users at gromacs.org Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem Hi Yu I simulated the both case (1), (2) for only all-atom ligand system and only protein system respectively you mentioned. I run the each case; the NVT and NPT equilibration with 200ps and 1ns respectively. And there are no problems during NVT and NPT equilibration. And while I wrote the ligand only topology file, I realized that there is specific order in writing topology file (before I don?t exactly know about the order.) Below is the last section of my topology file: ; Include Position restraint file #ifdef POSRES #include "../PROTEIN/posre.itp" #endif #include "../LIGAND/lig.itp" #ifdef POSRES_LIG #include "../LIGAND/lig_posre.itp" #endif ; Include water topology #include "gromos54a7_atb_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos54a7_atb_lipid.ff/ions.itp" [ system ] ; Name --- in water [ molecules ] ; Compound #mols Protein_chain_A 1 LIG 1 SOL 30059 NA 4 ????????????????????????????????????? Is there any problem with my topology file and Is it the right order? Thank you very much b, You > 2020. 4. 17. ?? 3:34, Yu Du ??: > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Mon Apr 20 12:41:50 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 20 Apr 2020 10:41:50 -0000 Subject: [gmx-users] How to solve the "LINCS WARNING" problem (???) In-Reply-To: References: Message-ID: <370e3738-4f57-1794-6e8f-2fc9eac123eb@vt.edu> On 4/20/20 3:51 AM, ??? wrote: > Hi Prasanth > > Firstly Sorry for late reply? > > The force field I used is Gromacs 5.x.x 54a7 came from ATB. > I downloaded and used the all-atom topology file(.itp) so I said that it is all-atom simulation. > By any chance, is it wrong approach?? > The GROMOS force fields are united-atom. I do not know why ATB offers all-atom topologies; they are in principle incompatible with the GROMOS biomolecular force field. -Justin >> 2020. 4. 17. ?? 7:58, Prasanth G, Research Scholar ??: >> >> Hi Jinyoung >> >> Can you please tell which forcefield you are using for these simulations >> As far as I remember atb server generates gromos compatible parameters, >> which is a United atom forcefield. Since you said you are interested in an >> all atom simulation, I'm slightly confused >> >> Regards. >> >> On Fri, 17 Apr, 2020, 2:17 PM , < >> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: >> So >>> Send gromacs.org_gmx-users mailing list submissions to >>> gromacs.org_gmx-users at maillist.sys.kth.se >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>> or, via email, send a message with subject or body 'help' to >>> gromacs.org_gmx-users-request at maillist.sys.kth.se >>> >>> You can reach the person managing the list at >>> gromacs.org_gmx-users-owner at maillist.sys.kth.se >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of gromacs.org_gmx-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: How to solve the "LINCS WARNING" problem (???) >>> 2. RIN (Residue interaction network) for protein ligand >>> interactions (Prasanth G, Research Scholar) >>> 3. atomselection for index group of cyclic rings >>> (Prasanth G, Research Scholar) >>> 4. Re: How to solve the "LINCS WARNING" problem (Yu Du) >>> 5. atomtype "OE" in charmm36 (Schirra, Simone) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Fri, 17 Apr 2020 13:30:14 +0900 >>> From: ??? >>> To: gmx-users at gromacs.org >>> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >>> Message-ID: >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Thank you Yu Du >>> I encountered the problem while I have tried to simulate the >>> protein-ligand complex system. >>> 1. I generated the all atom ligand topology file from the ATB website. And >>> I make both ligand .gro file and protein .gro file by using pdb2gmx and >>> editconf module. >>> 2. Then I run solvation, adding ion, energy minimization step with no >>> problem >>> 3. The problem I mailed is from NVT or NPT equilibration step. During >>> equilibration step, I met the problem mentioned. >>> >>> I attached my ligand topology file >>> -------------- next part -------------- >>> . >>> Is the problem from the wrong ligand topology (parameter) file? >>> >>> Thank you. >>> >>>> 2020. 4. 16. ?? 11:01, Yu Du ??: >>>> >>>> If you haven't solved your LINCS WARNING, you need to show more details >>> of how you got that problem, including the generation of your ligand >>> topology file. There are maybe some errors in your ligand topology that you >>> didn't figure out. >>>> Cheers, >>>> >>>> Yu >>>> ________________________________ >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < >>> byunjy0614 at gmail.com> >>>> Sent: Thursday, April 16, 2020 21:43 >>>> To: gmx-users at gromacs.org >>>> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >>>> >>>> Thank you for reply Du, You >>>> You said that "If you want more suggestion, you need to provide some >>> details of the generation of ligand's topology? >>>> Du you mean that I modify my topology file manually?? >>>> >>>> >>>>> 2020. 4. 14. ?? 5:08, Yu Du ??: >>>>> >>>>> Hi Jinyoung, >>>>> >>>>> I guess that the LINCS WARNING you encountered maybe came from hiden >>> errors in the configuration of either protein or ligand OR more directly >>> from the ligand's topology. You need to carefully check the configuration >>> of protein and ligand, e.g. side chain goes through benzene ring. >>>>> After a careful check, If you want more suggestion, you need to provide >>> some details of the generation of ligand's topology. >>>>> Du, Yu >>>>> PhD Student, >>>>> Shanghai Institute of Organic Chemistry >>>>> 345 Ling Ling Rd., Shanghai, China. >>>>> Zip: 200032, Tel: (86) 021 5492 5275 >>>>> ________________________________ >>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? < >>> byunjy0614 at gmail.com> >>>>> Sent: Tuesday, April 14, 2020 14:32 >>>>> To: gmx-users at gromacs.org >>>>> Subject: [gmx-users] How to solve the "LINCS WARNING" problem >>>>> >>>>> Dear GROMACS users, >>>>> >>>>> Since I have run the nvt and npt processes for the protein-ligand >>> interaction, I met the the warning messages below >>>>> Step 231785, time 463.57 (ps) LINCS WARNING >>>>> relative constraint deviation after LINCS: >>>>> rms 0.000176, max 0.003912 (between atoms 3035 and 3037) >>>>> bonds that rotated more than 30 degrees: >>>>> atom 1 atom 2 angle previous, current, constraint length >>>>> 3035 3036 34.0 0.1090 0.1087 0.1090 >>>>> >>>>> ?. >>>>> >>>>> Step 231825, time 463.65 (ps) LINCS WARNING >>>>> relative constraint deviation after LINCS: >>>>> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029) >>>>> bonds that rotated more than 30 degrees: >>>>> atom 1 atom 2 angle previous, current, constraint length >>>>> 3024 3025 90.0 0.1090 0.1236 0.1090 >>>>> 3026 3027 100.8 0.1090 6.6242 0.1090 >>>>> 3028 3029 162.5 1.7683 5245.4102 0.1090 >>>>> 3033 3034 106.7 0.1090 426.5654 0.1090 >>>>> 3035 3037 90.0 0.3851 0.7991 0.1090 >>>>> 3038 3039 90.0 0.6045 0.4497 0.1090 >>>>> 3038 3040 90.0 0.1123 0.2833 0.1090 >>>>> 3041 3042 59.0 0.1020 0.1020 0.1020 >>>>> Wrote pdb files with previous and current coordinates >>>>> >>>>> Step 231826, time 463.652 (ps) LINCS WARNING >>>>> relative constraint deviation after LINCS: >>>>> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and >>> 3034) >>>>> bonds that rotated more than 30 degrees: >>>>> atom 1 atom 2 angle previous, current, constraint length >>>>> 1423 1424 140.4 0.1000 503.9983 0.1000 >>>>> 3024 3025 61.1 0.1236 223337872.0000 0.1090 >>>>> 3026 3027 168.8 6.6242 149263.5000 0.1090 >>>>> 3028 3029 165.8 5245.4102 263929.4375 0.1090 >>>>> 3031 3032 116.2 0.1090 223428336.0000 0.1090 >>>>> 3033 3034 179.9 426.5654 446766720.0000 0.1090 >>>>> 3035 3036 35.3 29.6105 831.0708 0.1090 >>>>> 3035 3037 102.9 0.7991 775.3371 0.1090 >>>>> 3038 3039 90.0 0.4497 0.6355 0.1090 >>>>> 3038 3040 47.7 0.2833 0.1111 0.1090 >>>>> step 231826: One or more water molecules can not be settled. >>>>> Check for bad contacts and/or reduce the timestep if appropriate. >>>>> >>>>> So I checked the my input configuration. the 3035, 3028, 3035 atoms are >>> ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms. >>>>> Why does the LINCS warning occurs? and How I solve this problem? >>>>> >>>>> Many Thanks >>>>> >>>>> Jinyoung >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Fri, 17 Apr 2020 10:25:38 +0530 >>> From: "Prasanth G, Research Scholar" >>> To: gromacs.org_gmx-users at maillist.sys.kth.se >>> Subject: [gmx-users] RIN (Residue interaction network) for protein >>> ligand interactions >>> Message-ID: >>> < >>> CAGpSbSR1UhXoXuxOeAh7h0F2UKzTgJ_rfXm7zfYKDezxSH3oVQ at mail.gmail.com> >>> Content-Type: text/plain; charset="UTF-8" >>> >>> Dear All, >>> >>> I am interested in viewing the Residue Interaction network during a protein >>> - ligand simulation. Can someone suggest an easy way to go about it? >>> >>> I tried to use gRINN tool but I guess it doesn't work if ligands are >>> present. >>> Thanks in advance. >>> >>> -- >>> Regards, >>> Prasanth. >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Fri, 17 Apr 2020 10:27:52 +0530 >>> From: "Prasanth G, Research Scholar" >>> To: gromacs.org_gmx-users at maillist.sys.kth.se >>> Subject: [gmx-users] atomselection for index group of cyclic rings >>> Message-ID: >>> < >>> CAGpSbSSQBMcpnSvm5nvWq9ZqbiSvUrc1FktAhgwOTyqw6kP60g at mail.gmail.com> >>> Content-Type: text/plain; charset="UTF-8" >>> >>> Dear all, >>> I am interested in measuring the distance between two cyclic rings present >>> in the residues and ligands over time. Can you kindly suggest how to go >>> about this? >>> Specially, if i am interested in measuring the distance between the center >>> of the two rings over time. Thank you >>> >>> -- >>> Regards, >>> Prasanth. >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Fri, 17 Apr 2020 06:34:48 +0000 >>> From: Yu Du >>> To: "gmx-users at gromacs.org" >>> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem >>> Message-ID: >>> < >>> SL2PR04MB30335B7BE660077087DED2CEE0D90 at SL2PR04MB3033.apcprd04.prod.outlook.com >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Jinyoung, >>> >>> You made it clear. >>> >>> If you do not have special needs in all-atom version of the ligand, you >>> can also try the united-atom topology of the very same ligand. >>> >>> To check the origin of LINCS WARNING, I suggest running MD simulation with >>> only protein and only ligand in the same process you followed in a divide >>> and conquer strategy. >>> >>> Could you run the following simulation to pinpoint the error? >>> >>> (1) Simulation only all-atom ligand in the system. >>> (2) Simulation only protein in the system. >>> (3) Simulation only united-atom ligand in the system if it's possible. >>> >>> In the end, I noticed that you used ATB topology, so you need to strictly >>> follow the instruction in the ATB ff file folders for protein-ligand >>> simulation. >>> >>> PS: gmx-users mail list do not receive attachment. >>> >>> Cheers, >>> Yu >>> >>> >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Fri, 17 Apr 2020 08:45:26 +0000 >>> From: "Schirra, Simone" >>> To: "gromacs.org_gmx-users at maillist.sys.kth.se" >>> >>> Subject: [gmx-users] atomtype "OE" in charmm36 >>> Message-ID: >>> <412999B95FB6894AAB9B6283E4C20DA126065042 at XMBX3.uibk.ac.at> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Dear Gromacs users, >>> >>> I want to simulate polyethylene glycol and I am using a script to build my >>> .itp and .gro files. The script is designed to work with charmm35r, however >>> I only found charmm36 available now (I read, that c35r was only temporary). >>> I thought, it should work with this version as well. >>> When I try energy minimization, the atomtype OE is not found. OE is used >>> for the ether oxygen's in the itp file. >>> I also found an ether toppar file at MacKerell Lab Hompage, however it >>> seems to be designed for use with charmm rather than gromacs. >>> Is there a way to convert it for use with gromacs? Or is there another >>> definition I can use to work with my PEG? Or maybe c35r is still somewhere >>> around? >>> >>> I would be very grateful if someone could help me! >>> Simone >>> >>> >>> >>> ------------------------------ >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> >>> End of gromacs.org_gmx-users Digest, Vol 192, Issue 57 >>> ****************************************************** >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From b.mijiddorj at gmail.com Mon Apr 20 12:46:31 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Mon, 20 Apr 2020 10:46:31 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: Dear Justin, Thank you very much for your reply. I see. I cut trr file several ns before the stopped frame, and I would like to cut the corresponding checkpoint file before the stopped frame. Is it possible to get the specific frame checkpoint using gmx? I would like to re-perform the extended simulation again starting from another frame. Is it also possible to use the original checkpoint file as it is? Best regards, Mijiddorj ---------------------------- > > Message: 5 > Date: Sun, 19 Apr 2020 15:36:11 -0400 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > frame header > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 4/18/20 5:38 AM, Mijiddorj B wrote: > > Dear Justin, > > > > Thank you very much for your reply. I see. However, I have one more > > question. Is it caused by usage of -noappend or other reasons? > > No, it's because of the power failure likely causing an issue on the > filesystem or with your file directly. > > -Justin > > > Best regards, > > > > Mijiddorj > > > > --------------------------------------------------------- > >> Message: 1 > >> Date: Fri, 17 Apr 2020 11:51:25 -0400 > >> From: Justin Lemkul > >> To: gmx-users at gromacs.org > >> Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr > >> frame header > >> Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu> > >> Content-Type: text/plain; charset=utf-8; format=flowed > >> > >> > >> > >> On 4/17/20 10:13 AM, Mijiddorj B wrote: > >>> Dear GMX users, > >>> > >>> Hello, I performed MD simulation using gromacs 2018.7v. During this > >>> simulation, the calculation was stopped because of the electric cut. > >> Then, > >>> I continued the simulation using "gmx mdrun with -noappend" in order to > >> get > >>> separate trajectory for the safety of data. After that, I would like to > >>> concatenate the trr files. > >>> However, I received following error message. > >>> > >>> How, can I concatenate these trajectories. > >>> ********************************************** > >>> Program: gmx trjcat, version 2018.7 > >>> Source file: src/gromacs/fileio/trrio.cpp (line 114) > >>> > >>> Fatal error: > >>> Failed to find GROMACS magic number in trr frame header, so this is > not a > >>> trr > >>> file! > >>> > >>> For more information and tips for troubleshooting, please check the > >> GROMACS > >>> website at http://www.gromacs.org/Documentation/Errors > >>> ************************************************ > >> Your file is corrupted and you will have to run that portion of the > >> simulation again. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 71 > ****************************************************** > From jalemkul at vt.edu Mon Apr 20 13:04:01 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 20 Apr 2020 11:04:01 -0000 Subject: [gmx-users] Failed to find GROMACS magic number in trr frame header In-Reply-To: References: Message-ID: <749b5bc6-e683-a0ab-6985-6ef8da63440f@vt.edu> On 4/20/20 6:39 AM, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. I cut trr file several ns before > the stopped frame, and I would like to cut the corresponding checkpoint > file before the stopped frame. Checkpoint files are not trajectories; they only contain one frame. > Is it possible to get the specific frame checkpoint using gmx? Not without using the -cpnum option of mdrun. Checkpoint files are overwritten every few minutes so by default, you only ever have the current and previously saved states. > I would like to re-perform the extended simulation again starting from > another frame. Is it also possible to use the original checkpoint file as > it is? Not unless you have a checkpoint file that corresponds to exactly that frame, which is usually not the case. Checkpoint files are written every few minutes rather than at some fixed interval of time steps. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Mon Apr 20 13:41:09 2020 From: alexanderwien2k at gmail.com (Alex) Date: Mon, 20 Apr 2020 11:41:09 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi Magnus, Thanks. The problem raises only because of using the pull-pbc-ref-prev-step-com which needs the pull-group1-pbcatom to be -1 to be meaningful. For an identical system and mdp parameters using 2018 version of gromacs which is independent to the pull-pbc-ref-prev-step-com, I see no issue. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundborg at scilifelab.se> wrote: > Sorry, about the statement about pbcatom -1. I was thinking about 0. I > don't know if pbcatom -1 is good or not in this case. > > Regards, > > Magnus > > On 2020-04-20 09:24, Magnus Lundborg wrote: > > Hi Alex, > > > > I don't think this is related to using pull-pbc-ref-prev-step-com. > > Have you tried without it? However, it is risky using pbcatom -1, > > since you don't know what atom you are using as the initial reference. > > I would suggest picking an atom you know is located at the centre of > > the structure. > > > > I would think that the problem has to do with the comm removal. What > > are your parameters for comm-mode, nstcomm and comm-grps? It is > > possible that you need to lower your nstcomm. It is also possible, but > > not certain, the comm-mode Linear-acceleration-correction might help > > you. For some reason, it seems like I have sometimes avoided similar > > problems by using the sd integrator instead, but I haven't evaluated > > that properly - it might just have been coincidences. If you see a > > clear difference using the sd integrator it might be good if you'd > > file an issue about it on gitlab so that someone can look into if > > there is something wrong. > > > > Regards, > > Magnus > > > > On 2020-04-18 20:12, Alex wrote: > >> Dear all, > >> To generate the initial configurations for umbrella sampling, I > >> conducted a > >> simple pulling simulation by which a single-small molecule (mol_A) is > >> being > >> dragged along -Z from water into the body of a thin film. > >> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > >> yes" and > >> "pull-group1-pbcatom = -1"* which cause a net shifting of the > >> system > >> along the pulling direction as soon as the mol_A reach to the thin film, > >> please find below the pulling flags movie and plot in below links. > >> > >> Centering the thin film and mol_A could solve the issue, (echo 1 0 | > >> trjconv -center yes) to some extent but still COM changes in the early > >> stage below 2ns. , > >> COM: > >> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > >> > >> Movie in which the water molecules are hidden: > >> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > >> > >> - > >> gmx version 2020.1 > >> ----- > >> pull = yes > >> pull-print-com = no > >> pull-print-ref-value = yes > >> pull-print-components = Yes > >> pull-nstxout = 1000 > >> pull-nstfout = 1000 > >> pull-pbc-ref-prev-step-com = yes > >> pull-ngroups = 2 > >> pull-ncoords = 1 > >> pull-group1-name = Thin-film > >> pull-group1-pbcatom = -1 > >> pull-group2-name = mol_A > >> pull-group2-pbcatom = 0 > >> pull-coord1-type = umbrella > >> pull-coord1-geometry = direction > >> pull-coord1-groups = 1 2 > >> pull-coord1-dim = N N Y > >> pull-coord1-origin = 0.0 0.0 0.0 > >> pull-coord1-vec = 0.0 0.0 -1.0 > >> pull-coord1-start = yes > >> pull-coord1-init = 0 > >> pull-coord1-rate = 0.0005 > >> pull-coord1-k = 5000 > >> ----- > >> I wonder if I could extract correct initial configuration from this > >> trajectory? With correct initial configuration, I mean a set of gro > >> file in > >> which change from one from to another is the distance between the COM of > >> the thin-film and mol_A? > >> > >> Thank you > >> Alex > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From magnus.lundborg at scilifelab.se Mon Apr 20 14:46:07 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 20 Apr 2020 12:46:07 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi Alex, I don't see why it would need pull-group1-pbcatom = -1. Why not pick a central atom? Regards, Magnus On 2020-04-20 13:40, Alex wrote: > Hi Magnus, > Thanks. > The problem raises only because of using the pull-pbc-ref-prev-step-com > which needs the pull-group1-pbcatom to be -1 to be meaningful. > For an identical system and mdp parameters using 2018 version of gromacs > which is independent to the pull-pbc-ref-prev-step-com, I see no issue. > > Regards, > Alex > > On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < > magnus.lundborg at scilifelab.se> wrote: > >> Sorry, about the statement about pbcatom -1. I was thinking about 0. I >> don't know if pbcatom -1 is good or not in this case. >> >> Regards, >> >> Magnus >> >> On 2020-04-20 09:24, Magnus Lundborg wrote: >>> Hi Alex, >>> >>> I don't think this is related to using pull-pbc-ref-prev-step-com. >>> Have you tried without it? However, it is risky using pbcatom -1, >>> since you don't know what atom you are using as the initial reference. >>> I would suggest picking an atom you know is located at the centre of >>> the structure. >>> >>> I would think that the problem has to do with the comm removal. What >>> are your parameters for comm-mode, nstcomm and comm-grps? It is >>> possible that you need to lower your nstcomm. It is also possible, but >>> not certain, the comm-mode Linear-acceleration-correction might help >>> you. For some reason, it seems like I have sometimes avoided similar >>> problems by using the sd integrator instead, but I haven't evaluated >>> that properly - it might just have been coincidences. If you see a >>> clear difference using the sd integrator it might be good if you'd >>> file an issue about it on gitlab so that someone can look into if >>> there is something wrong. >>> >>> Regards, >>> Magnus >>> >>> On 2020-04-18 20:12, Alex wrote: >>>> Dear all, >>>> To generate the initial configurations for umbrella sampling, I >>>> conducted a >>>> simple pulling simulation by which a single-small molecule (mol_A) is >>>> being >>>> dragged along -Z from water into the body of a thin film. >>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = >>>> yes" and >>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the >>>> system >>>> along the pulling direction as soon as the mol_A reach to the thin film, >>>> please find below the pulling flags movie and plot in below links. >>>> >>>> Centering the thin film and mol_A could solve the issue, (echo 1 0 | >>>> trjconv -center yes) to some extent but still COM changes in the early >>>> stage below 2ns. , >>>> COM: >>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 >>>> >>>> Movie in which the water molecules are hidden: >>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv >>>> >>>> - >>>> gmx version 2020.1 >>>> ----- >>>> pull = yes >>>> pull-print-com = no >>>> pull-print-ref-value = yes >>>> pull-print-components = Yes >>>> pull-nstxout = 1000 >>>> pull-nstfout = 1000 >>>> pull-pbc-ref-prev-step-com = yes >>>> pull-ngroups = 2 >>>> pull-ncoords = 1 >>>> pull-group1-name = Thin-film >>>> pull-group1-pbcatom = -1 >>>> pull-group2-name = mol_A >>>> pull-group2-pbcatom = 0 >>>> pull-coord1-type = umbrella >>>> pull-coord1-geometry = direction >>>> pull-coord1-groups = 1 2 >>>> pull-coord1-dim = N N Y >>>> pull-coord1-origin = 0.0 0.0 0.0 >>>> pull-coord1-vec = 0.0 0.0 -1.0 >>>> pull-coord1-start = yes >>>> pull-coord1-init = 0 >>>> pull-coord1-rate = 0.0005 >>>> pull-coord1-k = 5000 >>>> ----- >>>> I wonder if I could extract correct initial configuration from this >>>> trajectory? With correct initial configuration, I mean a set of gro >>>> file in >>>> which change from one from to another is the distance between the COM of >>>> the thin-film and mol_A? >>>> >>>> Thank you >>>> Alex >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. From rollyng at gmail.com Tue Apr 21 08:08:10 2020 From: rollyng at gmail.com (Rolly Ng) Date: Tue, 21 Apr 2020 06:08:10 -0000 Subject: [gmx-users] Problem with Potential Mean Force calculation Message-ID: <007c01d617a3$39234850$ab69d8f0$@gmail.com> Dear Gromacs user and Dr. lemkul, I think my previous email is too large to send on the list. Could you please kindly look at the link for the plots? https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Po tential_Mean_Force_PMF_result I tried to applied the umbrella tutorial to my protein-protein system, and I am using GROMACS 2020 http://www.mdtutorials.com/gmx/umbrella/index.html I have very dense windows to 0.1nm as shown on the attached histogram, but as I look at the PMF curve, it is strange and incomplete? Could you please help me to check what has gone wrong? Thanks very much, Rolly Ng From johannes.hermann at tum.de Tue Apr 21 12:21:00 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Tue, 21 Apr 2020 10:21:00 -0000 Subject: [gmx-users] Appending crashed Replica Exchange Simulations: init_step/-replex is not equal for all subsystems In-Reply-To: <2163e31d-6726-197a-ed3f-b1b4890b007e@tum.de> References: <2163e31d-6726-197a-ed3f-b1b4890b007e@tum.de> Message-ID: <26f85261-66bd-d41a-d6c6-dc1e730d4c90@tum.de> Is there really no way to continue this simulation? Thanks in advance! On 17.04.20 11:35, Johannes Hermann wrote: > Dear all, > > I am doing free energy hamiltonian replica exchange simulations and > unfortunately my simulation crashed (not because of the MD system > itself but because of a hardware failure). The Problem is, that the > "first exchange step: init_step/-replex is not equal for all > subsystems" (log-file): > > first exchange step: init_step/-replex is not equal for all subsystems > ? subsystem 0: 10697 > ? subsystem 1: 10697 > ? subsystem 2: 10697 > ? subsystem 3: 10763 > ? subsystem 4: 10763 > > ..... > > Is there a way that I can manipulate (stripe?) my output files so that > I can append my simulation? Which files would I have to adapt? > > Thank you very much in advance! > > All the best > > Johannes > From jalemkul at vt.edu Tue Apr 21 13:09:31 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 21 Apr 2020 11:09:31 -0000 Subject: [gmx-users] Problem with Potential Mean Force calculation In-Reply-To: <007c01d617a3$39234850$ab69d8f0$@gmail.com> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> Message-ID: <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> On 4/21/20 2:08 AM, Rolly Ng wrote: > > Dear Gromacs user and Dr. lemkul, > > I think my previous email is too large to send on the list. Could you > please kindly look at the link for the plots? > > https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Potential_Mean_Force_PMF_result > I don't see how the PMF could possibly arise from your data. The reaction coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 - 10 nm. > I tried to applied the umbrella tutorial to my protein-protein system, > and I am using GROMACS 2020 > > http://www.mdtutorials.com/gmx/umbrella/index.html > > I have very dense windows to 0.1nm as shown on the attached histogram, > but as I look at the PMF curve, it is strange and incomplete? > I hope you're not directly applying the tutorial; there are some aspects of it (use of restraints, the window spacing, and the restraint only along z) that are not applicable to general protein-protein complexes. > Could you please help me to check what has gone wrong? > What was your gmx wham command? I really don't understand how it could have even produced that PMF given the data you have in the histograms. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From sranjan at iiserb.ac.in Tue Apr 21 14:07:37 2020 From: sranjan at iiserb.ac.in (Shashank Ranjan Srivastava) Date: Tue, 21 Apr 2020 12:07:37 -0000 Subject: [gmx-users] Regarding use of harmonic wall model In-Reply-To: <1587325451769.939397599@boxbe> References: <1587325451769.939397599@boxbe> Message-ID: Thank you so much Prof. Lemkul for your reply. As I don't know what and how to use this pull code, if you have any idea regarding what you have suggested will be of great help to me. Meanwhile I will read more about it. Thank You On Mon, Apr 20, 2020 at 1:14 AM Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule > > | More info > > > > On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote: > > Hello everyone, > > I want to create a gap between the first and last strand of a beta > barrel > > so that I can put a new strand in between. > > So, I have generated an input file using charmm-gui and using its gromacs > > production file (production.mdp) to run the simulation. I want to use a > > harmonic wall model to disrupt the bonding between the first and last > > strand of the beta barrel but not getting how to do it . > > I have asked it before as well but I did not get any suggestion. > > Please kindly help me with this query if anybody has any idea regarding > > this. > > I suggest using the pull code. The implementation of walls in GROMACS > does not do what you're asking. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Shashank Ranjan Srivastava Molecular Biophysics Laboratory Department of Biological Sciences, IISER-Bhopal, Madhya Pradesh From jalemkul at vt.edu Tue Apr 21 15:13:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 21 Apr 2020 13:13:05 -0000 Subject: [gmx-users] Regarding use of harmonic wall model In-Reply-To: References: <1587325451769.939397599@boxbe> Message-ID: <2e029980-f6dc-b997-a817-57b16843b7e6@vt.edu> On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote: > Thank you so much Prof. Lemkul for your reply. > As I don't know what and how to use this pull code, if you have any idea > regarding what you have suggested will be of great help to me. > Meanwhile I will read more about it. General principles here: http://www.mdtutorials.com/gmx/umbrella/index.html Obviously that's a very different approach from what you're trying to do but you can learn the basic syntax there. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Tue Apr 21 16:24:55 2020 From: alexanderwien2k at gmail.com (Alex) Date: Tue, 21 Apr 2020 14:24:55 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi Magnus, Actually I am confused with the available options for the "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when one of the group is large, even the 2020.1 version of grmacs would give a warning if one used No in a case of presence of a large group. Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 the middle atom (number wise) of the large group is used automatically which is safe only for small groups as manual states. So, only remaining option is -1. So, what I understood for a layered-large group similar to what I have one should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 which would cause moving the system along -Z during the pulling. Using gmx select, can I manually define a sub-group around the COM of the large group, and consider it as one of the pulling groups instead of the large group? Thank you Alex On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < magnus.lundborg at scilifelab.se> wrote: > Hi Alex, > > I don't see why it would need pull-group1-pbcatom = -1. Why not pick a > central atom? > > Regards, > > Magnus > > On 2020-04-20 13:40, Alex wrote: > > Hi Magnus, > > Thanks. > > The problem raises only because of using the pull-pbc-ref-prev-step-com > > which needs the pull-group1-pbcatom to be -1 to be meaningful. > > For an identical system and mdp parameters using 2018 version of gromacs > > which is independent to the pull-pbc-ref-prev-step-com, I see no issue. > > > > Regards, > > Alex > > > > On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < > > magnus.lundborg at scilifelab.se> wrote: > > > >> Sorry, about the statement about pbcatom -1. I was thinking about 0. I > >> don't know if pbcatom -1 is good or not in this case. > >> > >> Regards, > >> > >> Magnus > >> > >> On 2020-04-20 09:24, Magnus Lundborg wrote: > >>> Hi Alex, > >>> > >>> I don't think this is related to using pull-pbc-ref-prev-step-com. > >>> Have you tried without it? However, it is risky using pbcatom -1, > >>> since you don't know what atom you are using as the initial reference. > >>> I would suggest picking an atom you know is located at the centre of > >>> the structure. > >>> > >>> I would think that the problem has to do with the comm removal. What > >>> are your parameters for comm-mode, nstcomm and comm-grps? It is > >>> possible that you need to lower your nstcomm. It is also possible, but > >>> not certain, the comm-mode Linear-acceleration-correction might help > >>> you. For some reason, it seems like I have sometimes avoided similar > >>> problems by using the sd integrator instead, but I haven't evaluated > >>> that properly - it might just have been coincidences. If you see a > >>> clear difference using the sd integrator it might be good if you'd > >>> file an issue about it on gitlab so that someone can look into if > >>> there is something wrong. > >>> > >>> Regards, > >>> Magnus > >>> > >>> On 2020-04-18 20:12, Alex wrote: > >>>> Dear all, > >>>> To generate the initial configurations for umbrella sampling, I > >>>> conducted a > >>>> simple pulling simulation by which a single-small molecule (mol_A) is > >>>> being > >>>> dragged along -Z from water into the body of a thin film. > >>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > >>>> yes" and > >>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the > >>>> system > >>>> along the pulling direction as soon as the mol_A reach to the thin > film, > >>>> please find below the pulling flags movie and plot in below links. > >>>> > >>>> Centering the thin film and mol_A could solve the issue, (echo 1 0 | > >>>> trjconv -center yes) to some extent but still COM changes in the early > >>>> stage below 2ns. , > >>>> COM: > >>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > >>>> > >>>> Movie in which the water molecules are hidden: > >>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > >>>> > >>>> - > >>>> gmx version 2020.1 > >>>> ----- > >>>> pull = yes > >>>> pull-print-com = no > >>>> pull-print-ref-value = yes > >>>> pull-print-components = Yes > >>>> pull-nstxout = 1000 > >>>> pull-nstfout = 1000 > >>>> pull-pbc-ref-prev-step-com = yes > >>>> pull-ngroups = 2 > >>>> pull-ncoords = 1 > >>>> pull-group1-name = Thin-film > >>>> pull-group1-pbcatom = -1 > >>>> pull-group2-name = mol_A > >>>> pull-group2-pbcatom = 0 > >>>> pull-coord1-type = umbrella > >>>> pull-coord1-geometry = direction > >>>> pull-coord1-groups = 1 2 > >>>> pull-coord1-dim = N N Y > >>>> pull-coord1-origin = 0.0 0.0 0.0 > >>>> pull-coord1-vec = 0.0 0.0 -1.0 > >>>> pull-coord1-start = yes > >>>> pull-coord1-init = 0 > >>>> pull-coord1-rate = 0.0005 > >>>> pull-coord1-k = 5000 > >>>> ----- > >>>> I wonder if I could extract correct initial configuration from this > >>>> trajectory? With correct initial configuration, I mean a set of gro > >>>> file in > >>>> which change from one from to another is the distance between the COM > of > >>>> the thin-film and mol_A? > >>>> > >>>> Thank you > >>>> Alex > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From rollyng at gmail.com Tue Apr 21 16:40:41 2020 From: rollyng at gmail.com (Rolly Ng) Date: Tue, 21 Apr 2020 14:40:41 -0000 Subject: [gmx-users] =?gb2312?b?u9i4tDogIFByb2JsZW0gd2l0aCBQb3RlbnRpYWwg?= =?gb2312?b?TWVhbiBGb3JjZSBjYWxjdWxhdGlvbg==?= In-Reply-To: <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> Message-ID: <001201d617ea$d23800c0$76a80240$@gmail.com> Dear Justin, I cut the x-axis to 8nm but I have uploaded the original histogram plot to RG. Please have a look again, thank you. I used the following command for wham, gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal I used the AMBER99SB-ILDN forcefield and protein protein pair is KEAP1-NRF2 (2FLU) from https://www.rcsb.org/structure/2FLU I tried to pull the NRF2 from KEAP1, and I can visualize that it has been successfully pulled from the initial position, producing the force and COM plots which seem reasonable. How can I debug the problem? Which files should I check? Thanks, Rolly -----????----- ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se ?? Justin Lemkul ????: 2020?4?21???? ??7:09 ???: Discussion list for GROMACS users ??: Re: [gmx-users] Problem with Potential Mean Force calculation On 4/21/20 2:08 AM, Rolly Ng wrote: > > Dear Gromacs user and Dr. lemkul, > > I think my previous email is too large to send on the list. Could you > please kindly look at the link for the plots? > > https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_stra > nge_Potential_Mean_Force_PMF_result > I don't see how the PMF could possibly arise from your data. The reaction coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 - 10 nm. > I tried to applied the umbrella tutorial to my protein-protein system, > and I am using GROMACS 2020 > > http://www.mdtutorials.com/gmx/umbrella/index.html > > I have very dense windows to 0.1nm as shown on the attached histogram, > but as I look at the PMF curve, it is strange and incomplete? > I hope you're not directly applying the tutorial; there are some aspects of it (use of restraints, the window spacing, and the restraint only along z) that are not applicable to general protein-protein complexes. > Could you please help me to check what has gone wrong? > What was your gmx wham command? I really don't understand how it could have even produced that PMF given the data you have in the histograms. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jkozuch at zedat.fu-berlin.de Tue Apr 21 16:43:39 2020 From: jkozuch at zedat.fu-berlin.de (Jacek Artur Kozuch) Date: Tue, 21 Apr 2020 14:43:39 -0000 Subject: [gmx-users] Dihedral Restraints Message-ID: <55527.79.226.117.53.1587480216.webmail@webmail.zedat.fu-berlin.de> Dear all, I am a bit confused about [ dihedral constraints ]. I was planning to contraint a dihedral in a "flat-bottom" way, so that e.g. angles between 120 and 240 deg are sampled, but above 240 and below 140 are basically "not allowed". In other words, I just want a harmonic potential, where the point of zero-potential is stretched from a point Theta_0 to a range of Theta_0 +- delta_Theta. Dihedral restraints seemed to be what I need, at first glance, but I am confused about the resulting potential obtained from equation 12 in the manual: http://manual.gromacs.org/current/reference-manual/functions/restraints.html#dihedralrestraint The conditions - |Theta'| > delta_Theta - |Theta'| <= delta_Theta and the "(Theta' - delta_Theta)" in the first condition of eq. 12 will do it in an asymmetric way, with different behaviour at Theta' = + delta_Theta or Theta' = - delta_Theta. Therefore, is equation 12 just written in a strange way and it creates a symmetric flat-bottomed potential or will it really result in such an asymmetry? Thanks already for your help. Best wishes, Jacek ________________________________________________ Dr. Jacek Kozuch Freie Universit?t Berlin Fachbereich Physik Arnimallee 14 Raum 1.1.35 14 195 Berlin ________________________________________________ From jalemkul at vt.edu Tue Apr 21 16:49:02 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 21 Apr 2020 14:49:02 -0000 Subject: [gmx-users] =?utf-8?b?5Zue5aSNOiBQcm9ibGVtIHdpdGggUG90ZW50aWFs?= =?utf-8?q?_Mean_Force_calculation?= In-Reply-To: <001201d617ea$d23800c0$76a80240$@gmail.com> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> Message-ID: <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> On 4/21/20 10:40 AM, Rolly Ng wrote: > Dear Justin, > > I cut the x-axis to 8nm but I have uploaded the original histogram plot to > RG. Please have a look again, thank you. It's not a matter of changing the axis. Your histograms indicate sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you have a protein-protein complex, I doubt the COM distance can ever be zero. There is a disconnect between your files. -Justin > I used the following command for wham, > gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal > > I used the AMBER99SB-ILDN forcefield and protein protein pair is KEAP1-NRF2 > (2FLU) from https://www.rcsb.org/structure/2FLU > > I tried to pull the NRF2 from KEAP1, and I can visualize that it has been > successfully pulled from the initial position, producing the force and COM > plots which seem reasonable. > > How can I debug the problem? Which files should I check? > > Thanks, > Rolly > > -----????----- > ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > ?? Justin Lemkul > ????: 2020?4?21???? ??7:09 > ???: Discussion list for GROMACS users > ??: Re: [gmx-users] Problem with Potential Mean Force calculation > > > > On 4/21/20 2:08 AM, Rolly Ng wrote: >> Dear Gromacs user and Dr. lemkul, >> >> I think my previous email is too large to send on the list. Could you >> please kindly look at the link for the plots? >> >> https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_stra >> nge_Potential_Mean_Force_PMF_result >> > I don't see how the PMF could possibly arise from your data. The reaction > coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 > - 10 nm. > >> I tried to applied the umbrella tutorial to my protein-protein system, >> and I am using GROMACS 2020 >> >> http://www.mdtutorials.com/gmx/umbrella/index.html >> >> I have very dense windows to 0.1nm as shown on the attached histogram, >> but as I look at the PMF curve, it is strange and incomplete? >> > I hope you're not directly applying the tutorial; there are some aspects of > it (use of restraints, the window spacing, and the restraint only along z) > that are not applicable to general protein-protein complexes. > >> Could you please help me to check what has gone wrong? >> > What was your gmx wham command? I really don't understand how it could have > even produced that PMF given the data you have in the histograms. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-request at gromacs.org. > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From vuqv.phys at gmail.com Tue Apr 21 17:05:32 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Tue, 21 Apr 2020 15:05:32 -0000 Subject: [gmx-users] =?utf-8?b?5Zue5aSNOiBQcm9ibGVtIHdpdGggUG90ZW50aWFs?= =?utf-8?q?_Mean_Force_calculation?= In-Reply-To: <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> Message-ID: I think the output from WHAM in the terminal may give some information to detect the problem. WHAM will tell you the boundary he used to fit your PMF because your histogram and COM position both tell us your reaction coordinate is range from about 2-7nm but WHAM fit from 0-10nm is so strange Best regards, On Tue, Apr 21, 2020 at 4:49 PM Justin Lemkul wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > Dear Justin, > > > > I cut the x-axis to 8nm but I have uploaded the original histogram plot > to > > RG. Please have a look again, thank you. > > It's not a matter of changing the axis. Your histograms indicate > sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you have > a protein-protein complex, I doubt the COM distance can ever be zero. > There is a disconnect between your files. > > -Justin > > > I used the following command for wham, > > gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal > > > > I used the AMBER99SB-ILDN forcefield and protein protein pair is > KEAP1-NRF2 > > (2FLU) from https://www.rcsb.org/structure/2FLU > > > > I tried to pull the NRF2 from KEAP1, and I can visualize that it has been > > successfully pulled from the initial position, producing the force and > COM > > plots which seem reasonable. > > > > How can I debug the problem? Which files should I check? > > > > Thanks, > > Rolly > > > > -----????----- > > ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > ?? Justin Lemkul > > ????: 2020?4?21???? ??7:09 > > ???: Discussion list for GROMACS users > > ??: Re: [gmx-users] Problem with Potential Mean Force calculation > > > > > > > > On 4/21/20 2:08 AM, Rolly Ng wrote: > >> Dear Gromacs user and Dr. lemkul, > >> > >> I think my previous email is too large to send on the list. Could you > >> please kindly look at the link for the plots? > >> > >> https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_stra > >> nge_Potential_Mean_Force_PMF_result > >> > > I don't see how the PMF could possibly arise from your data. The reaction > > coordinate extends from 2 - 6 nm, but your PMF plot goes from 0 > > - 10 nm. > > > >> I tried to applied the umbrella tutorial to my protein-protein system, > >> and I am using GROMACS 2020 > >> > >> http://www.mdtutorials.com/gmx/umbrella/index.html > >> > >> I have very dense windows to 0.1nm as shown on the attached histogram, > >> but as I look at the PMF curve, it is strange and incomplete? > >> > > I hope you're not directly applying the tutorial; there are some aspects > of > > it (use of restraints, the window spacing, and the restraint only along > z) > > that are not applicable to general protein-protein complexes. > > > >> Could you please help me to check what has gone wrong? > >> > > What was your gmx wham command? I really don't understand how it could > have > > even produced that PMF given the data you have in the histograms. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a > > mail to gmx-users-request at gromacs.org. > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From rollyng at gmail.com Tue Apr 21 18:40:46 2020 From: rollyng at gmail.com (Rolly Ng) Date: Tue, 21 Apr 2020 16:40:46 -0000 Subject: [gmx-users] =?utf-8?b?5Zue5aSNOiAg5Zue5aSNOiBQcm9ibGVtIHdpdGgg?= =?utf-8?q?Potential_Mean_Force_calculation?= In-Reply-To: References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> Message-ID: <001a01d617fb$989e4e30$c9daea90$@gmail.com> Dear Justin and Vu, Thank you and I am checking the tpr and vxg files by reducing the number of files in the 2 dat files. The first 10 data points seems giving the correct PMF reading although the list is incomplete, so I suspect that some of my tpr and xvg files are bad for wham. I will report my finding after check all 51 tpr/vxg pairs. Thank you, Rolly -----????----- ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se ?? Quyen V. Vu ????: 2020?4?21???? ??11:10 ???: gmx-users at gromacs.org ??: Re: [gmx-users] ??: Problem with Potential Mean Force calculation I think the output from WHAM in the terminal may give some information to detect the problem. WHAM will tell you the boundary he used to fit your PMF because your histogram and COM position both tell us your reaction coordinate is range from about 2-7nm but WHAM fit from 0-10nm is so strange Best regards, On Tue, Apr 21, 2020 at 4:49 PM Justin Lemkul wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > Dear Justin, > > > > I cut the x-axis to 8nm but I have uploaded the original histogram > > plot > to > > RG. Please have a look again, thank you. > > It's not a matter of changing the axis. Your histograms indicate > sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you > have a protein-protein complex, I doubt the COM distance can ever be zero. > There is a disconnect between your files. > > -Justin > > > I used the following command for wham, gmx wham -it tpr-files.dat > > -if pullf-files.dat -o -hist -unit kCal > > > > I used the AMBER99SB-ILDN forcefield and protein protein pair is > KEAP1-NRF2 > > (2FLU) from https://www.rcsb.org/structure/2FLU > > > > I tried to pull the NRF2 from KEAP1, and I can visualize that it has > > been successfully pulled from the initial position, producing the > > force and > COM > > plots which seem reasonable. > > > > How can I debug the problem? Which files should I check? > > > > Thanks, > > Rolly > > > > -----????----- > > ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > ?? Justin Lemkul > > ????: 2020?4?21???? ??7:09 > > ???: Discussion list for GROMACS users > > ??: Re: [gmx-users] Problem with Potential Mean Force calculation > > > > > > > > On 4/21/20 2:08 AM, Rolly Ng wrote: > >> Dear Gromacs user and Dr. lemkul, > >> > >> I think my previous email is too large to send on the list. Could > >> you please kindly look at the link for the plots? > >> > >> https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_s > >> tra nge_Potential_Mean_Force_PMF_result > >> > > I don't see how the PMF could possibly arise from your data. The > > reaction coordinate extends from 2 - 6 nm, but your PMF plot goes > > from 0 > > - 10 nm. > > > >> I tried to applied the umbrella tutorial to my protein-protein > >> system, and I am using GROMACS 2020 > >> > >> http://www.mdtutorials.com/gmx/umbrella/index.html > >> > >> I have very dense windows to 0.1nm as shown on the attached > >> histogram, but as I look at the PMF curve, it is strange and incomplete? > >> > > I hope you're not directly applying the tutorial; there are some > > aspects > of > > it (use of restraints, the window spacing, and the restraint only > > along > z) > > that are not applicable to general protein-protein complexes. > > > >> Could you please help me to check what has gone wrong? > >> > > What was your gmx wham command? I really don't understand how it > > could > have > > even produced that PMF given the data you have in the histograms. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > send a > > mail to gmx-users-request at gromacs.org. > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From pall.szilard at gmail.com Wed Apr 22 00:15:55 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 21 Apr 2020 22:15:55 -0000 Subject: [gmx-users] Disabling MKL In-Reply-To: <1314707627.1382055.1587123896143@mail.yahoo.com> References: <1314707627.1382055.1587123896143.ref@mail.yahoo.com> <1314707627.1382055.1587123896143@mail.yahoo.com> Message-ID: Configure with -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF Cheers, -- Szil?rd On Fri, Apr 17, 2020 at 2:07 PM Mahmood Naderan wrote: > Hi > How can I disable MKL while building gromacs? With this configure command > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_FFT_LIBRARY=fftw3 > > > > I see > > -- The GROMACS-managed build of FFTW 3 will configure with the following > optimizations: --enable-sse2;--enable-avx;--enable-avx2 > -- Using external FFT library - FFTW3 build managed by GROMACS > -- Looking for sgemm_ > -- Looking for sgemm_ - not found > -- Looking for sgemm_ > -- Looking for sgemm_ - found > -- Found BLAS: > /share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_thread.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.so;/opt/intel/lib/intel64/libguide.so;-lpthread;-lm;-ldl > > > > > > Then I get these errors > > [100%] Linking CXX executable ../../bin/gmx > [100%] Linking CXX executable ../../bin/template > /bin/ld: warning: libmkl_intel_lp64.so, needed by > ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) > /bin/ld: warning: libmkl_intel_thread.so, needed by > ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) > /bin/ld: warning: libmkl_core.so, needed by ../../lib/libgromacs.so.4.0.0, > not found (try using -rpath or -rpath-link) > /bin/ld: warning: libguide.so, needed by ../../lib/libgromacs.so.4.0.0, > not found (try using -rpath or -rpath-link) > ../../lib/libgromacs.so.4.0.0: undefined reference to `ssteqr_' > ../../lib/libgromacs.so.4.0.0: undefined reference to `dsteqr_' > ../../lib/libgromacs.so.4.0.0: undefined reference to `sger_' > > > > > > > Regards, > Mahmood > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From pall.szilard at gmail.com Wed Apr 22 00:15:56 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 21 Apr 2020 22:15:56 -0000 Subject: [gmx-users] Disabling MKL In-Reply-To: <1314707627.1382055.1587123896143@mail.yahoo.com> References: <1314707627.1382055.1587123896143.ref@mail.yahoo.com> <1314707627.1382055.1587123896143@mail.yahoo.com> Message-ID: Configure with -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF Cheers, -- Szil?rd On Fri, Apr 17, 2020 at 2:07 PM Mahmood Naderan wrote: > Hi > How can I disable MKL while building gromacs? With this configure command > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_FFT_LIBRARY=fftw3 > > > > I see > > -- The GROMACS-managed build of FFTW 3 will configure with the following > optimizations: --enable-sse2;--enable-avx;--enable-avx2 > -- Using external FFT library - FFTW3 build managed by GROMACS > -- Looking for sgemm_ > -- Looking for sgemm_ - not found > -- Looking for sgemm_ > -- Looking for sgemm_ - found > -- Found BLAS: > /share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_lp64.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_intel_thread.so;/share/binary/intel/composer_xe_2015.0.090/mkl/lib/intel64/libmkl_core.so;/opt/intel/lib/intel64/libguide.so;-lpthread;-lm;-ldl > > > > > > Then I get these errors > > [100%] Linking CXX executable ../../bin/gmx > [100%] Linking CXX executable ../../bin/template > /bin/ld: warning: libmkl_intel_lp64.so, needed by > ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) > /bin/ld: warning: libmkl_intel_thread.so, needed by > ../../lib/libgromacs.so.4.0.0, not found (try using -rpath or -rpath-link) > /bin/ld: warning: libmkl_core.so, needed by ../../lib/libgromacs.so.4.0.0, > not found (try using -rpath or -rpath-link) > /bin/ld: warning: libguide.so, needed by ../../lib/libgromacs.so.4.0.0, > not found (try using -rpath or -rpath-link) > ../../lib/libgromacs.so.4.0.0: undefined reference to `ssteqr_' > ../../lib/libgromacs.so.4.0.0: undefined reference to `dsteqr_' > ../../lib/libgromacs.so.4.0.0: undefined reference to `sger_' > > > > > > > Regards, > Mahmood > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From pall.szilard at gmail.com Wed Apr 22 00:32:59 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 21 Apr 2020 22:32:59 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: <9bc1b76d-5a4b-78f4-eff1-dfd2a4bbf73f@gmail.com> References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> <9bc1b76d-5a4b-78f4-eff1-dfd2a4bbf73f@gmail.com> Message-ID: Hi, Note that the new generation Ryzen2-based CPUs perform even better than those we benchmarked for that paper. The 3900-series Threarippers are great for workstations, unless you need the workstation form-factor, you are better off with servers like the TYAN GA88B8021. If so, i EPYC 1P is what you should be looking at, e.g. EPYC 7402P. GPU-wise, depending on your timeline you can expect NVIDIA to release something this year, so you may want to time the purchase to either hit the curren-gen GPUs discounted or go for the next gen. Cheers, -- Szil?rd On Sat, Apr 18, 2020 at 7:56 AM Alex wrote: > From what I am seeing in this paper, we should just go with something > along the lines of Ryzen 1950x + 4 x 2080 or 2080Ti. There are > indications that Ryzen also rips (pun intended) Xeons in DFT/CC > calculations, so overall this combination sounds quite reasonable for > our purposes. This also outlines a path towards upgrading our existing > nodes. > > Thanks Kevin, this is very informative. > > Alex > > On 4/17/2020 8:52 PM, Kevin Boyd wrote: > > Yes, that's it. I think consumer-class Nvidia cards are still the best > > value, unless you have other applications that need the benefits of > > industrial cards. > > > > Cheers, > > > > Kevin > > > > On Fri, Apr 17, 2020 at 5:58 PM Alex wrote: > > > >> *Message sent from a system outside of UConn.* > >> > >> > >> Hi Kevin, > >> > >> Thanks for responding! RAM is mentioned for completeness. This amount is > >> not for gmx -- we do other, much more RAM-intensive calculations, in > >> fact 256 gigs is very modest for that. I have no doubt that AMD CPUs > >> would work with Nvidia GPUs, was mainly wondering if there would be any > >> additional speed boost if we also used AMD GPUs. > >> > >> Nope, haven't seen the paper, but quite interested in checking it out. > >> Is this the latest version? > >> https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 > >> > >> Thank you, > >> > >> Alex > >> > >> On 4/17/2020 6:29 PM, Kevin Boyd wrote: > >>> Hi, > >>> > >>> AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base > >>> regardless of the GPUs you end up choosing. In my experience AMD CPUs > >> have > >>> had great value. > >>> > >>> A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very > >> much > >>> overkill, but perhaps you have other uses for the machine that need it. > >>> > >>> Have you seen the updated "More bang for your buck" paper that goes > into > >>> optimizing compute nodes? > >>> > >>> > >>> See > >>> > >>> > >>> > >>> On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: > >>> > >>>> *Message sent from a system outside of UConn.* > >>>> > >>>> > >>>> Gromacs is totally compatible with nvidia based gpu. You need to > install > >>>> cuda drivers and you can build easily with cmake. For amd gpu you > would > >> be > >>>> needing openCL alongwith the sdk for amd gpu. I would suggest you to > use > >>>> nvidia acceleration for better performance. > >>>> > >>>> On Sat, Apr 18, 2020, 4:42 AM Alex wrote: > >>>> > >>>>> Hello all, > >>>>> > >>>>> Hope you're staying safe & healthy! We are starting to spec new > >> machines > >>>>> and our end goal is two machines, each featuring: > >>>>> > >>>>> 1. ~16-18 CPU cores w/hyperthreading > >>>>> > >>>>> 2. Four GPUs > >>>>> > >>>>> 3. ~256 gigs of RAM. > >>>>> > >>>>> A very approximate allocation of money is ~$15-20K per unit, but we > >>>>> could of course buy more if each machine turns out to be > significantly > >>>>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are > >>>>> welcome. We are somewhat open to AMD-based solutions, but wonder what > >>>>> the situation is with GPU acceleration, as so far we've been entirely > >>>>> Intel-based. Will it work with NVIDIA cards? Will we have to install > >> AMD > >>>>> GPUs? Does current Gromacs perform well on AMD-based rigs? > >>>>> > >>>>> Thank you! > >>>>> > >>>>> Alex > >>>>> > >>>>> -- > >>>>> Gromacs Users mailing list > >>>>> > >>>>> * Please search the archive at > >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>>> posting! > >>>>> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> * For (un)subscribe requests visit > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>> send a mail to gmx-users-request at gromacs.org. > >>>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nedomacho at gmail.com Wed Apr 22 07:42:14 2020 From: nedomacho at gmail.com (Alex) Date: Wed, 22 Apr 2020 05:42:14 -0000 Subject: [gmx-users] Spec'ing for new machines (again!) In-Reply-To: References: <1994569922.6241723.1587122056803.JavaMail.zimbra@savba.sk> <740d0a20-0c3d-0a87-ea5f-0fdbc4a5cdc6@vt.edu> <668854826.6270614.1587129399152.JavaMail.zimbra@savba.sk> <5c85f42b-a94c-9083-c75c-f8fd2ea99d67@vt.edu> <964435053.6336486.1587161044286.JavaMail.zimbra@savba.sk> <9bc1b76d-5a4b-78f4-eff1-dfd2a4bbf73f@gmail.com> Message-ID: <48571db1-9dcb-511f-8b61-bc8e7b36d92c@gmail.com> Hi Szil?rd, We haven't decided yet on what price point& performance level we would be settling on, but this is overall great advice, thanks a lot. Alex On 4/21/2020 4:32 PM, Szil?rd P?ll wrote: > Hi, > > Note that the new generation Ryzen2-based CPUs perform even better than > those we benchmarked for that paper. The 3900-series Threarippers are great > for workstations, unless you need the workstation form-factor, you are > better off with servers like the TYAN GA88B8021. If so, i EPYC 1P is what > you should be looking at, e.g. EPYC 7402P. > > GPU-wise, depending on your timeline you can expect NVIDIA to release > something this year, so you may want to time the purchase to either hit the > curren-gen GPUs discounted or go for the next gen. > > Cheers, > -- > Szil?rd > > > On Sat, Apr 18, 2020 at 7:56 AM Alex wrote: > >> From what I am seeing in this paper, we should just go with something >> along the lines of Ryzen 1950x + 4 x 2080 or 2080Ti. There are >> indications that Ryzen also rips (pun intended) Xeons in DFT/CC >> calculations, so overall this combination sounds quite reasonable for >> our purposes. This also outlines a path towards upgrading our existing >> nodes. >> >> Thanks Kevin, this is very informative. >> >> Alex >> >> On 4/17/2020 8:52 PM, Kevin Boyd wrote: >>> Yes, that's it. I think consumer-class Nvidia cards are still the best >>> value, unless you have other applications that need the benefits of >>> industrial cards. >>> >>> Cheers, >>> >>> Kevin >>> >>> On Fri, Apr 17, 2020 at 5:58 PM Alex wrote: >>> >>>> *Message sent from a system outside of UConn.* >>>> >>>> >>>> Hi Kevin, >>>> >>>> Thanks for responding! RAM is mentioned for completeness. This amount is >>>> not for gmx -- we do other, much more RAM-intensive calculations, in >>>> fact 256 gigs is very modest for that. I have no doubt that AMD CPUs >>>> would work with Nvidia GPUs, was mainly wondering if there would be any >>>> additional speed boost if we also used AMD GPUs. >>>> >>>> Nope, haven't seen the paper, but quite interested in checking it out. >>>> Is this the latest version? >>>> https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 >>>> >>>> Thank you, >>>> >>>> Alex >>>> >>>> On 4/17/2020 6:29 PM, Kevin Boyd wrote: >>>>> Hi, >>>>> >>>>> AMD CPUs work fine with Nvidia GPUs, so feel free to use AMD as a base >>>>> regardless of the GPUs you end up choosing. In my experience AMD CPUs >>>> have >>>>> had great value. >>>>> >>>>> A ratio of ~4 cores/ GPU shouldn't be a problem. 256 GB of RAM is very >>>> much >>>>> overkill, but perhaps you have other uses for the machine that need it. >>>>> >>>>> Have you seen the updated "More bang for your buck" paper that goes >> into >>>>> optimizing compute nodes? >>>>> >>>>> >>>>> See >>>>> >>>>> >>>>> >>>>> On Fri, Apr 17, 2020 at 4:17 PM FAISAL NABI wrote: >>>>> >>>>>> *Message sent from a system outside of UConn.* >>>>>> >>>>>> >>>>>> Gromacs is totally compatible with nvidia based gpu. You need to >> install >>>>>> cuda drivers and you can build easily with cmake. For amd gpu you >> would >>>> be >>>>>> needing openCL alongwith the sdk for amd gpu. I would suggest you to >> use >>>>>> nvidia acceleration for better performance. >>>>>> >>>>>> On Sat, Apr 18, 2020, 4:42 AM Alex wrote: >>>>>> >>>>>>> Hello all, >>>>>>> >>>>>>> Hope you're staying safe & healthy! We are starting to spec new >>>> machines >>>>>>> and our end goal is two machines, each featuring: >>>>>>> >>>>>>> 1. ~16-18 CPU cores w/hyperthreading >>>>>>> >>>>>>> 2. Four GPUs >>>>>>> >>>>>>> 3. ~256 gigs of RAM. >>>>>>> >>>>>>> A very approximate allocation of money is ~$15-20K per unit, but we >>>>>>> could of course buy more if each machine turns out to be >> significantly >>>>>>> cheaper. All suggestions for CPUs and GPUs (esp. from Szilard) are >>>>>>> welcome. We are somewhat open to AMD-based solutions, but wonder what >>>>>>> the situation is with GPU acceleration, as so far we've been entirely >>>>>>> Intel-based. Will it work with NVIDIA cards? Will we have to install >>>> AMD >>>>>>> GPUs? Does current Gromacs perform well on AMD-based rigs? >>>>>>> >>>>>>> Thank you! >>>>>>> >>>>>>> Alex >>>>>>> >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >>>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From rollyng at gmail.com Wed Apr 22 16:40:14 2020 From: rollyng at gmail.com (Rolly Ng) Date: Wed, 22 Apr 2020 14:40:14 -0000 Subject: [gmx-users] =?utf-8?b?5Zue5aSNOiAg5Zue5aSNOiBQcm9ibGVtIHdpdGgg?= =?utf-8?q?Potential_Mean_Force_calculation?= In-Reply-To: References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> Message-ID: <002201d618b3$ec0d3730$c427a590$@gmail.com> Dear Justin and Vu, I think I have solved part of my problem. The number of tpr/xvg pairs were too much in my case. Although I used the script to generate 50 pairs with 0.1nm setting, it turns out that only the first 27 pairs works. ./setupUmbrella.py summary_distances.dat 0.1 run-umbrella.sh &> caught-output.txt Please find my summary_distances.dat and caught-output.txt attached. I also found that the wham loops for very long time if there is problem with the tpr/xvg pairs. A normal run will last only tens of iteration. I have to check the pairs one by one in order to get a reasonable PMF. I have uploaded them to RG. What could be the problem with the tpr/xvg pairs? How can I avoid it the next time? Thanks, Rolly Thank you and I am checking the tpr and vxg files by reducing the number of files in the 2 dat files. The first 10 data points seems giving the correct PMF reading although the list is incomplete, so I suspect that some of my tpr and xvg files are bad for wham. I will report my finding after check all 51 tpr/vxg pairs. Thank you, Rolly -----????----- ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se ?? Quyen V. Vu ????: 2020?4?21???? ??11:10 ???: gmx-users at gromacs.org ??: Re: [gmx-users] ??: Problem with Potential Mean Force calculation I think the output from WHAM in the terminal may give some information to detect the problem. WHAM will tell you the boundary he used to fit your PMF because your histogram and COM position both tell us your reaction coordinate is range from about 2-7nm but WHAM fit from 0-10nm is so strange Best regards, On Tue, Apr 21, 2020 at 4:49 PM Justin Lemkul wrote: > > > On 4/21/20 10:40 AM, Rolly Ng wrote: > > Dear Justin, > > > > I cut the x-axis to 8nm but I have uploaded the original histogram > > plot > to > > RG. Please have a look again, thank you. > > It's not a matter of changing the axis. Your histograms indicate > sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm. If you > have a protein-protein complex, I doubt the COM distance can ever be zero. > There is a disconnect between your files. > > -Justin > > > I used the following command for wham, gmx wham -it tpr-files.dat > > -if pullf-files.dat -o -hist -unit kCal > > > > I used the AMBER99SB-ILDN forcefield and protein protein pair is > KEAP1-NRF2 > > (2FLU) from https://www.rcsb.org/structure/2FLU > > > > I tried to pull the NRF2 from KEAP1, and I can visualize that it has > > been successfully pulled from the initial position, producing the > > force and > COM > > plots which seem reasonable. > > > > How can I debug the problem? Which files should I check? > > > > Thanks, > > Rolly > > > > -----????----- > > ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > ?? Justin Lemkul > > ????: 2020?4?21???? ??7:09 > > ???: Discussion list for GROMACS users > > ??: Re: [gmx-users] Problem with Potential Mean Force calculation > > > > > > > > On 4/21/20 2:08 AM, Rolly Ng wrote: > >> Dear Gromacs user and Dr. lemkul, > >> > >> I think my previous email is too large to send on the list. Could > >> you please kindly look at the link for the plots? > >> > >> https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_s > >> tra nge_Potential_Mean_Force_PMF_result > >> > > I don't see how the PMF could possibly arise from your data. The > > reaction coordinate extends from 2 - 6 nm, but your PMF plot goes > > from 0 > > - 10 nm. > > > >> I tried to applied the umbrella tutorial to my protein-protein > >> system, and I am using GROMACS 2020 > >> > >> http://www.mdtutorials.com/gmx/umbrella/index.html > >> > >> I have very dense windows to 0.1nm as shown on the attached > >> histogram, but as I look at the PMF curve, it is strange and incomplete? > >> > > I hope you're not directly applying the tutorial; there are some > > aspects > of > > it (use of restraints, the window spacing, and the restraint only > > along > z) > > that are not applicable to general protein-protein complexes. > > > >> Could you please help me to check what has gone wrong? > >> > > What was your gmx wham command? I really don't understand how it > > could > have > > even produced that PMF given the data you have in the histograms. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalemkul at vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > send a > > mail to gmx-users-request at gromacs.org. > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: caught-output.txt URL: From subhamoy at ualberta.ca Wed Apr 22 23:40:06 2020 From: subhamoy at ualberta.ca (Subhamoy Mahajan) Date: Wed, 22 Apr 2020 21:40:06 -0000 Subject: [gmx-users] How to report bugs or issues? Message-ID: <8FAFBA60-B972-4393-8992-1C7B7E203EC1@ualberta.ca> Hello Everyone, I have not used the mailing list before. Could anyone give me some pointers on how to report a bug or issue that I have noticed in gromacs? I can?t seem to ?file a new issue? in redmine.gromacs.org . Thanking You, Subhamoy From magnus.lundborg at scilifelab.se Thu Apr 23 08:45:03 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Thu, 23 Apr 2020 06:45:03 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi Alex, pull-group1-pbcatom lets you specify the exact atom used as the PBC reference. Both 0 and -1 are special cases. For small molecules 0 is (almost?) always OK. Find one in the center of you membrane (in the pull direction). I'll actually have to check if -1 is even compatible with pull-pbc-ref-prev-step-com. It's possible that that combination should not be allowed even. As you say, you can define a subgroup within the larger membrane group, but that is mainly of use if you know that some atoms consistently in the center of the whole group and others are more flexible. Regards, Magnus On 2020-04-21 16:24, Alex wrote: > Hi Magnus, > Actually I am confused with the available options for the > "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". > For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when > one of the group is large, even the 2020.1 version of grmacs would give a > warning if one used No in a case of presence of a large group. > Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 > the middle atom (number wise) of the large group is used automatically > which is safe only for small groups as manual states. So, only > remaining option is -1. > So, what I understood for a layered-large group similar to what I have one > should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 > which would cause moving the system along -Z during the pulling. > > Using gmx select, can I manually define a sub-group around the COM of the > large group, and consider it as one of the pulling groups instead of the > large group? > > Thank you > Alex > > On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < > magnus.lundborg at scilifelab.se> wrote: > >> Hi Alex, >> >> I don't see why it would need pull-group1-pbcatom = -1. Why not pick a >> central atom? >> >> Regards, >> >> Magnus >> >> On 2020-04-20 13:40, Alex wrote: >>> Hi Magnus, >>> Thanks. >>> The problem raises only because of using the pull-pbc-ref-prev-step-com >>> which needs the pull-group1-pbcatom to be -1 to be meaningful. >>> For an identical system and mdp parameters using 2018 version of gromacs >>> which is independent to the pull-pbc-ref-prev-step-com, I see no issue. >>> >>> Regards, >>> Alex >>> >>> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < >>> magnus.lundborg at scilifelab.se> wrote: >>> >>>> Sorry, about the statement about pbcatom -1. I was thinking about 0. I >>>> don't know if pbcatom -1 is good or not in this case. >>>> >>>> Regards, >>>> >>>> Magnus >>>> >>>> On 2020-04-20 09:24, Magnus Lundborg wrote: >>>>> Hi Alex, >>>>> >>>>> I don't think this is related to using pull-pbc-ref-prev-step-com. >>>>> Have you tried without it? However, it is risky using pbcatom -1, >>>>> since you don't know what atom you are using as the initial reference. >>>>> I would suggest picking an atom you know is located at the centre of >>>>> the structure. >>>>> >>>>> I would think that the problem has to do with the comm removal. What >>>>> are your parameters for comm-mode, nstcomm and comm-grps? It is >>>>> possible that you need to lower your nstcomm. It is also possible, but >>>>> not certain, the comm-mode Linear-acceleration-correction might help >>>>> you. For some reason, it seems like I have sometimes avoided similar >>>>> problems by using the sd integrator instead, but I haven't evaluated >>>>> that properly - it might just have been coincidences. If you see a >>>>> clear difference using the sd integrator it might be good if you'd >>>>> file an issue about it on gitlab so that someone can look into if >>>>> there is something wrong. >>>>> >>>>> Regards, >>>>> Magnus >>>>> >>>>> On 2020-04-18 20:12, Alex wrote: >>>>>> Dear all, >>>>>> To generate the initial configurations for umbrella sampling, I >>>>>> conducted a >>>>>> simple pulling simulation by which a single-small molecule (mol_A) is >>>>>> being >>>>>> dragged along -Z from water into the body of a thin film. >>>>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = >>>>>> yes" and >>>>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the >>>>>> system >>>>>> along the pulling direction as soon as the mol_A reach to the thin >> film, >>>>>> please find below the pulling flags movie and plot in below links. >>>>>> >>>>>> Centering the thin film and mol_A could solve the issue, (echo 1 0 | >>>>>> trjconv -center yes) to some extent but still COM changes in the early >>>>>> stage below 2ns. , >>>>>> COM: >>>>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 >>>>>> >>>>>> Movie in which the water molecules are hidden: >>>>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv >>>>>> >>>>>> - >>>>>> gmx version 2020.1 >>>>>> ----- >>>>>> pull = yes >>>>>> pull-print-com = no >>>>>> pull-print-ref-value = yes >>>>>> pull-print-components = Yes >>>>>> pull-nstxout = 1000 >>>>>> pull-nstfout = 1000 >>>>>> pull-pbc-ref-prev-step-com = yes >>>>>> pull-ngroups = 2 >>>>>> pull-ncoords = 1 >>>>>> pull-group1-name = Thin-film >>>>>> pull-group1-pbcatom = -1 >>>>>> pull-group2-name = mol_A >>>>>> pull-group2-pbcatom = 0 >>>>>> pull-coord1-type = umbrella >>>>>> pull-coord1-geometry = direction >>>>>> pull-coord1-groups = 1 2 >>>>>> pull-coord1-dim = N N Y >>>>>> pull-coord1-origin = 0.0 0.0 0.0 >>>>>> pull-coord1-vec = 0.0 0.0 -1.0 >>>>>> pull-coord1-start = yes >>>>>> pull-coord1-init = 0 >>>>>> pull-coord1-rate = 0.0005 >>>>>> pull-coord1-k = 5000 >>>>>> ----- >>>>>> I wonder if I could extract correct initial configuration from this >>>>>> trajectory? With correct initial configuration, I mean a set of gro >>>>>> file in >>>>>> which change from one from to another is the distance between the COM >> of >>>>>> the thin-film and mol_A? >>>>>> >>>>>> Thank you >>>>>> Alex >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From ydu-sci at outlook.com Thu Apr 23 10:25:50 2020 From: ydu-sci at outlook.com (Yu Du) Date: Thu, 23 Apr 2020 08:25:50 -0000 Subject: [gmx-users] How to report bugs or issues? In-Reply-To: <55eb5cb1.34a90.171a622d510.Coremail.duyu@sioc.ac.cn> References: <55eb5cb1.34a90.171a622d510.Coremail.duyu@sioc.ac.cn> Message-ID: -----Original Messages----- From: "Paul bauer" Sent Time: 2020-03-25 00:40:13 (Wednesday) To: gromacs.org_gmx-users at maillist.sys.kth.se, "gmx-announce at gromacs.org" Cc: Subject: [gmx-users] GROMACS has switched to use Gitlab Hello gmx users! I just finished the transition of our project database to use the Gitlab servers. This means that from now on issues should be reported using the issue tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of redmine.gromacs.org. The redmine and gerrit servers have been set be read only from now on, so that you can still access information there, but it wont be able to report new things there any more. Cheers Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From Stephane.ABEL at cea.fr Thu Apr 23 11:43:02 2020 From: Stephane.ABEL at cea.fr (ABEL Stephane) Date: Thu, 23 Apr 2020 09:43:02 -0000 Subject: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion Message-ID: <3E39B768BB199548AB18F7289E7534AF560CD689@EXDAG0-B0.intra.cea.fr> Deal all, I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences for the bonded and non bonded terms For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below | mdin Single point &cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999 / But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 0 ; Maximum number of (minimization) steps to perform (should be 50000) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Group ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Cut-off ; Treatment of long range electrostatic interactions rcoulomb = 0 ; Short-range electrostatic cut-off rvdw = 0 ; Short-range Van der Waals cut-off rlist = 0 pbc = no ; P continuation = yes I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander Thanks in advance for your help and suggestions St?phane From jalemkul at vt.edu Thu Apr 23 12:17:11 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 23 Apr 2020 10:17:11 -0000 Subject: [gmx-users] =?utf-8?b?5Zue5aSNOiDlm57lpI06IFByb2JsZW0gd2l0aCBQ?= =?utf-8?q?otential_Mean_Force_calculation?= In-Reply-To: <002201d618b3$ec0d3730$c427a590$@gmail.com> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> <002201d618b3$ec0d3730$c427a590$@gmail.com> Message-ID: <5f479f44-56b4-e1f0-f4ae-ccdb62a238d2@vt.edu> On 4/22/20 10:40 AM, Rolly Ng wrote: > Dear Justin and Vu, > > I think I have solved part of my problem. The number of tpr/xvg pairs were too much in my case. Although I used the script to generate 50 pairs with 0.1nm setting, it turns out that only the first 27 pairs works. What does "only the first 27 pairs work" mean? > ./setupUmbrella.py summary_distances.dat 0.1 run-umbrella.sh &> caught-output.txt > > Please find my summary_distances.dat and caught-output.txt attached. > > I also found that the wham loops for very long time if there is problem with the tpr/xvg pairs. A normal run will last only tens of iteration. I have to check the pairs one by one in order to get a reasonable PMF. I have uploaded them to RG. > > What could be the problem with the tpr/xvg pairs? How can I avoid it the next time? The reaction coordinate you established with these 51 .tpr files is consistent with the histograms you showed - sampling roughly between 2 - 8 nm. The PMF is still basically an impossibility based on these data. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Thu Apr 23 12:18:44 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 23 Apr 2020 10:18:44 -0000 Subject: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion In-Reply-To: <3E39B768BB199548AB18F7289E7534AF560CD689@EXDAG0-B0.intra.cea.fr> References: <3E39B768BB199548AB18F7289E7534AF560CD689@EXDAG0-B0.intra.cea.fr> Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4fdcc@vt.edu> On 4/23/20 5:42 AM, ABEL Stephane wrote: > Deal all, > > I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences for the bonded and non bonded terms > > For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below > > | mdin Single point > &cntrl > imin=0, > maxcyc=0, > ntmin=2, > ntb=0, > igb=0, > cut=999 > / > > But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms > > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 0 ; Maximum number of (minimization) steps to perform (should be 50000) > > ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long range forces > cutoff-scheme = Group ; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, grid) > coulombtype = Cut-off ; Treatment of long range electrostatic interactions > rcoulomb = 0 ; Short-range electrostatic cut-off > rvdw = 0 ; Short-range Van der Waals cut-off > rlist = 0 > pbc = no ; P > continuation = yes > > I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander Why is it incompatible with mdrun -rerun? Do you get an error? You also shouldn't use a minimizer when doing a zero-point energy. Use the md integrator. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Thu Apr 23 12:52:57 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Thu, 23 Apr 2020 10:52:57 -0000 Subject: [gmx-users] Problem C-H bonds of Benzene after minimization Message-ID: Dear Gromacs Users, I am trying to perform MD simulations of benzene molecule in a cube of water just for practicing. By following the tutorial https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup the residue Benzene within Amber99 force field. After the minimization however I got the C-H bonds of benzene distorted and unusually stretched. During the grompp procedure I got the following note: " In moleculetype 'Other' 6 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom." Could it be related to the problem I am facing? Here the starting .pdb file of benzene: COMPND BENZENE REMARK 1 File created by GaussView 6.0.16 HETATM 1 C1 C6H6 0 0.968 1.903 0.000 C HETATM 2 C2 C6H6 0 2.363 1.903 0.000 C HETATM 3 C3 C6H6 0 3.060 3.111 0.000 C HETATM 4 C4 C6H6 0 2.363 4.319 -0.001 C HETATM 5 C5 C6H6 0 0.968 4.319 -0.002 C HETATM 6 C6 C6H6 0 0.270 3.111 -0.001 C HETATM 7 H1 C6H6 0 0.418 0.951 0.000 H HETATM 8 H2 C6H6 0 2.912 0.951 0.001 H HETATM 9 H3 C6H6 0 4.160 3.111 0.001 H HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 H HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 H HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 H END CONECT 1 2 6 7 CONECT 2 1 3 8 CONECT 3 2 4 9 CONECT 4 3 5 10 CONECT 5 4 6 11 CONECT 6 1 5 12 CONECT 7 1 CONECT 8 2 CONECT 9 3 CONECT 10 4 CONECT 11 5 CONECT 12 6 Here the .rtp file included in Amber99.ff: [ C6H6 ] [ atoms ] C1 CA -0.1285 1 C2 CA -0.1285 2 C3 CA -0.1285 3 C4 CA -0.1285 4 C5 CA -0.1285 5 C6 CA -0.1285 6 H1 HA 0.1285 7 H2 HA 0.1285 8 H3 HA 0.1285 9 H4 HA 0.1285 10 H5 HA 0.1285 11 H6 HA 0.1285 12 [ bonds ] C1 H7 C1 C2 C1 C6 C2 C8 C2 C1 C2 C3 C3 H9 C3 C2 C3 C4 C4 H10 C4 C3 C4 C5 C5 H11 C5 C4 C5 C6 C6 H12 C6 C5 C6 C1 Can somebody help me to figure out such issue? Thanks. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Thu Apr 23 12:54:46 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 23 Apr 2020 10:54:46 -0000 Subject: [gmx-users] Problem C-H bonds of Benzene after minimization In-Reply-To: References: Message-ID: <5b6850d5-d8b6-a81d-f311-6fd3c83189e3@vt.edu> On 4/23/20 6:52 AM, Paolo Costa wrote: > Dear Gromacs Users, > > I am trying to perform MD simulations of benzene molecule in a cube of > water just for practicing. > By following the tutorial > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup > the residue Benzene within Amber99 force field. After the minimization > however I got the C-H bonds of benzene distorted and unusually stretched. > During the grompp procedure I got the following note: > > " In moleculetype 'Other' 6 atoms are not bound by a potential or > constraint to any other atom in the same moleculetype. Although > technically this might not cause issues in a simulation, this often means > that the user forgot to add a bond/potential/constraint or put multiple > molecules in the same moleculetype definition by mistake. Run with -v to > get information for each atom." > > Could it be related to the problem I am facing? > > Here the starting .pdb file of benzene: > COMPND BENZENE > REMARK 1 File created by GaussView 6.0.16 > HETATM 1 C1 C6H6 0 0.968 1.903 0.000 C > HETATM 2 C2 C6H6 0 2.363 1.903 0.000 C > HETATM 3 C3 C6H6 0 3.060 3.111 0.000 C > HETATM 4 C4 C6H6 0 2.363 4.319 -0.001 C > HETATM 5 C5 C6H6 0 0.968 4.319 -0.002 C > HETATM 6 C6 C6H6 0 0.270 3.111 -0.001 C > HETATM 7 H1 C6H6 0 0.418 0.951 0.000 H > HETATM 8 H2 C6H6 0 2.912 0.951 0.001 H > HETATM 9 H3 C6H6 0 4.160 3.111 0.001 H > HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 H > HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 H > HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 H > END > CONECT 1 2 6 7 > CONECT 2 1 3 8 > CONECT 3 2 4 9 > CONECT 4 3 5 10 > CONECT 5 4 6 11 > CONECT 6 1 5 12 > CONECT 7 1 > CONECT 8 2 > CONECT 9 3 > CONECT 10 4 > CONECT 11 5 > CONECT 12 6 > > Here the .rtp file included in Amber99.ff: > [ C6H6 ] > [ atoms ] > C1 CA -0.1285 1 > C2 CA -0.1285 2 > C3 CA -0.1285 3 > C4 CA -0.1285 4 > C5 CA -0.1285 5 > C6 CA -0.1285 6 > H1 HA 0.1285 7 > H2 HA 0.1285 8 > H3 HA 0.1285 9 > H4 HA 0.1285 10 > H5 HA 0.1285 11 > H6 HA 0.1285 12 > [ bonds ] > C1 H7 > C1 C2 > C1 C6 > C2 C8 > C2 C1 > C2 C3 > C3 H9 > C3 C2 > C3 C4 > C4 H10 > C4 C3 > C4 C5 > C5 H11 > C5 C4 > C5 C6 > C6 H12 > C6 C5 > C6 C1 > > Can somebody help me to figure out such issue? The bonds in the .rtp file are wrong. The hydrogen nomenclature is incorrect so you do not have any C-H bonds in the topology. You can verify this for yourself. You probably have 6 bonds instead of 12. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Thu Apr 23 13:05:36 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Thu, 23 Apr 2020 11:05:36 -0000 Subject: [gmx-users] Problem C-H bonds of Benzene after minimization In-Reply-To: <5b6850d5-d8b6-a81d-f311-6fd3c83189e3@vt.edu> References: <5b6850d5-d8b6-a81d-f311-6fd3c83189e3@vt.edu> Message-ID: Hi Justin, indeed there are only six bonds in the topology files! As you said the hydrogen nomenclature in .rtp file is wrong. Thanks a lot! Paolo Il giorno gio 23 apr 2020 alle ore 12:55 Justin Lemkul ha scritto: > > > On 4/23/20 6:52 AM, Paolo Costa wrote: > > Dear Gromacs Users, > > > > I am trying to perform MD simulations of benzene molecule in a cube of > > water just for practicing. > > By following the tutorial > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I > setup > > the residue Benzene within Amber99 force field. After the minimization > > however I got the C-H bonds of benzene distorted and unusually stretched. > > During the grompp procedure I got the following note: > > > > " In moleculetype 'Other' 6 atoms are not bound by a potential or > > constraint to any other atom in the same moleculetype. Although > > technically this might not cause issues in a simulation, this often > means > > that the user forgot to add a bond/potential/constraint or put > multiple > > molecules in the same moleculetype definition by mistake. Run with -v > to > > get information for each atom." > > > > Could it be related to the problem I am facing? > > > > Here the starting .pdb file of benzene: > > COMPND BENZENE > > REMARK 1 File created by GaussView 6.0.16 > > HETATM 1 C1 C6H6 0 0.968 1.903 0.000 > C > > HETATM 2 C2 C6H6 0 2.363 1.903 0.000 > C > > HETATM 3 C3 C6H6 0 3.060 3.111 0.000 > C > > HETATM 4 C4 C6H6 0 2.363 4.319 -0.001 > C > > HETATM 5 C5 C6H6 0 0.968 4.319 -0.002 > C > > HETATM 6 C6 C6H6 0 0.270 3.111 -0.001 > C > > HETATM 7 H1 C6H6 0 0.418 0.951 0.000 > H > > HETATM 8 H2 C6H6 0 2.912 0.951 0.001 > H > > HETATM 9 H3 C6H6 0 4.160 3.111 0.001 > H > > HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 > H > > HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 > H > > HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 > H > > END > > CONECT 1 2 6 7 > > CONECT 2 1 3 8 > > CONECT 3 2 4 9 > > CONECT 4 3 5 10 > > CONECT 5 4 6 11 > > CONECT 6 1 5 12 > > CONECT 7 1 > > CONECT 8 2 > > CONECT 9 3 > > CONECT 10 4 > > CONECT 11 5 > > CONECT 12 6 > > > > Here the .rtp file included in Amber99.ff: > > [ C6H6 ] > > [ atoms ] > > C1 CA -0.1285 1 > > C2 CA -0.1285 2 > > C3 CA -0.1285 3 > > C4 CA -0.1285 4 > > C5 CA -0.1285 5 > > C6 CA -0.1285 6 > > H1 HA 0.1285 7 > > H2 HA 0.1285 8 > > H3 HA 0.1285 9 > > H4 HA 0.1285 10 > > H5 HA 0.1285 11 > > H6 HA 0.1285 12 > > [ bonds ] > > C1 H7 > > C1 C2 > > C1 C6 > > C2 C8 > > C2 C1 > > C2 C3 > > C3 H9 > > C3 C2 > > C3 C4 > > C4 H10 > > C4 C3 > > C4 C5 > > C5 H11 > > C5 C4 > > C5 C6 > > C6 H12 > > C6 C5 > > C6 C1 > > > > Can somebody help me to figure out such issue? > > The bonds in the .rtp file are wrong. The hydrogen nomenclature is > incorrect so you do not have any C-H bonds in the topology. You can > verify this for yourself. You probably have 6 bonds instead of 12. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From halverson at Princeton.EDU Thu Apr 23 18:40:41 2020 From: halverson at Princeton.EDU (Jonathan D. Halverson) Date: Thu, 23 Apr 2020 16:40:41 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node Message-ID: We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running RHEL 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel nodes. Everything below is about of the POWER9/V100 node. We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 CPU-core and 1 GPU (ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives 102 ns/day. The difference in performance is roughly the same for the larger ADH benchmark and when different numbers of CPU-cores are used. GROMACS is always underperforming on our POWER9/V100 nodes. We have pinning turned on (see Slurm script at bottom). Below is our build procedure on the POWER9/V100 node: version_gmx=2019.6 wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz tar zxvf gromacs-${version_gmx}.tar.gz cd gromacs-${version_gmx} mkdir build && cd build module purge module load rh/devtoolset/7 module load cudatoolkit/10.2 OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" cmake3 .. -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ -DGMX_OPENMP_MAX_THREADS=128 \ -DCMAKE_INSTALL_PREFIX=$HOME/.local \ -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON make -j 10 make check make install 45 of the 46 tests pass with the exception being HardwareUnitTests. There are several posts about this and apparently it is not a concern. The full build log is here: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log Here is more info about our POWER9/V100 node: $ lscpu Architecture: ppc64le Byte Order: Little Endian CPU(s): 128 On-line CPU(s) list: 0-127 Thread(s) per core: 4 Core(s) per socket: 16 Socket(s): 2 NUMA node(s): 6 Model: 2.3 (pvr 004e 1203) Model name: POWER9, altivec supported CPU max MHz: 3800.0000 CPU min MHz: 2300.0000 You see that we have 4 hardware threads per physical core. If we use 4 hardware threads on the RNASE benchmark instead of 1 the performance goes to 119 ns/day which is still about 20% less than the Broadwell/P100 value. When using multiple CPU-cores on the POWER9/V100 there is significant variation in the execution time of the code. There are four GPUs per POWER9/V100 node: $ nvidia-smi -q Driver Version : 440.33.01 CUDA Version : 10.2 GPU 00000004:04:00.0 Product Name : Tesla V100-SXM2-32GB The GPUs have been shown to perform as expected on other applications. The following lines are found in md.log for the POWER9/V100 run: Overriding thread affinity set outside gmx mdrun Pinning threads with an auto-selected logical core stride of 128 NOTE: Thread affinity was not set. The full md.log is available here: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log Below are the MegaFlops Accounting for the POWER9/V100 versus Broadwell/P100: ================ IBM POWER9 WITH NVIDIA V100 ================ Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 297.763872 2679.875 0.0 NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 98.0 NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 1.6 1,4 nonbonded interactions 53.415341 4807.381 0.0 Shift-X 3.029040 18.174 0.0 Angles 37.043704 6223.342 0.0 Propers 55.825582 12784.058 0.1 Impropers 4.220422 877.848 0.0 Virial 2.432585 43.787 0.0 Stop-CM 2.452080 24.521 0.0 Calc-Ekin 48.128080 1299.458 0.0 Lincs 20.536159 1232.170 0.0 Lincs-Mat 444.613344 1778.453 0.0 Constraint-V 261.192228 2089.538 0.0 Constraint-Vir 2.430161 58.324 0.0 Settle 73.382008 23702.389 0.1 ----------------------------------------------------------------------------- Total 16441499.096 100.0 ----------------------------------------------------------------------------- ================ INTEL BROADWELL WITH NVIDIA P100 ================ Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Pair Search distance check 271.334272 2442.008 0.0 NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 98.0 NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 1.6 1,4 nonbonded interactions 53.415341 4807.381 0.0 Shift-X 3.029040 18.174 0.0 Bonds 10.541054 621.922 0.0 Angles 37.043704 6223.342 0.0 Propers 55.825582 12784.058 0.1 Impropers 4.220422 877.848 0.0 Virial 2.432585 43.787 0.0 Stop-CM 2.452080 24.521 0.0 Calc-Ekin 48.128080 1299.458 0.0 Lincs 9.992997 599.580 0.0 Lincs-Mat 50.775228 203.101 0.0 Constraint-V 240.108012 1920.864 0.0 Constraint-Vir 2.323707 55.769 0.0 Settle 73.382008 23702.389 0.2 ----------------------------------------------------------------------------- Total 12909529.017 100.0 ----------------------------------------------------------------------------- Some of the rows are identical between the two tables above. The largest difference is observed for the "NxN Ewald Elec. + LJ [F]" row. Here is our Slurm script: #!/bin/bash #SBATCH --job-name=gmx # create a short name for your job #SBATCH --nodes=1 # node count #SBATCH --ntasks=1 # total number of tasks across all nodes #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if multi-threaded tasks) #SBATCH --mem=4G # memory per node (4G per cpu-core is default) #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) #SBATCH --gres=gpu:1 # number of gpus per node module purge module load cudatoolkit/10.2 BCH=../rnase_cubic gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o bench.tpr gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s bench.tpr How do we get optimal performance out of GROMACS on our POWER9/V100 nodes? Jon From Stephane.ABEL at cea.fr Thu Apr 23 19:28:22 2020 From: Stephane.ABEL at cea.fr (ABEL Stephane) Date: Thu, 23 Apr 2020 17:28:22 -0000 Subject: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion Message-ID: <3E39B768BB199548AB18F7289E7534AF560CD7CB@EXDAG0-B0.intra.cea.fr> Hi Justin I obtained the following error with the following command and the mdp mentioned below gmx mdrun -s 1_OGNG_GLYCAM_SPE_GMX.tpr -rerun 1_OGNG_Amber.pdb Thank you St?phane ------------------------------------------------------------------ Program: gmx mdrun, version 2018.1 Source file: src/programs/mdrun/runner.cpp (line 736) Fatal error: The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors >> You also shouldn't use a minimizer when doing a zero-point energy. Use the md integrator. OK I try your suggestion ---------------------------------------------------------------------- And the mdp Message: 1 Date: Thu, 23 Apr 2020 06:18:33 -0400 From: Justin Lemkul To: gmx-users at gromacs.org Subject: Re: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4fdcc at vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 4/23/20 5:42 AM, ABEL Stephane wrote: > Deal all, > > I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and GROMACS codes and thus computes the energy differences for the bonded and non bonded terms > > For the former test I using the prmtop and inpcrd files generated with tleap and sander with the minimal commands below > > | mdin Single point > &cntrl > imin=0, > maxcyc=0, > ntmin=2, > ntb=0, > igb=0, > cut=999 > / > > But For GROMACS vers > 5.0 and 2018.x , I did not find the equivalent mdp parameters that can be used for doing the same task. I I used the minimal file below The bonded energy terms are very similar between the two codes but not the non bonded terms > > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 0 ; Maximum number of (minimization) steps to perform (should be 50000) > > ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long range forces > cutoff-scheme = Group ; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, grid) > coulombtype = Cut-off ; Treatment of long range electrostatic interactions > rcoulomb = 0 ; Short-range electrostatic cut-off > rvdw = 0 ; Short-range Van der Waals cut-off > rlist = 0 > pbc = no ; P > continuation = yes > > I also also notice that a tpr generated with this mdp can not be used with -rerun argument so how I can compute a SPE equivalent to Sander Why is it incompatible with mdrun -rerun? Do you get an error? You also shouldn't use a minimizer when doing a zero-point energy. Use the md integrator. -Justin From lamonteserincastanedo at gmail.com Thu Apr 23 21:01:55 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 23 Apr 2020 19:01:55 -0000 Subject: [gmx-users] about error running temperature equilibration Message-ID: I am trying to run a temperature equilibration of my system and I get the following error: ======================= NOTE 1 [file nvt.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file nvt.mdp]: Center of mass removal not necessary for Andersen. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur. ERROR 1 [file nvt.mdp]: nstcomm must be 1, not 100 for Andersen, as velocities of atoms in coupled groups are randomized every time step ======================= but I don't even have in my nvt.mdp any values for the nstcomm or restriction of center of masses translations or rotation. So I honestly do not know what is happening here. Do anybody have an idea of what is going on? This are the parameters for my cvt.mdp: ====================================================== define = -DPOSRES ; position restrain for waters ; Run parameters integrator = md-vv ; velocity Verlet algorithm nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 1 fs, largely irrelevant with Verlet rcoulomb = 333.3 ; short-range electrostatic cutoff (in nm) rvdw = 333.3 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = cutoff ; cutoff treatment ; Temperature coupling is on tcoupl = andersen ; Andersen thermostat tc-grps = System ; couple system to bath tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K nstcomm = 1 ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ===================================================================== Kindly, Lazaro From jalemkul at vt.edu Thu Apr 23 21:04:22 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 23 Apr 2020 19:04:22 -0000 Subject: [gmx-users] about error running temperature equilibration In-Reply-To: References: Message-ID: <2750018b-19ca-6787-7893-e23574d59f6b@vt.edu> On 4/23/20 3:01 PM, lazaro monteserin wrote: > I am trying to run a temperature equilibration of my system and I get the > following error: > > ======================= > NOTE 1 [file nvt.mdp]: > nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting > nstcomm to nstcalcenergy > > NOTE 2 [file nvt.mdp]: > Center of mass removal not necessary for Andersen. All velocities of > coupled groups are rerandomized periodically, so flying ice cube errors > will not occur. > > ERROR 1 [file nvt.mdp]: > nstcomm must be 1, not 100 for Andersen, as velocities of atoms in > coupled groups are randomized every time step > ======================= > but I don't even have in my nvt.mdp any values for the nstcomm or > restriction of center of masses translations or rotation. So I honestly do > not know what is happening here. > > Do anybody have an idea of what is going on? For any settings no explicitly listed, the defaults are used. See the manual: http://manual.gromacs.org/current/user-guide/mdp-options.html -Justin > This are the parameters for my cvt.mdp: > > ====================================================== > define = -DPOSRES ; position restrain for waters > ; Run parameters > integrator = md-vv ; velocity Verlet algorithm > nsteps = 50000 ; 2 * 50000 = 100 ps > dt = 0.002 ; 2 fs > ; Output control > nstxout = 500 ; save coordinates every 1.0 ps > nstvout = 500 ; save velocities every 1.0 ps > nstenergy = 500 ; save energies every 1.0 ps > nstlog = 500 ; update log file every 1.0 ps > ; Bond parameters > continuation = no ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = h-bonds ; bonds involving H are constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Nonbonded settings > cutoff-scheme = Verlet ; Buffered neighbor searching > ns_type = grid ; search neighboring grid cells > nstlist = 10 ; 1 fs, largely irrelevant with Verlet > rcoulomb = 333.3 ; short-range electrostatic cutoff (in > nm) > rvdw = 333.3 ; short-range van der Waals cutoff (in > nm) > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Electrostatics > coulombtype = cutoff ; cutoff treatment > ; Temperature coupling is on > tcoupl = andersen ; Andersen thermostat > tc-grps = System ; couple system to bath > tau_t = 0.1 ; time constant, in ps > ref_t = 300 ; reference temperature, one for each > group, in K > nstcomm = 1 > ; Pressure coupling is off > pcoupl = no ; no pressure coupling in NVT > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Velocity generation > gen_vel = yes ; assign velocities from Maxwell > distribution > gen_temp = 300 ; temperature for Maxwell distribution > gen_seed = -1 ; generate a random seed > > ===================================================================== > > Kindly, Lazaro -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ernestocamparolla2 at gmail.com Thu Apr 23 23:59:05 2020 From: ernestocamparolla2 at gmail.com (Ernesto Camparolla) Date: Thu, 23 Apr 2020 21:59:05 -0000 Subject: [gmx-users] Umbrella Sampling with 2 reaction coordinates Message-ID: Dear gromacs users, I've performed umbrella sampling using 2 reaction coordinates (of the same geometry and dimensions and which I previously used for pulling in two phase spaces). Now I am trying to recover the PMF. Does g_wham support this scheme? Is it correct to obtain a 1D PMF by supplying g_wham with pullf and pullx files obtained from a 2 reaction coordinate pulling setup? Thank you. From ekh58 at cornell.edu Fri Apr 24 00:05:23 2020 From: ekh58 at cornell.edu (Erik Henze) Date: Thu, 23 Apr 2020 22:05:23 -0000 Subject: [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries Message-ID: Hi, I am attempting to study permeation events in an ion channel where the filter is located in the extracellular region, far away from the middle of the transmembrane regions. My question is two-fold: 1) Where is the optimal place to set up the compartment boundaries? If I place the compartment boundaries in the middle of the membrane (as where most channel filters would approximately be) then, given that the pore of the channel is very large in this region, I will be swapping lots of ions which aren't actually permeating the channel. This doesn't necessarily seem like a problem, given that COMPEL can record the permeation events separately with the cylinder you define. I was concerned, however, that this constant swapping that COMPEL has to do will make the simulation very computationally costly/inefficient in some way. This brings me to my next question: 2) Can you define the cylinder in a way that is independent of the center of the channel, so that I can place the cylinder in a region centered near the extracellular region? Any thoughts/advice on this would be greatly appreciated, thanks! -Erik H From kevin.boyd at uconn.edu Fri Apr 24 03:09:14 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Fri, 24 Apr 2020 01:09:14 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: Hi, Can you post the full log for the Intel system? I typically find the real cycle and time accounting section a better place to start debugging performance issues. A couple quick notes, but need a side-by-side comparison for more useful analysis, and these points may apply to both systems so may not be your root cause: * At first glance, your Power system spends 1/3 of its time in constraint calculation, which is unusual. This can be reduced 2 ways - first, by adding more CPU cores. It doesn't make a ton of sense to benchmark on one core if your applications will use more. Second, if you upgrade to Gromacs 2020 you can probably put the constraint calculation on the GPU with -update GPU. * The Power system log has this line: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 indicating that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or some other core) to specify where you want the process pinned. Kevin On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < halverson at princeton.edu> wrote: > *Message sent from a system outside of UConn.* > > > We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an > IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running RHEL > 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > nodes. Everything below is about of the POWER9/V100 node. > > We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > CPU-core and 1 GPU ( > ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives 102 > ns/day. The difference in performance is roughly the same for the larger > ADH benchmark and when different numbers of CPU-cores are used. GROMACS is > always underperforming on our POWER9/V100 nodes. We have pinning turned on > (see Slurm script at bottom). > > Below is our build procedure on the POWER9/V100 node: > > version_gmx=2019.6 > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > tar zxvf gromacs-${version_gmx}.tar.gz > cd gromacs-${version_gmx} > mkdir build && cd build > > module purge > module load rh/devtoolset/7 > module load cudatoolkit/10.2 > > OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > > cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > -DGMX_BUILD_OWN_FFTW=ON \ > -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > -DGMX_OPENMP_MAX_THREADS=128 \ > -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > > make -j 10 > make check > make install > > 45 of the 46 tests pass with the exception being HardwareUnitTests. There > are several posts about this and apparently it is not a concern. The full > build log is here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > > > > Here is more info about our POWER9/V100 node: > > $ lscpu > Architecture: ppc64le > Byte Order: Little Endian > CPU(s): 128 > On-line CPU(s) list: 0-127 > Thread(s) per core: 4 > Core(s) per socket: 16 > Socket(s): 2 > NUMA node(s): 6 > Model: 2.3 (pvr 004e 1203) > Model name: POWER9, altivec supported > CPU max MHz: 3800.0000 > CPU min MHz: 2300.0000 > > You see that we have 4 hardware threads per physical core. If we use 4 > hardware threads on the RNASE benchmark instead of 1 the performance goes > to 119 ns/day which is still about 20% less than the Broadwell/P100 value. > When using multiple CPU-cores on the POWER9/V100 there is significant > variation in the execution time of the code. > > There are four GPUs per POWER9/V100 node: > > $ nvidia-smi -q > Driver Version : 440.33.01 > CUDA Version : 10.2 > GPU 00000004:04:00.0 > Product Name : Tesla V100-SXM2-32GB > > The GPUs have been shown to perform as expected on other applications. > > > > > The following lines are found in md.log for the POWER9/V100 run: > > Overriding thread affinity set outside gmx mdrun > Pinning threads with an auto-selected logical core stride of 128 > NOTE: Thread affinity was not set. > > The full md.log is available here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > > > Below are the MegaFlops Accounting for the POWER9/V100 versus > Broadwell/P100: > > ================ IBM POWER9 WITH NVIDIA V100 ================ > Computing: M-Number M-Flops % Flops > > ----------------------------------------------------------------------------- > Pair Search distance check 297.763872 2679.875 0.0 > NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 98.0 > NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 1.6 > 1,4 nonbonded interactions 53.415341 4807.381 0.0 > Shift-X 3.029040 18.174 0.0 > Angles 37.043704 6223.342 0.0 > Propers 55.825582 12784.058 0.1 > Impropers 4.220422 877.848 0.0 > Virial 2.432585 43.787 0.0 > Stop-CM 2.452080 24.521 0.0 > Calc-Ekin 48.128080 1299.458 0.0 > Lincs 20.536159 1232.170 0.0 > Lincs-Mat 444.613344 1778.453 0.0 > Constraint-V 261.192228 2089.538 0.0 > Constraint-Vir 2.430161 58.324 0.0 > Settle 73.382008 23702.389 0.1 > > ----------------------------------------------------------------------------- > Total 16441499.096 100.0 > > ----------------------------------------------------------------------------- > > > ================ INTEL BROADWELL WITH NVIDIA P100 ================ > Computing: M-Number M-Flops % Flops > > ----------------------------------------------------------------------------- > Pair Search distance check 271.334272 2442.008 0.0 > NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 98.0 > NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 1.6 > 1,4 nonbonded interactions 53.415341 4807.381 0.0 > Shift-X 3.029040 18.174 0.0 > Bonds 10.541054 621.922 0.0 > Angles 37.043704 6223.342 0.0 > Propers 55.825582 12784.058 0.1 > Impropers 4.220422 877.848 0.0 > Virial 2.432585 43.787 0.0 > Stop-CM 2.452080 24.521 0.0 > Calc-Ekin 48.128080 1299.458 0.0 > Lincs 9.992997 599.580 0.0 > Lincs-Mat 50.775228 203.101 0.0 > Constraint-V 240.108012 1920.864 0.0 > Constraint-Vir 2.323707 55.769 0.0 > Settle 73.382008 23702.389 0.2 > > ----------------------------------------------------------------------------- > Total 12909529.017 100.0 > > ----------------------------------------------------------------------------- > > Some of the rows are identical between the two tables above. The largest > difference > is observed for the "NxN Ewald Elec. + LJ [F]" row. > > > > Here is our Slurm script: > > #!/bin/bash > #SBATCH --job-name=gmx # create a short name for your job > #SBATCH --nodes=1 # node count > #SBATCH --ntasks=1 # total number of tasks across all nodes > #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > multi-threaded tasks) > #SBATCH --mem=4G # memory per node (4G per cpu-core is > default) > #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > #SBATCH --gres=gpu:1 # number of gpus per node > > module purge > module load cudatoolkit/10.2 > > BCH=../rnase_cubic > gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > bench.tpr > gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > bench.tpr > > > > How do we get optimal performance out of GROMACS on our POWER9/V100 nodes? > > Jon > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From halverson at Princeton.EDU Fri Apr 24 03:43:05 2020 From: halverson at Princeton.EDU (Jonathan D. Halverson) Date: Fri, 24 Apr 2020 01:43:05 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: , Message-ID: Hi Kevin, md.log for the Intel run is here: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 Thanks for the info on constraints with 2020. I'll try some runs with different values of -pinoffset for 2019.6. I know a group at NIST is having the same or similar problems with POWER9/V100. Jon ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Kevin Boyd Sent: Thursday, April 23, 2020 9:08 PM To: gmx-users at gromacs.org Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node Hi, Can you post the full log for the Intel system? I typically find the real cycle and time accounting section a better place to start debugging performance issues. A couple quick notes, but need a side-by-side comparison for more useful analysis, and these points may apply to both systems so may not be your root cause: * At first glance, your Power system spends 1/3 of its time in constraint calculation, which is unusual. This can be reduced 2 ways - first, by adding more CPU cores. It doesn't make a ton of sense to benchmark on one core if your applications will use more. Second, if you upgrade to Gromacs 2020 you can probably put the constraint calculation on the GPU with -update GPU. * The Power system log has this line: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 indicating that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or some other core) to specify where you want the process pinned. Kevin On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < halverson at princeton.edu> wrote: > *Message sent from a system outside of UConn.* > > > We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an > IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running RHEL > 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > nodes. Everything below is about of the POWER9/V100 node. > > We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > CPU-core and 1 GPU ( > ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives 102 > ns/day. The difference in performance is roughly the same for the larger > ADH benchmark and when different numbers of CPU-cores are used. GROMACS is > always underperforming on our POWER9/V100 nodes. We have pinning turned on > (see Slurm script at bottom). > > Below is our build procedure on the POWER9/V100 node: > > version_gmx=2019.6 > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > tar zxvf gromacs-${version_gmx}.tar.gz > cd gromacs-${version_gmx} > mkdir build && cd build > > module purge > module load rh/devtoolset/7 > module load cudatoolkit/10.2 > > OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > > cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > -DGMX_BUILD_OWN_FFTW=ON \ > -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > -DGMX_OPENMP_MAX_THREADS=128 \ > -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > > make -j 10 > make check > make install > > 45 of the 46 tests pass with the exception being HardwareUnitTests. There > are several posts about this and apparently it is not a concern. The full > build log is here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > > > > Here is more info about our POWER9/V100 node: > > $ lscpu > Architecture: ppc64le > Byte Order: Little Endian > CPU(s): 128 > On-line CPU(s) list: 0-127 > Thread(s) per core: 4 > Core(s) per socket: 16 > Socket(s): 2 > NUMA node(s): 6 > Model: 2.3 (pvr 004e 1203) > Model name: POWER9, altivec supported > CPU max MHz: 3800.0000 > CPU min MHz: 2300.0000 > > You see that we have 4 hardware threads per physical core. If we use 4 > hardware threads on the RNASE benchmark instead of 1 the performance goes > to 119 ns/day which is still about 20% less than the Broadwell/P100 value. > When using multiple CPU-cores on the POWER9/V100 there is significant > variation in the execution time of the code. > > There are four GPUs per POWER9/V100 node: > > $ nvidia-smi -q > Driver Version : 440.33.01 > CUDA Version : 10.2 > GPU 00000004:04:00.0 > Product Name : Tesla V100-SXM2-32GB > > The GPUs have been shown to perform as expected on other applications. > > > > > The following lines are found in md.log for the POWER9/V100 run: > > Overriding thread affinity set outside gmx mdrun > Pinning threads with an auto-selected logical core stride of 128 > NOTE: Thread affinity was not set. > > The full md.log is available here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > > > Below are the MegaFlops Accounting for the POWER9/V100 versus > Broadwell/P100: > > ================ IBM POWER9 WITH NVIDIA V100 ================ > Computing: M-Number M-Flops % Flops > > ----------------------------------------------------------------------------- > Pair Search distance check 297.763872 2679.875 0.0 > NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 98.0 > NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 1.6 > 1,4 nonbonded interactions 53.415341 4807.381 0.0 > Shift-X 3.029040 18.174 0.0 > Angles 37.043704 6223.342 0.0 > Propers 55.825582 12784.058 0.1 > Impropers 4.220422 877.848 0.0 > Virial 2.432585 43.787 0.0 > Stop-CM 2.452080 24.521 0.0 > Calc-Ekin 48.128080 1299.458 0.0 > Lincs 20.536159 1232.170 0.0 > Lincs-Mat 444.613344 1778.453 0.0 > Constraint-V 261.192228 2089.538 0.0 > Constraint-Vir 2.430161 58.324 0.0 > Settle 73.382008 23702.389 0.1 > > ----------------------------------------------------------------------------- > Total 16441499.096 100.0 > > ----------------------------------------------------------------------------- > > > ================ INTEL BROADWELL WITH NVIDIA P100 ================ > Computing: M-Number M-Flops % Flops > > ----------------------------------------------------------------------------- > Pair Search distance check 271.334272 2442.008 0.0 > NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 98.0 > NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 1.6 > 1,4 nonbonded interactions 53.415341 4807.381 0.0 > Shift-X 3.029040 18.174 0.0 > Bonds 10.541054 621.922 0.0 > Angles 37.043704 6223.342 0.0 > Propers 55.825582 12784.058 0.1 > Impropers 4.220422 877.848 0.0 > Virial 2.432585 43.787 0.0 > Stop-CM 2.452080 24.521 0.0 > Calc-Ekin 48.128080 1299.458 0.0 > Lincs 9.992997 599.580 0.0 > Lincs-Mat 50.775228 203.101 0.0 > Constraint-V 240.108012 1920.864 0.0 > Constraint-Vir 2.323707 55.769 0.0 > Settle 73.382008 23702.389 0.2 > > ----------------------------------------------------------------------------- > Total 12909529.017 100.0 > > ----------------------------------------------------------------------------- > > Some of the rows are identical between the two tables above. The largest > difference > is observed for the "NxN Ewald Elec. + LJ [F]" row. > > > > Here is our Slurm script: > > #!/bin/bash > #SBATCH --job-name=gmx # create a short name for your job > #SBATCH --nodes=1 # node count > #SBATCH --ntasks=1 # total number of tasks across all nodes > #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > multi-threaded tasks) > #SBATCH --mem=4G # memory per node (4G per cpu-core is > default) > #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > #SBATCH --gres=gpu:1 # number of gpus per node > > module purge > module load cudatoolkit/10.2 > > BCH=../rnase_cubic > gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > bench.tpr > gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > bench.tpr > > > > How do we get optimal performance out of GROMACS on our POWER9/V100 nodes? > > Jon > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From m.b.abdelaal at gmail.com Fri Apr 24 04:29:02 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Fri, 24 Apr 2020 02:29:02 -0000 Subject: [gmx-users] Periodic boundary conditions during the simulation Message-ID: Hello everybody, I know that due to periodic boundary conditions the molecules move from one side of the box to the other side and moves outside the box. I also know how to use trjconv to solve this problem and I usually do this step at the end of the simulation. However I have noticed that after the energy minimization, some molecules which were position restrained at the bottom of the box have been moved to the top of the box. I knew that I have this periodic boundary condition problem not just from visualization of the structure after the energy minimization, but also from the atoms coordinates in the .gro file after the energy minimization, the z coordinate of some atoms have been changed from bottom to top as below: before energy minimization: (the z coordinate was always zero) 1GRM C1 1 0.061 0.071 0.000 1GRM C2 2 0.184 0.142 0.000 1GRM C3 3 0.184 0.284 0.000 1GRM C4 4 0.061 0.355 0.000 2GRM C1 5 0.061 0.497 0.000 after energy minimization: (z coordinate of some atoms have been changed into 14 which is at the top of the box) 1GRM C1 1 0.061 0.071 14.000 1GRM C2 2 0.184 0.142 14.000 1GRM C3 3 0.184 0.284 0.000 1GRM C4 4 0.061 0.355 0.000 2GRM C1 5 0.061 0.497 14.000 Do I need to solve this PBC problem between the different steps (energy min, NVT, NPT, production run) or it is okay to continue my simulation (even if the molecules have moved) and solve this problem at the end ? Many thanks, Mohamed From sranjan at iiserb.ac.in Fri Apr 24 05:11:55 2020 From: sranjan at iiserb.ac.in (Shashank Ranjan Srivastava) Date: Fri, 24 Apr 2020 03:11:55 -0000 Subject: [gmx-users] Regarding use of harmonic wall model In-Reply-To: <1587475534223.939397599@boxbe> References: <1587325451769.939397599@boxbe> <1587475534223.939397599@boxbe> Message-ID: Thank you so much. I will work on it. Thank you On Tue, 21 Apr 2020, 18:55 Justin Lemkul, wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalemkul at vt.edu) Add cleanup rule > > | More info > > > > On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote: > > Thank you so much Prof. Lemkul for your reply. > > As I don't know what and how to use this pull code, if you have any idea > > regarding what you have suggested will be of great help to me. > > Meanwhile I will read more about it. > > General principles here: > http://www.mdtutorials.com/gmx/umbrella/index.html > > Obviously that's a very different approach from what you're trying to do > but you can learn the basic syntax there. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From kevin.boyd at uconn.edu Fri Apr 24 05:38:02 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Fri, 24 Apr 2020 03:38:02 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: I'm not entirely sure how thread-pinning plays with slurm allocations on partial nodes. I always reserve the entire node when I use thread pinning, and run a bunch of simulations by pinning to different cores manually, rather than relying on slurm to divvy up resources for multiple jobs. Looking at both logs now, a few more points * Your benchmarks are short enough that little things like cores spinning up frequencies can matter. I suggest running longer (increase nsteps in the mdp or at the command line), and throwing away your initial benchmark data (see -resetstep and -resethway) to avoid artifacts * Your benchmark system is quite small for such a powerful GPU. I might expect better performance running multiple simulations per-GPU if the workflows being run can rely on replicates, and a larger system would probably scale better to the V100. * The P100/intel system appears to have pinned cores properly, it's unclear whether it had a real impact on these benchmarks * It looks like the CPU-based computations were the primary contributors to the observed difference in performance. That should decrease or go away with increased core counts and shifting the update phase to the GPU. It may be (I have no prior experience to indicate either way) that the intel cores are simply better on a 1-1 basis than the Power cores. If you have 4-8 cores per simulation (try -ntomp 4 and increasing the allocation of your slurm job), the individual core performance shouldn't matter too much, you're just certainly bottlenecked on one CPU core per GPU, which can emphasize performance differences.. Kevin On Thu, Apr 23, 2020 at 6:43 PM Jonathan D. Halverson < halverson at princeton.edu> wrote: > *Message sent from a system outside of UConn.* > > > Hi Kevin, > > md.log for the Intel run is here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 > > Thanks for the info on constraints with 2020. I'll try some runs with > different values of -pinoffset for 2019.6. > > I know a group at NIST is having the same or similar problems with > POWER9/V100. > > Jon > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin > Boyd > Sent: Thursday, April 23, 2020 9:08 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node > > Hi, > > Can you post the full log for the Intel system? I typically find the real > cycle and time accounting section a better place to start debugging > performance issues. > > A couple quick notes, but need a side-by-side comparison for more useful > analysis, and these points may apply to both systems so may not be your > root cause: > * At first glance, your Power system spends 1/3 of its time in constraint > calculation, which is unusual. This can be reduced 2 ways - first, by > adding more CPU cores. It doesn't make a ton of sense to benchmark on one > core if your applications will use more. Second, if you upgrade to Gromacs > 2020 you can probably put the constraint calculation on the GPU with > -update GPU. > * The Power system log has this line: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 > indicating > that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or > some other core) to specify where you want the process pinned. > > Kevin > > On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < > halverson at princeton.edu> wrote: > > > *Message sent from a system outside of UConn.* > > > > > > We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an > > IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running > RHEL > > 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > > nodes. Everything below is about of the POWER9/V100 node. > > > > We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > > CPU-core and 1 GPU ( > > ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > > found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives > 102 > > ns/day. The difference in performance is roughly the same for the larger > > ADH benchmark and when different numbers of CPU-cores are used. GROMACS > is > > always underperforming on our POWER9/V100 nodes. We have pinning turned > on > > (see Slurm script at bottom). > > > > Below is our build procedure on the POWER9/V100 node: > > > > version_gmx=2019.6 > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > > tar zxvf gromacs-${version_gmx}.tar.gz > > cd gromacs-${version_gmx} > > mkdir build && cd build > > > > module purge > > module load rh/devtoolset/7 > > module load cudatoolkit/10.2 > > > > OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > > > > cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > > -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > > -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > > -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > > -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > > -DGMX_BUILD_OWN_FFTW=ON \ > > -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > > -DGMX_OPENMP_MAX_THREADS=128 \ > > -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > > -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > > > > make -j 10 > > make check > > make install > > > > 45 of the 46 tests pass with the exception being HardwareUnitTests. There > > are several posts about this and apparently it is not a concern. The full > > build log is here: > > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > > > > > > > > Here is more info about our POWER9/V100 node: > > > > $ lscpu > > Architecture: ppc64le > > Byte Order: Little Endian > > CPU(s): 128 > > On-line CPU(s) list: 0-127 > > Thread(s) per core: 4 > > Core(s) per socket: 16 > > Socket(s): 2 > > NUMA node(s): 6 > > Model: 2.3 (pvr 004e 1203) > > Model name: POWER9, altivec supported > > CPU max MHz: 3800.0000 > > CPU min MHz: 2300.0000 > > > > You see that we have 4 hardware threads per physical core. If we use 4 > > hardware threads on the RNASE benchmark instead of 1 the performance goes > > to 119 ns/day which is still about 20% less than the Broadwell/P100 > value. > > When using multiple CPU-cores on the POWER9/V100 there is significant > > variation in the execution time of the code. > > > > There are four GPUs per POWER9/V100 node: > > > > $ nvidia-smi -q > > Driver Version : 440.33.01 > > CUDA Version : 10.2 > > GPU 00000004:04:00.0 > > Product Name : Tesla V100-SXM2-32GB > > > > The GPUs have been shown to perform as expected on other applications. > > > > > > > > > > The following lines are found in md.log for the POWER9/V100 run: > > > > Overriding thread affinity set outside gmx mdrun > > Pinning threads with an auto-selected logical core stride of 128 > > NOTE: Thread affinity was not set. > > > > The full md.log is available here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > > > > > > > > Below are the MegaFlops Accounting for the POWER9/V100 versus > > Broadwell/P100: > > > > ================ IBM POWER9 WITH NVIDIA V100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 297.763872 2679.875 > 0.0 > > NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 20.536159 1232.170 > 0.0 > > Lincs-Mat 444.613344 1778.453 > 0.0 > > Constraint-V 261.192228 2089.538 > 0.0 > > Constraint-Vir 2.430161 58.324 > 0.0 > > Settle 73.382008 23702.389 > 0.1 > > > > > ----------------------------------------------------------------------------- > > Total 16441499.096 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > > > ================ INTEL BROADWELL WITH NVIDIA P100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 271.334272 2442.008 > 0.0 > > NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Bonds 10.541054 621.922 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 9.992997 599.580 > 0.0 > > Lincs-Mat 50.775228 203.101 > 0.0 > > Constraint-V 240.108012 1920.864 > 0.0 > > Constraint-Vir 2.323707 55.769 > 0.0 > > Settle 73.382008 23702.389 > 0.2 > > > > > ----------------------------------------------------------------------------- > > Total 12909529.017 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > Some of the rows are identical between the two tables above. The largest > > difference > > is observed for the "NxN Ewald Elec. + LJ [F]" row. > > > > > > > > Here is our Slurm script: > > > > #!/bin/bash > > #SBATCH --job-name=gmx # create a short name for your job > > #SBATCH --nodes=1 # node count > > #SBATCH --ntasks=1 # total number of tasks across all nodes > > #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > > multi-threaded tasks) > > #SBATCH --mem=4G # memory per node (4G per cpu-core is > > default) > > #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > > #SBATCH --gres=gpu:1 # number of gpus per node > > > > module purge > > module load cudatoolkit/10.2 > > > > BCH=../rnase_cubic > > gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > > bench.tpr > > gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > > bench.tpr > > > > > > > > How do we get optimal performance out of GROMACS on our POWER9/V100 > nodes? > > > > Jon > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nedomacho at gmail.com Fri Apr 24 05:54:47 2020 From: nedomacho at gmail.com (Alex) Date: Fri, 24 Apr 2020 03:54:47 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: <0cdf1551-a223-de2a-a599-75612dd9c3de@gmail.com> Hi Kevin, We've been having issues with Power9/V100 very similar to what Jon described and basically settled on what I believe is sub-par performance. We tested it on systems with ~30-50K particles and threads simply cannot be pinned. As far as Gromacs is concerned, our brand-new Power9 nodes operate as if they were based on Intel CPUs (two threads per core) and zero advantage of IBM parallelization is being taken. Other users of the same nodes reported similar issues with other software, which to me suggests that our sysadmins don't really know how to set these nodes up. At this point, if someone could figure out a clear set of build instructions in combination with slurm/mdrun inputs, it would be very much appreciated. Alex On 4/23/2020 9:37 PM, Kevin Boyd wrote: > I'm not entirely sure how thread-pinning plays with slurm allocations on > partial nodes. I always reserve the entire node when I use thread pinning, > and run a bunch of simulations by pinning to different cores manually, > rather than relying on slurm to divvy up resources for multiple jobs. > > Looking at both logs now, a few more points > > * Your benchmarks are short enough that little things like cores spinning > up frequencies can matter. I suggest running longer (increase nsteps in the > mdp or at the command line), and throwing away your initial benchmark data > (see -resetstep and -resethway) to avoid artifacts > * Your benchmark system is quite small for such a powerful GPU. I might > expect better performance running multiple simulations per-GPU if the > workflows being run can rely on replicates, and a larger system would > probably scale better to the V100. > * The P100/intel system appears to have pinned cores properly, it's > unclear whether it had a real impact on these benchmarks > * It looks like the CPU-based computations were the primary contributors to > the observed difference in performance. That should decrease or go away > with increased core counts and shifting the update phase to the GPU. It may > be (I have no prior experience to indicate either way) that the intel cores > are simply better on a 1-1 basis than the Power cores. If you have 4-8 > cores per simulation (try -ntomp 4 and increasing the allocation of your > slurm job), the individual core performance shouldn't matter too > much, you're just certainly bottlenecked on one CPU core per GPU, which can > emphasize performance differences.. > > Kevin > > On Thu, Apr 23, 2020 at 6:43 PM Jonathan D. Halverson < > halverson at princeton.edu> wrote: > >> *Message sent from a system outside of UConn.* >> >> >> Hi Kevin, >> >> md.log for the Intel run is here: >> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 >> >> Thanks for the info on constraints with 2020. I'll try some runs with >> different values of -pinoffset for 2019.6. >> >> I know a group at NIST is having the same or similar problems with >> POWER9/V100. >> >> Jon >> ________________________________ >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin >> Boyd >> Sent: Thursday, April 23, 2020 9:08 PM >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node >> >> Hi, >> >> Can you post the full log for the Intel system? I typically find the real >> cycle and time accounting section a better place to start debugging >> performance issues. >> >> A couple quick notes, but need a side-by-side comparison for more useful >> analysis, and these points may apply to both systems so may not be your >> root cause: >> * At first glance, your Power system spends 1/3 of its time in constraint >> calculation, which is unusual. This can be reduced 2 ways - first, by >> adding more CPU cores. It doesn't make a ton of sense to benchmark on one >> core if your applications will use more. Second, if you upgrade to Gromacs >> 2020 you can probably put the constraint calculation on the GPU with >> -update GPU. >> * The Power system log has this line: >> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 >> indicating >> that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or >> some other core) to specify where you want the process pinned. >> >> Kevin >> >> On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < >> halverson at princeton.edu> wrote: >> >>> *Message sent from a system outside of UConn.* >>> >>> >>> We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an >>> IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running >> RHEL >>> 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel >>> nodes. Everything below is about of the POWER9/V100 node. >>> >>> We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 >>> CPU-core and 1 GPU ( >>> ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and >>> found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives >> 102 >>> ns/day. The difference in performance is roughly the same for the larger >>> ADH benchmark and when different numbers of CPU-cores are used. GROMACS >> is >>> always underperforming on our POWER9/V100 nodes. We have pinning turned >> on >>> (see Slurm script at bottom). >>> >>> Below is our build procedure on the POWER9/V100 node: >>> >>> version_gmx=2019.6 >>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz >>> tar zxvf gromacs-${version_gmx}.tar.gz >>> cd gromacs-${version_gmx} >>> mkdir build && cd build >>> >>> module purge >>> module load rh/devtoolset/7 >>> module load cudatoolkit/10.2 >>> >>> OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" >>> >>> cmake3 .. -DCMAKE_BUILD_TYPE=Release \ >>> -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ >>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ >>> -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ >>> -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ >>> -DGMX_BUILD_OWN_FFTW=ON \ >>> -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ >>> -DGMX_OPENMP_MAX_THREADS=128 \ >>> -DCMAKE_INSTALL_PREFIX=$HOME/.local \ >>> -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON >>> >>> make -j 10 >>> make check >>> make install >>> >>> 45 of the 46 tests pass with the exception being HardwareUnitTests. There >>> are several posts about this and apparently it is not a concern. The full >>> build log is here: >>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log >>> >>> >>> Here is more info about our POWER9/V100 node: >>> >>> $ lscpu >>> Architecture: ppc64le >>> Byte Order: Little Endian >>> CPU(s): 128 >>> On-line CPU(s) list: 0-127 >>> Thread(s) per core: 4 >>> Core(s) per socket: 16 >>> Socket(s): 2 >>> NUMA node(s): 6 >>> Model: 2.3 (pvr 004e 1203) >>> Model name: POWER9, altivec supported >>> CPU max MHz: 3800.0000 >>> CPU min MHz: 2300.0000 >>> >>> You see that we have 4 hardware threads per physical core. If we use 4 >>> hardware threads on the RNASE benchmark instead of 1 the performance goes >>> to 119 ns/day which is still about 20% less than the Broadwell/P100 >> value. >>> When using multiple CPU-cores on the POWER9/V100 there is significant >>> variation in the execution time of the code. >>> >>> There are four GPUs per POWER9/V100 node: >>> >>> $ nvidia-smi -q >>> Driver Version : 440.33.01 >>> CUDA Version : 10.2 >>> GPU 00000004:04:00.0 >>> Product Name : Tesla V100-SXM2-32GB >>> >>> The GPUs have been shown to perform as expected on other applications. >>> >>> >>> >>> >>> The following lines are found in md.log for the POWER9/V100 run: >>> >>> Overriding thread affinity set outside gmx mdrun >>> Pinning threads with an auto-selected logical core stride of 128 >>> NOTE: Thread affinity was not set. >>> >>> The full md.log is available here: >>> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log >>> >>> >>> >>> >>> Below are the MegaFlops Accounting for the POWER9/V100 versus >>> Broadwell/P100: >>> >>> ================ IBM POWER9 WITH NVIDIA V100 ================ >>> Computing: M-Number M-Flops % >> Flops >>> >> ----------------------------------------------------------------------------- >>> Pair Search distance check 297.763872 2679.875 >> 0.0 >>> NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 >> 98.0 >>> NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 >> 1.6 >>> 1,4 nonbonded interactions 53.415341 4807.381 >> 0.0 >>> Shift-X 3.029040 18.174 >> 0.0 >>> Angles 37.043704 6223.342 >> 0.0 >>> Propers 55.825582 12784.058 >> 0.1 >>> Impropers 4.220422 877.848 >> 0.0 >>> Virial 2.432585 43.787 >> 0.0 >>> Stop-CM 2.452080 24.521 >> 0.0 >>> Calc-Ekin 48.128080 1299.458 >> 0.0 >>> Lincs 20.536159 1232.170 >> 0.0 >>> Lincs-Mat 444.613344 1778.453 >> 0.0 >>> Constraint-V 261.192228 2089.538 >> 0.0 >>> Constraint-Vir 2.430161 58.324 >> 0.0 >>> Settle 73.382008 23702.389 >> 0.1 >>> >> ----------------------------------------------------------------------------- >>> Total 16441499.096 >> 100.0 >>> >> ----------------------------------------------------------------------------- >>> >>> ================ INTEL BROADWELL WITH NVIDIA P100 ================ >>> Computing: M-Number M-Flops % >> Flops >>> >> ----------------------------------------------------------------------------- >>> Pair Search distance check 271.334272 2442.008 >> 0.0 >>> NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 >> 98.0 >>> NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 >> 1.6 >>> 1,4 nonbonded interactions 53.415341 4807.381 >> 0.0 >>> Shift-X 3.029040 18.174 >> 0.0 >>> Bonds 10.541054 621.922 >> 0.0 >>> Angles 37.043704 6223.342 >> 0.0 >>> Propers 55.825582 12784.058 >> 0.1 >>> Impropers 4.220422 877.848 >> 0.0 >>> Virial 2.432585 43.787 >> 0.0 >>> Stop-CM 2.452080 24.521 >> 0.0 >>> Calc-Ekin 48.128080 1299.458 >> 0.0 >>> Lincs 9.992997 599.580 >> 0.0 >>> Lincs-Mat 50.775228 203.101 >> 0.0 >>> Constraint-V 240.108012 1920.864 >> 0.0 >>> Constraint-Vir 2.323707 55.769 >> 0.0 >>> Settle 73.382008 23702.389 >> 0.2 >>> >> ----------------------------------------------------------------------------- >>> Total 12909529.017 >> 100.0 >>> >> ----------------------------------------------------------------------------- >>> Some of the rows are identical between the two tables above. The largest >>> difference >>> is observed for the "NxN Ewald Elec. + LJ [F]" row. >>> >>> >>> >>> Here is our Slurm script: >>> >>> #!/bin/bash >>> #SBATCH --job-name=gmx # create a short name for your job >>> #SBATCH --nodes=1 # node count >>> #SBATCH --ntasks=1 # total number of tasks across all nodes >>> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if >>> multi-threaded tasks) >>> #SBATCH --mem=4G # memory per node (4G per cpu-core is >>> default) >>> #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) >>> #SBATCH --gres=gpu:1 # number of gpus per node >>> >>> module purge >>> module load cudatoolkit/10.2 >>> >>> BCH=../rnase_cubic >>> gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o >>> bench.tpr >>> gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s >>> bench.tpr >>> >>> >>> >>> How do we get optimal performance out of GROMACS on our POWER9/V100 >> nodes? >>> Jon >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From dallas.warren at monash.edu Fri Apr 24 13:22:21 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Fri, 24 Apr 2020 11:22:21 -0000 Subject: [gmx-users] Periodic boundary conditions during the simulation In-Reply-To: References: Message-ID: Boundaries of the box used for visualisation are totally arbitrary, it makes not difference when the various simulations are being performed. Most efficient to simply process it at the end to get the visual representation you want Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.warren at monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 24 Apr 2020 at 12:29, Mohamed Abdelaal wrote: > Hello everybody, > > I know that due to periodic boundary conditions the molecules move from one > side of the box to the other side and moves outside the box. I also know > how to use trjconv to solve this problem and I usually do this step at the > end of the simulation. However I have noticed that after the energy > minimization, some molecules which were position restrained at the bottom > of the box have been moved to the top of the box. I knew that I have this > periodic boundary condition problem not just from visualization of the > structure after the energy minimization, but also from the atoms > coordinates in the .gro file after the energy minimization, the z > coordinate of some atoms have been changed from bottom to top as below: > > before energy minimization: (the z coordinate was always zero) > > 1GRM C1 1 0.061 0.071 0.000 > 1GRM C2 2 0.184 0.142 0.000 > 1GRM C3 3 0.184 0.284 0.000 > 1GRM C4 4 0.061 0.355 0.000 > 2GRM C1 5 0.061 0.497 0.000 > > > after energy minimization: (z coordinate of some atoms have been changed > into 14 which is at the top of the box) > > 1GRM C1 1 0.061 0.071 14.000 > 1GRM C2 2 0.184 0.142 14.000 > 1GRM C3 3 0.184 0.284 0.000 > 1GRM C4 4 0.061 0.355 0.000 > 2GRM C1 5 0.061 0.497 14.000 > > > > Do I need to solve this PBC problem between the different steps (energy > min, NVT, NPT, production run) or it is okay to continue my simulation > (even if the molecules have moved) and solve this problem at the end ? > > Many thanks, > Mohamed > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From ckutzne at gwdg.de Fri Apr 24 14:07:29 2020 From: ckutzne at gwdg.de (Kutzner, Carsten) Date: Fri, 24 Apr 2020 12:07:29 -0000 Subject: [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries In-Reply-To: References: Message-ID: Hi Erik, I am not sure that the CompEl code as it is can deal with the setup you are describing (but I may be wrong). Below are a few thoughts and things you might want to try. > Am 24.04.2020 um 00:05 schrieb Erik Henze : > > Hi, > I am attempting to study permeation events in an ion channel where the > filter is located in the extracellular region, far away from the middle of > the transmembrane regions. My question is two-fold: > > 1) Where is the optimal place to set up the compartment boundaries? The compartment boundaries should always be within the membranes, otherwise the exchanges of waters with ions won't make any sense as the system is effectively short-circuited. > > If I place the compartment boundaries in the middle of the membrane (as > where most channel filters would approximately be) then, given that the > pore of the channel is very large in this region, I will be swapping lots > of ions which aren't actually permeating the channel. This doesn't > necessarily seem like a problem, given that COMPEL can record the > permeation events separately with the cylinder you define. I was concerned, > however, that this constant swapping that COMPEL has to do will make the > simulation very computationally costly/inefficient in some way. No, probably not, because typically you check for that every 100+ steps, so it will only be a small performance penalty. > This brings > me to my next question: > > 2) Can you define the cylinder in a way that is independent of the center > of the channel, so that I can place the cylinder in a region centered near > the extracellular region? You can try with the cyl-up and cyl-down settings and adjust the bulk-offset parameter accordingly (look at Fig. 3 in https://pure.mpg.de/rest/items/item_2249662_6/component/file_2399280/content for the meaning of these parameters). Best, Carsten > > Any thoughts/advice on this would be greatly appreciated, thanks! > -Erik H > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From pall.szilard at gmail.com Fri Apr 24 16:24:03 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 14:24:03 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: Using a single thread per GPU as the linked log files show is not sufficient for GROMACS (and any modern machine should have more than that anyway), but I imply from your mail that this only meant to debug performance instability? Your performance variations with Power9 may be related that you are either not setting affinities or the affinity settings is not correct. However, you also have some job scheduler in the way (that I suspect is either not configured well or is not passed the required options to correctly assign resources to jobs) and obfuscates machine layout and makes things look weird to mdrun [1]. I suggest to simplify the problem and try to debug it step-by-step. Start with allocating full nodes and test that you can pin (either with mdurun -pin on or hwloc) and avoid [1], get an understanding of what should you expect from the node sharing that seem to not work correctly. Building GROMACS with hwloc may help as you get better reporting in the log. [1] https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100#L58 -- Szil?rd On Fri, Apr 24, 2020 at 3:43 AM Jonathan D. Halverson < halverson at princeton.edu> wrote: > Hi Kevin, > > md.log for the Intel run is here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 > > Thanks for the info on constraints with 2020. I'll try some runs with > different values of -pinoffset for 2019.6. > > I know a group at NIST is having the same or similar problems with > POWER9/V100. > > Jon > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin > Boyd > Sent: Thursday, April 23, 2020 9:08 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node > > Hi, > > Can you post the full log for the Intel system? I typically find the real > cycle and time accounting section a better place to start debugging > performance issues. > > A couple quick notes, but need a side-by-side comparison for more useful > analysis, and these points may apply to both systems so may not be your > root cause: > * At first glance, your Power system spends 1/3 of its time in constraint > calculation, which is unusual. This can be reduced 2 ways - first, by > adding more CPU cores. It doesn't make a ton of sense to benchmark on one > core if your applications will use more. Second, if you upgrade to Gromacs > 2020 you can probably put the constraint calculation on the GPU with > -update GPU. > * The Power system log has this line: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 > indicating > that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or > some other core) to specify where you want the process pinned. > > Kevin > > On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < > halverson at princeton.edu> wrote: > > > *Message sent from a system outside of UConn.* > > > > > > We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an > > IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running > RHEL > > 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > > nodes. Everything below is about of the POWER9/V100 node. > > > > We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > > CPU-core and 1 GPU ( > > ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > > found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives > 102 > > ns/day. The difference in performance is roughly the same for the larger > > ADH benchmark and when different numbers of CPU-cores are used. GROMACS > is > > always underperforming on our POWER9/V100 nodes. We have pinning turned > on > > (see Slurm script at bottom). > > > > Below is our build procedure on the POWER9/V100 node: > > > > version_gmx=2019.6 > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > > tar zxvf gromacs-${version_gmx}.tar.gz > > cd gromacs-${version_gmx} > > mkdir build && cd build > > > > module purge > > module load rh/devtoolset/7 > > module load cudatoolkit/10.2 > > > > OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > > > > cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > > -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > > -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > > -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > > -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > > -DGMX_BUILD_OWN_FFTW=ON \ > > -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > > -DGMX_OPENMP_MAX_THREADS=128 \ > > -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > > -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > > > > make -j 10 > > make check > > make install > > > > 45 of the 46 tests pass with the exception being HardwareUnitTests. There > > are several posts about this and apparently it is not a concern. The full > > build log is here: > > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > > > > > > > > Here is more info about our POWER9/V100 node: > > > > $ lscpu > > Architecture: ppc64le > > Byte Order: Little Endian > > CPU(s): 128 > > On-line CPU(s) list: 0-127 > > Thread(s) per core: 4 > > Core(s) per socket: 16 > > Socket(s): 2 > > NUMA node(s): 6 > > Model: 2.3 (pvr 004e 1203) > > Model name: POWER9, altivec supported > > CPU max MHz: 3800.0000 > > CPU min MHz: 2300.0000 > > > > You see that we have 4 hardware threads per physical core. If we use 4 > > hardware threads on the RNASE benchmark instead of 1 the performance goes > > to 119 ns/day which is still about 20% less than the Broadwell/P100 > value. > > When using multiple CPU-cores on the POWER9/V100 there is significant > > variation in the execution time of the code. > > > > There are four GPUs per POWER9/V100 node: > > > > $ nvidia-smi -q > > Driver Version : 440.33.01 > > CUDA Version : 10.2 > > GPU 00000004:04:00.0 > > Product Name : Tesla V100-SXM2-32GB > > > > The GPUs have been shown to perform as expected on other applications. > > > > > > > > > > The following lines are found in md.log for the POWER9/V100 run: > > > > Overriding thread affinity set outside gmx mdrun > > Pinning threads with an auto-selected logical core stride of 128 > > NOTE: Thread affinity was not set. > > > > The full md.log is available here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > > > > > > > > Below are the MegaFlops Accounting for the POWER9/V100 versus > > Broadwell/P100: > > > > ================ IBM POWER9 WITH NVIDIA V100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 297.763872 2679.875 > 0.0 > > NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 20.536159 1232.170 > 0.0 > > Lincs-Mat 444.613344 1778.453 > 0.0 > > Constraint-V 261.192228 2089.538 > 0.0 > > Constraint-Vir 2.430161 58.324 > 0.0 > > Settle 73.382008 23702.389 > 0.1 > > > > > ----------------------------------------------------------------------------- > > Total 16441499.096 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > > > ================ INTEL BROADWELL WITH NVIDIA P100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 271.334272 2442.008 > 0.0 > > NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Bonds 10.541054 621.922 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 9.992997 599.580 > 0.0 > > Lincs-Mat 50.775228 203.101 > 0.0 > > Constraint-V 240.108012 1920.864 > 0.0 > > Constraint-Vir 2.323707 55.769 > 0.0 > > Settle 73.382008 23702.389 > 0.2 > > > > > ----------------------------------------------------------------------------- > > Total 12909529.017 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > Some of the rows are identical between the two tables above. The largest > > difference > > is observed for the "NxN Ewald Elec. + LJ [F]" row. > > > > > > > > Here is our Slurm script: > > > > #!/bin/bash > > #SBATCH --job-name=gmx # create a short name for your job > > #SBATCH --nodes=1 # node count > > #SBATCH --ntasks=1 # total number of tasks across all nodes > > #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > > multi-threaded tasks) > > #SBATCH --mem=4G # memory per node (4G per cpu-core is > > default) > > #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > > #SBATCH --gres=gpu:1 # number of gpus per node > > > > module purge > > module load cudatoolkit/10.2 > > > > BCH=../rnase_cubic > > gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > > bench.tpr > > gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > > bench.tpr > > > > > > > > How do we get optimal performance out of GROMACS on our POWER9/V100 > nodes? > > > > Jon > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From rollyng at gmail.com Fri Apr 24 17:47:46 2020 From: rollyng at gmail.com (Rolly Ng) Date: Fri, 24 Apr 2020 15:47:46 -0000 Subject: [gmx-users] =?gb2312?b?u9i4tDogILvYuLQ6ILvYuLQ6IFByb2JsZW0gd2l0?= =?gb2312?b?aCBQb3RlbnRpYWwgTWVhbiBGb3JjZSBjYWxjdWxhdGlvbg==?= In-Reply-To: <5f479f44-56b4-e1f0-f4ae-ccdb62a238d2@vt.edu> References: <007c01d617a3$39234850$ab69d8f0$@gmail.com> <630431a3-9597-294b-fea0-fd60b3e33d32@vt.edu> <001201d617ea$d23800c0$76a80240$@gmail.com> <09b9c81e-3b4f-dd30-33a8-6f8762929bb4@vt.edu> <002201d618b3$ec0d3730$c427a590$@gmail.com> <5f479f44-56b4-e1f0-f4ae-ccdb62a238d2@vt.edu> Message-ID: <007201d61a4f$b0d25040$1276f0c0$@gmail.com> Dear Justin, Please refer to my figures on RG, https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Po tential_Mean_Force_PMF_result The 1st plot of my question shows the pull force of the Steered MD of 500 ps, and I have visualized that the guest was gradually moved away from the host. By looking at the pull force, I suppose that the frames from 0 to about 250 ps are sufficient for the umbrella sampling and your tutorial was 0 to 160 ps. So, I suppose only the linear section of the pull force frames are need. When I was checking the tpr/xvg pairs, instead of using all frames, I reduced the umber of file pairs to 27. Whereas the 51 pairs are for the entire 500 ps. Thank you very much for your patient and I have also updated my answer on RG with two new plots showing the PMF (free_energy.png) and histogram (histo.png) from 0 to 5 nm. Regards, Rolly -----????----- ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se ?? Justin Lemkul ????: 2020?4?23???? ??6:17 ???: gmx-users at gromacs.org ??: Re: [gmx-users] ??: ??: Problem with Potential Mean Force calculation On 4/22/20 10:40 AM, Rolly Ng wrote: > Dear Justin and Vu, > > I think I have solved part of my problem. The number of tpr/xvg pairs were too much in my case. Although I used the script to generate 50 pairs with 0. 1nm setting, it turns out that only the first 27 pairs works. What does "only the first 27 pairs work" mean? > ./setupUmbrella.py summary_distances.dat 0.1 run-umbrella.sh &> > caught-output.txt > > Please find my summary_distances.dat and caught-output.txt attached. > > I also found that the wham loops for very long time if there is problem with the tpr/xvg pairs. A normal run will last only tens of iteration. I have to check the pairs one by one in order to get a reasonable PMF. I have uploaded them to RG. > > What could be the problem with the tpr/xvg pairs? How can I avoid it the next time? The reaction coordinate you established with these 51 .tpr files is consistent with the histograms you showed - sampling roughly between 2 - 8 nm. The PMF is still basically an impossibility based on these data. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From halverson at Princeton.EDU Fri Apr 24 19:27:54 2020 From: halverson at Princeton.EDU (Jonathan D. Halverson) Date: Fri, 24 Apr 2020 17:27:54 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: , Message-ID: I cannot force the pinning via GROMACS so I will look at what can be done with hwloc. On the POWER9 the hardware appears to be detected correctly (only Intel gives note): Running on 1 node with total 128 cores, 128 logical cores, 1 compatible GPU But during the build it fails the HarwareUnitTests: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log#L3338 Here are more benchmarks based on Kevin and Szil?rd's suggestions: ADH (134177 atoms, ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz) 2019.6, PME and cubic box nsteps = 40000 Intel Broadwell-NVIDIA P100 ntomp (rate, wall time) 1 (21 ns/day, 323 s) 4 (56 ns/day, 123 s) 8 (69 ns/day, 100 s) IBM POWER9-NVIDIA V100 ntomp (rate, wall time) 1 (14 ns/day, 500 s) 1 (14 ns/day, 502 s) 1 (14 ns/day, 510 s) 4 (19 ns/day, 357 s) 4 (17 ns/day, 397 s) 4 (20 ns/day, 346 s) 8 (30 ns/day, 232 s) 8 (24 ns/day, 288 s) 8 (31 ns/day, 222 s) 16 (59 ns/day, 117 s) 16 (65 ns/day, 107 s) 16 (63 ns/day, 110 s) [md.log on GitHub is https://bit.ly/3aCm1gw] 32 (89 ns/day, 76 s) 32 (93 ns/day, 75 s) 32 (89 ns/day, 78 s) 64 (57 ns/day, 122 s) 64 (43 ns/day, 159 s) 64 (46 ns/day, 152 s) Yes, there is variability between identical runs for POWER9/V100. For the Intel case, ntomp equals the number of physical cores. For the IBM case, ntomp is equal to the number of hardware threads (4 hardware threads per physical core). On a physical core basis, these number are looking better but clearly there are still problems. I tried different values for -pinoffset but didn't see performance gains that could't be explained by the variation from run to run. I've written to contacts at ORNL and IBM. Jon ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Szil?rd P?ll Sent: Friday, April 24, 2020 10:23 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node Using a single thread per GPU as the linked log files show is not sufficient for GROMACS (and any modern machine should have more than that anyway), but I imply from your mail that this only meant to debug performance instability? Your performance variations with Power9 may be related that you are either not setting affinities or the affinity settings is not correct. However, you also have some job scheduler in the way (that I suspect is either not configured well or is not passed the required options to correctly assign resources to jobs) and obfuscates machine layout and makes things look weird to mdrun [1]. I suggest to simplify the problem and try to debug it step-by-step. Start with allocating full nodes and test that you can pin (either with mdurun -pin on or hwloc) and avoid [1], get an understanding of what should you expect from the node sharing that seem to not work correctly. Building GROMACS with hwloc may help as you get better reporting in the log. [1] https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100#L58 -- Szil?rd On Fri, Apr 24, 2020 at 3:43 AM Jonathan D. Halverson < halverson at princeton.edu> wrote: > Hi Kevin, > > md.log for the Intel run is here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 > > Thanks for the info on constraints with 2020. I'll try some runs with > different values of -pinoffset for 2019.6. > > I know a group at NIST is having the same or similar problems with > POWER9/V100. > > Jon > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin > Boyd > Sent: Thursday, April 23, 2020 9:08 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node > > Hi, > > Can you post the full log for the Intel system? I typically find the real > cycle and time accounting section a better place to start debugging > performance issues. > > A couple quick notes, but need a side-by-side comparison for more useful > analysis, and these points may apply to both systems so may not be your > root cause: > * At first glance, your Power system spends 1/3 of its time in constraint > calculation, which is unusual. This can be reduced 2 ways - first, by > adding more CPU cores. It doesn't make a ton of sense to benchmark on one > core if your applications will use more. Second, if you upgrade to Gromacs > 2020 you can probably put the constraint calculation on the GPU with > -update GPU. > * The Power system log has this line: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 > indicating > that threads perhaps were not actually pinned. Try adding -pinoffset 0 (or > some other core) to specify where you want the process pinned. > > Kevin > > On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < > halverson at princeton.edu> wrote: > > > *Message sent from a system outside of UConn.* > > > > > > We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on an > > IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running > RHEL > > 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > > nodes. Everything below is about of the POWER9/V100 node. > > > > We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > > CPU-core and 1 GPU ( > > ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > > found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives > 102 > > ns/day. The difference in performance is roughly the same for the larger > > ADH benchmark and when different numbers of CPU-cores are used. GROMACS > is > > always underperforming on our POWER9/V100 nodes. We have pinning turned > on > > (see Slurm script at bottom). > > > > Below is our build procedure on the POWER9/V100 node: > > > > version_gmx=2019.6 > > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > > tar zxvf gromacs-${version_gmx}.tar.gz > > cd gromacs-${version_gmx} > > mkdir build && cd build > > > > module purge > > module load rh/devtoolset/7 > > module load cudatoolkit/10.2 > > > > OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > > > > cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > > -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > > -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > > -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > > -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > > -DGMX_BUILD_OWN_FFTW=ON \ > > -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > > -DGMX_OPENMP_MAX_THREADS=128 \ > > -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > > -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > > > > make -j 10 > > make check > > make install > > > > 45 of the 46 tests pass with the exception being HardwareUnitTests. There > > are several posts about this and apparently it is not a concern. The full > > build log is here: > > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > > > > > > > > Here is more info about our POWER9/V100 node: > > > > $ lscpu > > Architecture: ppc64le > > Byte Order: Little Endian > > CPU(s): 128 > > On-line CPU(s) list: 0-127 > > Thread(s) per core: 4 > > Core(s) per socket: 16 > > Socket(s): 2 > > NUMA node(s): 6 > > Model: 2.3 (pvr 004e 1203) > > Model name: POWER9, altivec supported > > CPU max MHz: 3800.0000 > > CPU min MHz: 2300.0000 > > > > You see that we have 4 hardware threads per physical core. If we use 4 > > hardware threads on the RNASE benchmark instead of 1 the performance goes > > to 119 ns/day which is still about 20% less than the Broadwell/P100 > value. > > When using multiple CPU-cores on the POWER9/V100 there is significant > > variation in the execution time of the code. > > > > There are four GPUs per POWER9/V100 node: > > > > $ nvidia-smi -q > > Driver Version : 440.33.01 > > CUDA Version : 10.2 > > GPU 00000004:04:00.0 > > Product Name : Tesla V100-SXM2-32GB > > > > The GPUs have been shown to perform as expected on other applications. > > > > > > > > > > The following lines are found in md.log for the POWER9/V100 run: > > > > Overriding thread affinity set outside gmx mdrun > > Pinning threads with an auto-selected logical core stride of 128 > > NOTE: Thread affinity was not set. > > > > The full md.log is available here: > > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > > > > > > > > Below are the MegaFlops Accounting for the POWER9/V100 versus > > Broadwell/P100: > > > > ================ IBM POWER9 WITH NVIDIA V100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 297.763872 2679.875 > 0.0 > > NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 20.536159 1232.170 > 0.0 > > Lincs-Mat 444.613344 1778.453 > 0.0 > > Constraint-V 261.192228 2089.538 > 0.0 > > Constraint-Vir 2.430161 58.324 > 0.0 > > Settle 73.382008 23702.389 > 0.1 > > > > > ----------------------------------------------------------------------------- > > Total 16441499.096 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > > > ================ INTEL BROADWELL WITH NVIDIA P100 ================ > > Computing: M-Number M-Flops % > Flops > > > > > ----------------------------------------------------------------------------- > > Pair Search distance check 271.334272 2442.008 > 0.0 > > NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 > 98.0 > > NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 > 1.6 > > 1,4 nonbonded interactions 53.415341 4807.381 > 0.0 > > Shift-X 3.029040 18.174 > 0.0 > > Bonds 10.541054 621.922 > 0.0 > > Angles 37.043704 6223.342 > 0.0 > > Propers 55.825582 12784.058 > 0.1 > > Impropers 4.220422 877.848 > 0.0 > > Virial 2.432585 43.787 > 0.0 > > Stop-CM 2.452080 24.521 > 0.0 > > Calc-Ekin 48.128080 1299.458 > 0.0 > > Lincs 9.992997 599.580 > 0.0 > > Lincs-Mat 50.775228 203.101 > 0.0 > > Constraint-V 240.108012 1920.864 > 0.0 > > Constraint-Vir 2.323707 55.769 > 0.0 > > Settle 73.382008 23702.389 > 0.2 > > > > > ----------------------------------------------------------------------------- > > Total 12909529.017 > 100.0 > > > > > ----------------------------------------------------------------------------- > > > > Some of the rows are identical between the two tables above. The largest > > difference > > is observed for the "NxN Ewald Elec. + LJ [F]" row. > > > > > > > > Here is our Slurm script: > > > > #!/bin/bash > > #SBATCH --job-name=gmx # create a short name for your job > > #SBATCH --nodes=1 # node count > > #SBATCH --ntasks=1 # total number of tasks across all nodes > > #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > > multi-threaded tasks) > > #SBATCH --mem=4G # memory per node (4G per cpu-core is > > default) > > #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > > #SBATCH --gres=gpu:1 # number of gpus per node > > > > module purge > > module load cudatoolkit/10.2 > > > > BCH=../rnase_cubic > > gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > > bench.tpr > > gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > > bench.tpr > > > > > > > > How do we get optimal performance out of GROMACS on our POWER9/V100 > nodes? > > > > Jon > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From alexanderwien2k at gmail.com Fri Apr 24 20:33:14 2020 From: alexanderwien2k at gmail.com (Alex) Date: Fri, 24 Apr 2020 18:33:14 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi Magnus, I see, many thanks for the insights. On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < magnus.lundborg at scilifelab.se> wrote: > Hi Alex, > > pull-group1-pbcatom lets you specify the exact atom used as the PBC > reference. Both 0 and -1 are special cases. For small molecules 0 is > (almost?) always OK. Find one in the center of you membrane (in the pull > direction). I'll actually have to check if -1 is even compatible with > pull-pbc-ref-prev-step-com. It's possible that that combination should > not be allowed even. > So, the pull-group1-pbcatm could be any other number as atom number rather than 0 and -1. > > As you say, you can define a subgroup within the larger membrane group, > but that is mainly of use if you know that some atoms consistently in > the center of the whole group and others are more flexible. > In this case where the subgroup defined in index.ndx file has more than one atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to the pull-group1-pbcatom? If I am not mistaken, here, the entry number in index.ndx file belong to the subgroup should be assigned to the pull-group1-pbcatom. [ system ] [ Other ] .... [ non-water ] [ subgroup ] Would you please confirm if I am correct? Thank you Alex > Regards, > > Magnus > > On 2020-04-21 16:24, Alex wrote: > > Hi Magnus, > > Actually I am confused with the available options for the > > "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". > > For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when > > one of the group is large, even the 2020.1 version of grmacs would give a > > warning if one used No in a case of presence of a large group. > > Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 > > the middle atom (number wise) of the large group is used automatically > > which is safe only for small groups as manual states. So, only > > remaining option is -1. > > So, what I understood for a layered-large group similar to what I have > one > > should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 > > which would cause moving the system along -Z during the pulling. > > > > Using gmx select, can I manually define a sub-group around the COM of the > > large group, and consider it as one of the pulling groups instead of the > > large group? > > > > Thank you > > Alex > > > > On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < > > magnus.lundborg at scilifelab.se> wrote: > > > >> Hi Alex, > >> > >> I don't see why it would need pull-group1-pbcatom = -1. Why not pick a > >> central atom? > >> > >> Regards, > >> > >> Magnus > >> > >> On 2020-04-20 13:40, Alex wrote: > >>> Hi Magnus, > >>> Thanks. > >>> The problem raises only because of using the pull-pbc-ref-prev-step-com > >>> which needs the pull-group1-pbcatom to be -1 to be meaningful. > >>> For an identical system and mdp parameters using 2018 version of > gromacs > >>> which is independent to the pull-pbc-ref-prev-step-com, I see no issue. > >>> > >>> Regards, > >>> Alex > >>> > >>> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < > >>> magnus.lundborg at scilifelab.se> wrote: > >>> > >>>> Sorry, about the statement about pbcatom -1. I was thinking about 0. I > >>>> don't know if pbcatom -1 is good or not in this case. > >>>> > >>>> Regards, > >>>> > >>>> Magnus > >>>> > >>>> On 2020-04-20 09:24, Magnus Lundborg wrote: > >>>>> Hi Alex, > >>>>> > >>>>> I don't think this is related to using pull-pbc-ref-prev-step-com. > >>>>> Have you tried without it? However, it is risky using pbcatom -1, > >>>>> since you don't know what atom you are using as the initial > reference. > >>>>> I would suggest picking an atom you know is located at the centre of > >>>>> the structure. > >>>>> > >>>>> I would think that the problem has to do with the comm removal. What > >>>>> are your parameters for comm-mode, nstcomm and comm-grps? It is > >>>>> possible that you need to lower your nstcomm. It is also possible, > but > >>>>> not certain, the comm-mode Linear-acceleration-correction might help > >>>>> you. For some reason, it seems like I have sometimes avoided similar > >>>>> problems by using the sd integrator instead, but I haven't evaluated > >>>>> that properly - it might just have been coincidences. If you see a > >>>>> clear difference using the sd integrator it might be good if you'd > >>>>> file an issue about it on gitlab so that someone can look into if > >>>>> there is something wrong. > >>>>> > >>>>> Regards, > >>>>> Magnus > >>>>> > >>>>> On 2020-04-18 20:12, Alex wrote: > >>>>>> Dear all, > >>>>>> To generate the initial configurations for umbrella sampling, I > >>>>>> conducted a > >>>>>> simple pulling simulation by which a single-small molecule (mol_A) > is > >>>>>> being > >>>>>> dragged along -Z from water into the body of a thin film. > >>>>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = > >>>>>> yes" and > >>>>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the > >>>>>> system > >>>>>> along the pulling direction as soon as the mol_A reach to the thin > >> film, > >>>>>> please find below the pulling flags movie and plot in below links. > >>>>>> > >>>>>> Centering the thin film and mol_A could solve the issue, (echo 1 0 > | > >>>>>> trjconv -center yes) to some extent but still COM changes in the > early > >>>>>> stage below 2ns. , > >>>>>> COM: > >>>>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > >>>>>> > >>>>>> Movie in which the water molecules are hidden: > >>>>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > >>>>>> > >>>>>> - > >>>>>> gmx version 2020.1 > >>>>>> ----- > >>>>>> pull = yes > >>>>>> pull-print-com = no > >>>>>> pull-print-ref-value = yes > >>>>>> pull-print-components = Yes > >>>>>> pull-nstxout = 1000 > >>>>>> pull-nstfout = 1000 > >>>>>> pull-pbc-ref-prev-step-com = yes > >>>>>> pull-ngroups = 2 > >>>>>> pull-ncoords = 1 > >>>>>> pull-group1-name = Thin-film > >>>>>> pull-group1-pbcatom = -1 > >>>>>> pull-group2-name = mol_A > >>>>>> pull-group2-pbcatom = 0 > >>>>>> pull-coord1-type = umbrella > >>>>>> pull-coord1-geometry = direction > >>>>>> pull-coord1-groups = 1 2 > >>>>>> pull-coord1-dim = N N Y > >>>>>> pull-coord1-origin = 0.0 0.0 0.0 > >>>>>> pull-coord1-vec = 0.0 0.0 -1.0 > >>>>>> pull-coord1-start = yes > >>>>>> pull-coord1-init = 0 > >>>>>> pull-coord1-rate = 0.0005 > >>>>>> pull-coord1-k = 5000 > >>>>>> ----- > >>>>>> I wonder if I could extract correct initial configuration from this > >>>>>> trajectory? With correct initial configuration, I mean a set of gro > >>>>>> file in > >>>>>> which change from one from to another is the distance between the > COM > >> of > >>>>>> the thin-film and mol_A? > >>>>>> > >>>>>> Thank you > >>>>>> Alex > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pall.szilard at gmail.com Fri Apr 24 22:31:29 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 20:31:29 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: <0cdf1551-a223-de2a-a599-75612dd9c3de@gmail.com> References: <0cdf1551-a223-de2a-a599-75612dd9c3de@gmail.com> Message-ID: On Fri, Apr 24, 2020 at 5:55 AM Alex wrote: > Hi Kevin, > > We've been having issues with Power9/V100 very similar to what Jon > described and basically settled on what I believe is sub-par > performance. We tested it on systems with ~30-50K particles and threads > simply cannot be pinned. What does that mean, how did you verify that? The Linux kernel can in general set affinities on ppc64el, whether that's requested by mdrun or some other tool, so if you have observed that the affinity mask is not respected (or it does not change), that more likely OS / setup issue, I'd think. What is different compared to x86 is that the hardware thread layout is different on Power9 (with default Linux kernel configs) and hardware threads are exposed as consecutive "CPUs" by the OS rather than strided by #cores. I could try to sum up some details on how to sett affinities (with mdrun or external tools), if that is of interest. However, it really should be something that's possible to do even using the job scheduler (+ along reasonable system configuration). > As far as Gromacs is concerned, our brand-new > Power9 nodes operate as if they were based on Intel CPUs (two threads > per core) Unless the hardware thread layout has been changed, that's perhaps not the case, see above. > and zero advantage of IBM parallelization is being taken. > You mean the SMT4? > Other users of the same nodes reported similar issues with other > software, which to me suggests that our sysadmins don't really know how > to set these nodes up. > > At this point, if someone could figure out a clear set of build > instructions in combination with slurm/mdrun inputs, it would be very > much appreciated. > Have you checked public documentation on ORNL's sites? GROMACS has been used successfully on Summit. What about IBM support? -- Szil?rd > > Alex > > On 4/23/2020 9:37 PM, Kevin Boyd wrote: > > I'm not entirely sure how thread-pinning plays with slurm allocations on > > partial nodes. I always reserve the entire node when I use thread > pinning, > > and run a bunch of simulations by pinning to different cores manually, > > rather than relying on slurm to divvy up resources for multiple jobs. > > > > Looking at both logs now, a few more points > > > > * Your benchmarks are short enough that little things like cores spinning > > up frequencies can matter. I suggest running longer (increase nsteps in > the > > mdp or at the command line), and throwing away your initial benchmark > data > > (see -resetstep and -resethway) to avoid artifacts > > * Your benchmark system is quite small for such a powerful GPU. I might > > expect better performance running multiple simulations per-GPU if the > > workflows being run can rely on replicates, and a larger system would > > probably scale better to the V100. > > * The P100/intel system appears to have pinned cores properly, it's > > unclear whether it had a real impact on these benchmarks > > * It looks like the CPU-based computations were the primary contributors > to > > the observed difference in performance. That should decrease or go away > > with increased core counts and shifting the update phase to the GPU. It > may > > be (I have no prior experience to indicate either way) that the intel > cores > > are simply better on a 1-1 basis than the Power cores. If you have 4-8 > > cores per simulation (try -ntomp 4 and increasing the allocation of your > > slurm job), the individual core performance shouldn't matter too > > much, you're just certainly bottlenecked on one CPU core per GPU, which > can > > emphasize performance differences.. > > > > Kevin > > > > On Thu, Apr 23, 2020 at 6:43 PM Jonathan D. Halverson < > > halverson at princeton.edu> wrote: > > > >> *Message sent from a system outside of UConn.* > >> > >> > >> Hi Kevin, > >> > >> md.log for the Intel run is here: > >> > >> > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 > >> > >> Thanks for the info on constraints with 2020. I'll try some runs with > >> different values of -pinoffset for 2019.6. > >> > >> I know a group at NIST is having the same or similar problems with > >> POWER9/V100. > >> > >> Jon > >> ________________________________ > >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin > >> Boyd > >> Sent: Thursday, April 23, 2020 9:08 PM > >> To: gmx-users at gromacs.org > >> Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node > >> > >> Hi, > >> > >> Can you post the full log for the Intel system? I typically find the > real > >> cycle and time accounting section a better place to start debugging > >> performance issues. > >> > >> A couple quick notes, but need a side-by-side comparison for more useful > >> analysis, and these points may apply to both systems so may not be your > >> root cause: > >> * At first glance, your Power system spends 1/3 of its time in > constraint > >> calculation, which is unusual. This can be reduced 2 ways - first, by > >> adding more CPU cores. It doesn't make a ton of sense to benchmark on > one > >> core if your applications will use more. Second, if you upgrade to > Gromacs > >> 2020 you can probably put the constraint calculation on the GPU with > >> -update GPU. > >> * The Power system log has this line: > >> > >> > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 > >> indicating > >> that threads perhaps were not actually pinned. Try adding -pinoffset 0 > (or > >> some other core) to specify where you want the process pinned. > >> > >> Kevin > >> > >> On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < > >> halverson at princeton.edu> wrote: > >> > >>> *Message sent from a system outside of UConn.* > >>> > >>> > >>> We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on > an > >>> IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running > >> RHEL > >>> 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel > >>> nodes. Everything below is about of the POWER9/V100 node. > >>> > >>> We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 > >>> CPU-core and 1 GPU ( > >>> ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and > >>> found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives > >> 102 > >>> ns/day. The difference in performance is roughly the same for the > larger > >>> ADH benchmark and when different numbers of CPU-cores are used. GROMACS > >> is > >>> always underperforming on our POWER9/V100 nodes. We have pinning turned > >> on > >>> (see Slurm script at bottom). > >>> > >>> Below is our build procedure on the POWER9/V100 node: > >>> > >>> version_gmx=2019.6 > >>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz > >>> tar zxvf gromacs-${version_gmx}.tar.gz > >>> cd gromacs-${version_gmx} > >>> mkdir build && cd build > >>> > >>> module purge > >>> module load rh/devtoolset/7 > >>> module load cudatoolkit/10.2 > >>> > >>> OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" > >>> > >>> cmake3 .. -DCMAKE_BUILD_TYPE=Release \ > >>> -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ > >>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ > >>> -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ > >>> -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ > >>> -DGMX_BUILD_OWN_FFTW=ON \ > >>> -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ > >>> -DGMX_OPENMP_MAX_THREADS=128 \ > >>> -DCMAKE_INSTALL_PREFIX=$HOME/.local \ > >>> -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON > >>> > >>> make -j 10 > >>> make check > >>> make install > >>> > >>> 45 of the 46 tests pass with the exception being HardwareUnitTests. > There > >>> are several posts about this and apparently it is not a concern. The > full > >>> build log is here: > >>> > >> > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log > >>> > >>> > >>> Here is more info about our POWER9/V100 node: > >>> > >>> $ lscpu > >>> Architecture: ppc64le > >>> Byte Order: Little Endian > >>> CPU(s): 128 > >>> On-line CPU(s) list: 0-127 > >>> Thread(s) per core: 4 > >>> Core(s) per socket: 16 > >>> Socket(s): 2 > >>> NUMA node(s): 6 > >>> Model: 2.3 (pvr 004e 1203) > >>> Model name: POWER9, altivec supported > >>> CPU max MHz: 3800.0000 > >>> CPU min MHz: 2300.0000 > >>> > >>> You see that we have 4 hardware threads per physical core. If we use 4 > >>> hardware threads on the RNASE benchmark instead of 1 the performance > goes > >>> to 119 ns/day which is still about 20% less than the Broadwell/P100 > >> value. > >>> When using multiple CPU-cores on the POWER9/V100 there is significant > >>> variation in the execution time of the code. > >>> > >>> There are four GPUs per POWER9/V100 node: > >>> > >>> $ nvidia-smi -q > >>> Driver Version : 440.33.01 > >>> CUDA Version : 10.2 > >>> GPU 00000004:04:00.0 > >>> Product Name : Tesla V100-SXM2-32GB > >>> > >>> The GPUs have been shown to perform as expected on other applications. > >>> > >>> > >>> > >>> > >>> The following lines are found in md.log for the POWER9/V100 run: > >>> > >>> Overriding thread affinity set outside gmx mdrun > >>> Pinning threads with an auto-selected logical core stride of 128 > >>> NOTE: Thread affinity was not set. > >>> > >>> The full md.log is available here: > >>> > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > >>> > >>> > >>> > >>> > >>> Below are the MegaFlops Accounting for the POWER9/V100 versus > >>> Broadwell/P100: > >>> > >>> ================ IBM POWER9 WITH NVIDIA V100 ================ > >>> Computing: M-Number M-Flops % > >> Flops > >>> > >> > ----------------------------------------------------------------------------- > >>> Pair Search distance check 297.763872 2679.875 > >> 0.0 > >>> NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 > >> 98.0 > >>> NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 > >> 1.6 > >>> 1,4 nonbonded interactions 53.415341 4807.381 > >> 0.0 > >>> Shift-X 3.029040 18.174 > >> 0.0 > >>> Angles 37.043704 6223.342 > >> 0.0 > >>> Propers 55.825582 12784.058 > >> 0.1 > >>> Impropers 4.220422 877.848 > >> 0.0 > >>> Virial 2.432585 43.787 > >> 0.0 > >>> Stop-CM 2.452080 24.521 > >> 0.0 > >>> Calc-Ekin 48.128080 1299.458 > >> 0.0 > >>> Lincs 20.536159 1232.170 > >> 0.0 > >>> Lincs-Mat 444.613344 1778.453 > >> 0.0 > >>> Constraint-V 261.192228 2089.538 > >> 0.0 > >>> Constraint-Vir 2.430161 58.324 > >> 0.0 > >>> Settle 73.382008 23702.389 > >> 0.1 > >>> > >> > ----------------------------------------------------------------------------- > >>> Total 16441499.096 > >> 100.0 > >>> > >> > ----------------------------------------------------------------------------- > >>> > >>> ================ INTEL BROADWELL WITH NVIDIA P100 ================ > >>> Computing: M-Number M-Flops % > >> Flops > >>> > >> > ----------------------------------------------------------------------------- > >>> Pair Search distance check 271.334272 2442.008 > >> 0.0 > >>> NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 > >> 98.0 > >>> NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 > >> 1.6 > >>> 1,4 nonbonded interactions 53.415341 4807.381 > >> 0.0 > >>> Shift-X 3.029040 18.174 > >> 0.0 > >>> Bonds 10.541054 621.922 > >> 0.0 > >>> Angles 37.043704 6223.342 > >> 0.0 > >>> Propers 55.825582 12784.058 > >> 0.1 > >>> Impropers 4.220422 877.848 > >> 0.0 > >>> Virial 2.432585 43.787 > >> 0.0 > >>> Stop-CM 2.452080 24.521 > >> 0.0 > >>> Calc-Ekin 48.128080 1299.458 > >> 0.0 > >>> Lincs 9.992997 599.580 > >> 0.0 > >>> Lincs-Mat 50.775228 203.101 > >> 0.0 > >>> Constraint-V 240.108012 1920.864 > >> 0.0 > >>> Constraint-Vir 2.323707 55.769 > >> 0.0 > >>> Settle 73.382008 23702.389 > >> 0.2 > >>> > >> > ----------------------------------------------------------------------------- > >>> Total 12909529.017 > >> 100.0 > >>> > >> > ----------------------------------------------------------------------------- > >>> Some of the rows are identical between the two tables above. The > largest > >>> difference > >>> is observed for the "NxN Ewald Elec. + LJ [F]" row. > >>> > >>> > >>> > >>> Here is our Slurm script: > >>> > >>> #!/bin/bash > >>> #SBATCH --job-name=gmx # create a short name for your job > >>> #SBATCH --nodes=1 # node count > >>> #SBATCH --ntasks=1 # total number of tasks across all > nodes > >>> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if > >>> multi-threaded tasks) > >>> #SBATCH --mem=4G # memory per node (4G per cpu-core is > >>> default) > >>> #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) > >>> #SBATCH --gres=gpu:1 # number of gpus per node > >>> > >>> module purge > >>> module load cudatoolkit/10.2 > >>> > >>> BCH=../rnase_cubic > >>> gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o > >>> bench.tpr > >>> gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s > >>> bench.tpr > >>> > >>> > >>> > >>> How do we get optimal performance out of GROMACS on our POWER9/V100 > >> nodes? > >>> Jon > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-request at gromacs.org. > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pall.szilard at gmail.com Fri Apr 24 22:53:03 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 20:53:03 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: > The following lines are found in md.log for the POWER9/V100 run: > > Overriding thread affinity set outside gmx mdrun > Pinning threads with an auto-selected logical core stride of 128 > NOTE: Thread affinity was not set. > > The full md.log is available here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log I glanced over that at first, will see if I can reproduce it, though I only have access to a Raptor Talos, not an IBM machine with Ubuntu. What OS are you using? -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From pall.szilard at gmail.com Fri Apr 24 22:53:05 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 20:53:05 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: > The following lines are found in md.log for the POWER9/V100 run: > > Overriding thread affinity set outside gmx mdrun > Pinning threads with an auto-selected logical core stride of 128 > NOTE: Thread affinity was not set. > > The full md.log is available here: > https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log I glanced over that at first, will see if I can reproduce it, though I only have access to a Raptor Talos, not an IBM machine with Ubuntu. What OS are you using? -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jun.zhou at monash.edu Fri Apr 24 23:00:25 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Fri, 24 Apr 2020 21:00:25 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 192, Issue 89 In-Reply-To: References: Message-ID: <605B450B-2AB4-4CA1-8C34-4869C227E80B@monash.edu> Hi, I use gromacs-2019.4. Sent from my iPhone > On 25 Apr 2020, at 6:54 am, gromacs.org_gmx-users-request at maillist.sys.kth.se wrote: > > ?Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > 2. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > 3. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Apr 2020 22:31:11 +0200 > From: Szil?rd P?ll > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 > node > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> On Fri, Apr 24, 2020 at 5:55 AM Alex wrote: >> >> Hi Kevin, >> >> We've been having issues with Power9/V100 very similar to what Jon >> described and basically settled on what I believe is sub-par >> performance. We tested it on systems with ~30-50K particles and threads >> simply cannot be pinned. > > > What does that mean, how did you verify that? > The Linux kernel can in general set affinities on ppc64el, whether that's > requested by mdrun or some other tool, so if you have observed that the > affinity mask is not respected (or it does not change), that more likely OS > / setup issue, I'd think. > > What is different compared to x86 is that the hardware thread layout is > different on Power9 (with default Linux kernel configs) and hardware > threads are exposed as consecutive "CPUs" by the OS rather than strided by > #cores. > > I could try to sum up some details on how to sett affinities (with mdrun or > external tools), if that is of interest. However, it really should be > something that's possible to do even using the job scheduler (+ along > reasonable system configuration). > > >> As far as Gromacs is concerned, our brand-new >> Power9 nodes operate as if they were based on Intel CPUs (two threads >> per core) > > > Unless the hardware thread layout has been changed, that's perhaps not the > case, see above. > > >> and zero advantage of IBM parallelization is being taken. >> > > You mean the SMT4? > > >> Other users of the same nodes reported similar issues with other >> software, which to me suggests that our sysadmins don't really know how >> to set these nodes up. >> >> At this point, if someone could figure out a clear set of build >> instructions in combination with slurm/mdrun inputs, it would be very >> much appreciated. >> > > Have you checked public documentation on ORNL's sites? GROMACS has been > used successfully on Summit. What about IBM support? > > -- > Szil?rd > > >> >> Alex >> >>> On 4/23/2020 9:37 PM, Kevin Boyd wrote: >>> I'm not entirely sure how thread-pinning plays with slurm allocations on >>> partial nodes. I always reserve the entire node when I use thread >> pinning, >>> and run a bunch of simulations by pinning to different cores manually, >>> rather than relying on slurm to divvy up resources for multiple jobs. >>> >>> Looking at both logs now, a few more points >>> >>> * Your benchmarks are short enough that little things like cores spinning >>> up frequencies can matter. I suggest running longer (increase nsteps in >> the >>> mdp or at the command line), and throwing away your initial benchmark >> data >>> (see -resetstep and -resethway) to avoid artifacts >>> * Your benchmark system is quite small for such a powerful GPU. I might >>> expect better performance running multiple simulations per-GPU if the >>> workflows being run can rely on replicates, and a larger system would >>> probably scale better to the V100. >>> * The P100/intel system appears to have pinned cores properly, it's >>> unclear whether it had a real impact on these benchmarks >>> * It looks like the CPU-based computations were the primary contributors >> to >>> the observed difference in performance. That should decrease or go away >>> with increased core counts and shifting the update phase to the GPU. It >> may >>> be (I have no prior experience to indicate either way) that the intel >> cores >>> are simply better on a 1-1 basis than the Power cores. If you have 4-8 >>> cores per simulation (try -ntomp 4 and increasing the allocation of your >>> slurm job), the individual core performance shouldn't matter too >>> much, you're just certainly bottlenecked on one CPU core per GPU, which >> can >>> emphasize performance differences.. >>> >>> Kevin >>> >>> On Thu, Apr 23, 2020 at 6:43 PM Jonathan D. Halverson < >>> halverson at princeton.edu> wrote: >>> >>>> *Message sent from a system outside of UConn.* >>>> >>>> >>>> Hi Kevin, >>>> >>>> md.log for the Intel run is here: >>>> >>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 >>>> >>>> Thanks for the info on constraints with 2020. I'll try some runs with >>>> different values of -pinoffset for 2019.6. >>>> >>>> I know a group at NIST is having the same or similar problems with >>>> POWER9/V100. >>>> >>>> Jon >>>> ________________________________ >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin >>>> Boyd >>>> Sent: Thursday, April 23, 2020 9:08 PM >>>> To: gmx-users at gromacs.org >>>> Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node >>>> >>>> Hi, >>>> >>>> Can you post the full log for the Intel system? I typically find the >> real >>>> cycle and time accounting section a better place to start debugging >>>> performance issues. >>>> >>>> A couple quick notes, but need a side-by-side comparison for more useful >>>> analysis, and these points may apply to both systems so may not be your >>>> root cause: >>>> * At first glance, your Power system spends 1/3 of its time in >> constraint >>>> calculation, which is unusual. This can be reduced 2 ways - first, by >>>> adding more CPU cores. It doesn't make a ton of sense to benchmark on >> one >>>> core if your applications will use more. Second, if you upgrade to >> Gromacs >>>> 2020 you can probably put the constraint calculation on the GPU with >>>> -update GPU. >>>> * The Power system log has this line: >>>> >>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 >>>> indicating >>>> that threads perhaps were not actually pinned. Try adding -pinoffset 0 >> (or >>>> some other core) to specify where you want the process pinned. >>>> >>>> Kevin >>>> >>>> On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < >>>> halverson at princeton.edu> wrote: >>>> >>>>> *Message sent from a system outside of UConn.* >>>>> >>>>> >>>>> We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on >> an >>>>> IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running >>>> RHEL >>>>> 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel >>>>> nodes. Everything below is about of the POWER9/V100 node. >>>>> >>>>> We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 >>>>> CPU-core and 1 GPU ( >>>>> ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and >>>>> found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives >>>> 102 >>>>> ns/day. The difference in performance is roughly the same for the >> larger >>>>> ADH benchmark and when different numbers of CPU-cores are used. GROMACS >>>> is >>>>> always underperforming on our POWER9/V100 nodes. We have pinning turned >>>> on >>>>> (see Slurm script at bottom). >>>>> >>>>> Below is our build procedure on the POWER9/V100 node: >>>>> >>>>> version_gmx=2019.6 >>>>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz >>>>> tar zxvf gromacs-${version_gmx}.tar.gz >>>>> cd gromacs-${version_gmx} >>>>> mkdir build && cd build >>>>> >>>>> module purge >>>>> module load rh/devtoolset/7 >>>>> module load cudatoolkit/10.2 >>>>> >>>>> OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" >>>>> >>>>> cmake3 .. -DCMAKE_BUILD_TYPE=Release \ >>>>> -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ >>>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ >>>>> -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ >>>>> -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ >>>>> -DGMX_BUILD_OWN_FFTW=ON \ >>>>> -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ >>>>> -DGMX_OPENMP_MAX_THREADS=128 \ >>>>> -DCMAKE_INSTALL_PREFIX=$HOME/.local \ >>>>> -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON >>>>> >>>>> make -j 10 >>>>> make check >>>>> make install >>>>> >>>>> 45 of the 46 tests pass with the exception being HardwareUnitTests. >> There >>>>> are several posts about this and apparently it is not a concern. The >> full >>>>> build log is here: >>>>> >>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log >>>>> >>>>> >>>>> Here is more info about our POWER9/V100 node: >>>>> >>>>> $ lscpu >>>>> Architecture: ppc64le >>>>> Byte Order: Little Endian >>>>> CPU(s): 128 >>>>> On-line CPU(s) list: 0-127 >>>>> Thread(s) per core: 4 >>>>> Core(s) per socket: 16 >>>>> Socket(s): 2 >>>>> NUMA node(s): 6 >>>>> Model: 2.3 (pvr 004e 1203) >>>>> Model name: POWER9, altivec supported >>>>> CPU max MHz: 3800.0000 >>>>> CPU min MHz: 2300.0000 >>>>> >>>>> You see that we have 4 hardware threads per physical core. If we use 4 >>>>> hardware threads on the RNASE benchmark instead of 1 the performance >> goes >>>>> to 119 ns/day which is still about 20% less than the Broadwell/P100 >>>> value. >>>>> When using multiple CPU-cores on the POWER9/V100 there is significant >>>>> variation in the execution time of the code. >>>>> >>>>> There are four GPUs per POWER9/V100 node: >>>>> >>>>> $ nvidia-smi -q >>>>> Driver Version : 440.33.01 >>>>> CUDA Version : 10.2 >>>>> GPU 00000004:04:00.0 >>>>> Product Name : Tesla V100-SXM2-32GB >>>>> >>>>> The GPUs have been shown to perform as expected on other applications. >>>>> >>>>> >>>>> >>>>> >>>>> The following lines are found in md.log for the POWER9/V100 run: >>>>> >>>>> Overriding thread affinity set outside gmx mdrun >>>>> Pinning threads with an auto-selected logical core stride of 128 >>>>> NOTE: Thread affinity was not set. >>>>> >>>>> The full md.log is available here: >>>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log >>>>> >>>>> >>>>> >>>>> >>>>> Below are the MegaFlops Accounting for the POWER9/V100 versus >>>>> Broadwell/P100: >>>>> >>>>> ================ IBM POWER9 WITH NVIDIA V100 ================ >>>>> Computing: M-Number M-Flops % >>>> Flops >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> Pair Search distance check 297.763872 2679.875 >>>> 0.0 >>>>> NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 >>>> 98.0 >>>>> NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 >>>> 1.6 >>>>> 1,4 nonbonded interactions 53.415341 4807.381 >>>> 0.0 >>>>> Shift-X 3.029040 18.174 >>>> 0.0 >>>>> Angles 37.043704 6223.342 >>>> 0.0 >>>>> Propers 55.825582 12784.058 >>>> 0.1 >>>>> Impropers 4.220422 877.848 >>>> 0.0 >>>>> Virial 2.432585 43.787 >>>> 0.0 >>>>> Stop-CM 2.452080 24.521 >>>> 0.0 >>>>> Calc-Ekin 48.128080 1299.458 >>>> 0.0 >>>>> Lincs 20.536159 1232.170 >>>> 0.0 >>>>> Lincs-Mat 444.613344 1778.453 >>>> 0.0 >>>>> Constraint-V 261.192228 2089.538 >>>> 0.0 >>>>> Constraint-Vir 2.430161 58.324 >>>> 0.0 >>>>> Settle 73.382008 23702.389 >>>> 0.1 >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> Total 16441499.096 >>>> 100.0 >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> >>>>> ================ INTEL BROADWELL WITH NVIDIA P100 ================ >>>>> Computing: M-Number M-Flops % >>>> Flops >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> Pair Search distance check 271.334272 2442.008 >>>> 0.0 >>>>> NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 >>>> 98.0 >>>>> NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 >>>> 1.6 >>>>> 1,4 nonbonded interactions 53.415341 4807.381 >>>> 0.0 >>>>> Shift-X 3.029040 18.174 >>>> 0.0 >>>>> Bonds 10.541054 621.922 >>>> 0.0 >>>>> Angles 37.043704 6223.342 >>>> 0.0 >>>>> Propers 55.825582 12784.058 >>>> 0.1 >>>>> Impropers 4.220422 877.848 >>>> 0.0 >>>>> Virial 2.432585 43.787 >>>> 0.0 >>>>> Stop-CM 2.452080 24.521 >>>> 0.0 >>>>> Calc-Ekin 48.128080 1299.458 >>>> 0.0 >>>>> Lincs 9.992997 599.580 >>>> 0.0 >>>>> Lincs-Mat 50.775228 203.101 >>>> 0.0 >>>>> Constraint-V 240.108012 1920.864 >>>> 0.0 >>>>> Constraint-Vir 2.323707 55.769 >>>> 0.0 >>>>> Settle 73.382008 23702.389 >>>> 0.2 >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> Total 12909529.017 >>>> 100.0 >>>>> >>>> >> ----------------------------------------------------------------------------- >>>>> Some of the rows are identical between the two tables above. The >> largest >>>>> difference >>>>> is observed for the "NxN Ewald Elec. + LJ [F]" row. >>>>> >>>>> >>>>> >>>>> Here is our Slurm script: >>>>> >>>>> #!/bin/bash >>>>> #SBATCH --job-name=gmx # create a short name for your job >>>>> #SBATCH --nodes=1 # node count >>>>> #SBATCH --ntasks=1 # total number of tasks across all >> nodes >>>>> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if >>>>> multi-threaded tasks) >>>>> #SBATCH --mem=4G # memory per node (4G per cpu-core is >>>>> default) >>>>> #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) >>>>> #SBATCH --gres=gpu:1 # number of gpus per node >>>>> >>>>> module purge >>>>> module load cudatoolkit/10.2 >>>>> >>>>> BCH=../rnase_cubic >>>>> gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o >>>>> bench.tpr >>>>> gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s >>>>> bench.tpr >>>>> >>>>> >>>>> >>>>> How do we get optimal performance out of GROMACS on our POWER9/V100 >>>> nodes? >>>>> Jon >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-request at gromacs.org. >>>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Apr 2020 22:52:48 +0200 > From: Szil?rd P?ll > To: Discussion list for GROMACS users > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 > node > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> The following lines are found in md.log for the POWER9/V100 run: >> >> Overriding thread affinity set outside gmx mdrun >> Pinning threads with an auto-selected logical core stride of 128 >> NOTE: Thread affinity was not set. >> >> The full md.log is available here: >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > I glanced over that at first, will see if I can reproduce it, though I only > have access to a Raptor Talos, not an IBM machine with Ubuntu. > > What OS are you using? > > > -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > > > ------------------------------ > > Message: 3 > Date: Fri, 24 Apr 2020 22:52:48 +0200 > From: Szil?rd P?ll > To: Discussion list for GROMACS users > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 > node > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> The following lines are found in md.log for the POWER9/V100 run: >> >> Overriding thread affinity set outside gmx mdrun >> Pinning threads with an auto-selected logical core stride of 128 >> NOTE: Thread affinity was not set. >> >> The full md.log is available here: >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > I glanced over that at first, will see if I can reproduce it, though I only > have access to a Raptor Talos, not an IBM machine with Ubuntu. > > What OS are you using? > > > -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 89 > ****************************************************** From pall.szilard at gmail.com Sat Apr 25 00:13:03 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 22:13:03 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: Hi, Affinity settings on the Talos II with Ubuntu 18.04 kernel 5.0 works fine. I get threads pinned where they should be (hwloc confirmed) and consistent results. I also get reasonable thread placement even without pinning (i.e. the kernel scatters first until #threads <= #hwthreads). I see only a minor penalty to not pinning -- not too surprising given that I have a single NUMA node and the kernel is doing its job. Here are my quick the test results run on an 8-core Talos II Power9 + a GPU, using the adh_cubic input: $ grep Perf *.log test_1x1_rep1.log:Performance: 16.617 test_1x1_rep2.log:Performance: 16.479 test_1x1_rep3.log:Performance: 16.520 test_1x2_rep1.log:Performance: 32.034 test_1x2_rep2.log:Performance: 32.389 test_1x2_rep3.log:Performance: 32.340 test_1x4_rep1.log:Performance: 62.341 test_1x4_rep2.log:Performance: 62.569 test_1x4_rep3.log:Performance: 62.476 test_1x8_rep1.log:Performance: 97.049 test_1x8_rep2.log:Performance: 96.653 test_1x8_rep3.log:Performance: 96.889 This seems to point towards some issue with the OS or setup on the IBM machines you have -- and the unit test error may be one of the symptoms of it (as it suggests something is off with the hardware topology and a NUMA node is missing from it). I'd still suggest checking if a full not allocation with all threads, memory, etc passed to the job results in successful affinity settings i) in mdrun ii) in some other tool. Please update this thread if you have further findings. Cheers, -- Szil?rd On Fri, Apr 24, 2020 at 10:52 PM Szil?rd P?ll wrote: > > The following lines are found in md.log for the POWER9/V100 run: >> >> Overriding thread affinity set outside gmx mdrun >> Pinning threads with an auto-selected logical core stride of 128 >> NOTE: Thread affinity was not set. >> >> The full md.log is available here: >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > I glanced over that at first, will see if I can reproduce it, though I > only have access to a Raptor Talos, not an IBM machine with Ubuntu. > > What OS are you using? > > > -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > From pall.szilard at gmail.com Sat Apr 25 00:14:39 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 24 Apr 2020 22:14:39 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: Message-ID: Hi, Affinity settings on the Talos II with Ubuntu 18.04 kernel 5.0 works fine. I get threads pinned where they should be (hwloc confirmed) and consistent results. I also get reasonable thread placement even without pinning (i.e. the kernel scatters first until #threads <= #hwthreads). I see only a minor penalty to not pinning -- not too surprising given that I have a single NUMA node and the kernel is doing its job. Here are my quick the test results run on an 8-core Talos II Power9 + a GPU, using the adh_cubic input: $ grep Perf *.log test_1x1_rep1.log:Performance: 16.617 test_1x1_rep2.log:Performance: 16.479 test_1x1_rep3.log:Performance: 16.520 test_1x2_rep1.log:Performance: 32.034 test_1x2_rep2.log:Performance: 32.389 test_1x2_rep3.log:Performance: 32.340 test_1x4_rep1.log:Performance: 62.341 test_1x4_rep2.log:Performance: 62.569 test_1x4_rep3.log:Performance: 62.476 test_1x8_rep1.log:Performance: 97.049 test_1x8_rep2.log:Performance: 96.653 test_1x8_rep3.log:Performance: 96.889 This seems to point towards some issue with the OS or setup on the IBM machines you have -- and the unit test error may be one of the symptoms of it (as it suggests something is off with the hardware topology and a NUMA node is missing from it). I'd still suggest checking if a full not allocation with all threads, memory, etc passed to the job results in successful affinity settings i) in mdrun ii) in some other tool. Please update this thread if you have further findings. Cheers, -- Szil?rd On Fri, Apr 24, 2020 at 10:52 PM Szil?rd P?ll wrote: > > The following lines are found in md.log for the POWER9/V100 run: >> >> Overriding thread affinity set outside gmx mdrun >> Pinning threads with an auto-selected logical core stride of 128 >> NOTE: Thread affinity was not set. >> >> The full md.log is available here: >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > I glanced over that at first, will see if I can reproduce it, though I > only have access to a Raptor Talos, not an IBM machine with Ubuntu. > > What OS are you using? > > > -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > From nedomacho at gmail.com Sat Apr 25 02:19:38 2020 From: nedomacho at gmail.com (Alex) Date: Sat, 25 Apr 2020 00:19:38 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: <0cdf1551-a223-de2a-a599-75612dd9c3de@gmail.com> Message-ID: <2525d754-c1da-52e8-fba0-d0a2047f416a@gmail.com> Hi Szil?rd, My comment was as follows: 1. We have been unable to pin threads (mdrun overrides -pin on) with or without stride set to 4. 2. We basically accepted that power9/V100 performance (in ns/day) on identical systems is much worse than that we get from an Intel-based machine. Both jobs are set with -nt 32 and using four GPUs. 3. We have not tried to reach out to IBM or take any other steps. As I said, we accepted crappy performance. We would of course very much appreciate any further clarification from you -- without pointing to the specific issue (e.g., with OS), I am unable to productively bug our sysadmins (the cluster is institution-wide and there are only two people who have to deal with all the users). I myself do not have admin privileges on this machine. The only reason I commented was that Jon revitalized my old thread. ;) Alex On 4/24/2020 2:31 PM, Szil?rd P?ll wrote: > On Fri, Apr 24, 2020 at 5:55 AM Alex wrote: > >> Hi Kevin, >> >> We've been having issues with Power9/V100 very similar to what Jon >> described and basically settled on what I believe is sub-par >> performance. We tested it on systems with ~30-50K particles and threads >> simply cannot be pinned. > > What does that mean, how did you verify that? > The Linux kernel can in general set affinities on ppc64el, whether that's > requested by mdrun or some other tool, so if you have observed that the > affinity mask is not respected (or it does not change), that more likely OS > / setup issue, I'd think. > > What is different compared to x86 is that the hardware thread layout is > different on Power9 (with default Linux kernel configs) and hardware > threads are exposed as consecutive "CPUs" by the OS rather than strided by > #cores. > > I could try to sum up some details on how to sett affinities (with mdrun or > external tools), if that is of interest. However, it really should be > something that's possible to do even using the job scheduler (+ along > reasonable system configuration). > > >> As far as Gromacs is concerned, our brand-new >> Power9 nodes operate as if they were based on Intel CPUs (two threads >> per core) > > Unless the hardware thread layout has been changed, that's perhaps not the > case, see above. > > >> and zero advantage of IBM parallelization is being taken. >> > You mean the SMT4? > > >> Other users of the same nodes reported similar issues with other >> software, which to me suggests that our sysadmins don't really know how >> to set these nodes up. >> >> At this point, if someone could figure out a clear set of build >> instructions in combination with slurm/mdrun inputs, it would be very >> much appreciated. >> > Have you checked public documentation on ORNL's sites? GROMACS has been > used successfully on Summit. What about IBM support? > > -- > Szil?rd > > >> Alex >> >> On 4/23/2020 9:37 PM, Kevin Boyd wrote: >>> I'm not entirely sure how thread-pinning plays with slurm allocations on >>> partial nodes. I always reserve the entire node when I use thread >> pinning, >>> and run a bunch of simulations by pinning to different cores manually, >>> rather than relying on slurm to divvy up resources for multiple jobs. >>> >>> Looking at both logs now, a few more points >>> >>> * Your benchmarks are short enough that little things like cores spinning >>> up frequencies can matter. I suggest running longer (increase nsteps in >> the >>> mdp or at the command line), and throwing away your initial benchmark >> data >>> (see -resetstep and -resethway) to avoid artifacts >>> * Your benchmark system is quite small for such a powerful GPU. I might >>> expect better performance running multiple simulations per-GPU if the >>> workflows being run can rely on replicates, and a larger system would >>> probably scale better to the V100. >>> * The P100/intel system appears to have pinned cores properly, it's >>> unclear whether it had a real impact on these benchmarks >>> * It looks like the CPU-based computations were the primary contributors >> to >>> the observed difference in performance. That should decrease or go away >>> with increased core counts and shifting the update phase to the GPU. It >> may >>> be (I have no prior experience to indicate either way) that the intel >> cores >>> are simply better on a 1-1 basis than the Power cores. If you have 4-8 >>> cores per simulation (try -ntomp 4 and increasing the allocation of your >>> slurm job), the individual core performance shouldn't matter too >>> much, you're just certainly bottlenecked on one CPU core per GPU, which >> can >>> emphasize performance differences.. >>> >>> Kevin >>> >>> On Thu, Apr 23, 2020 at 6:43 PM Jonathan D. Halverson < >>> halverson at princeton.edu> wrote: >>> >>>> *Message sent from a system outside of UConn.* >>>> >>>> >>>> Hi Kevin, >>>> >>>> md.log for the Intel run is here: >>>> >>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.intel-broadwell-P100 >>>> Thanks for the info on constraints with 2020. I'll try some runs with >>>> different values of -pinoffset for 2019.6. >>>> >>>> I know a group at NIST is having the same or similar problems with >>>> POWER9/V100. >>>> >>>> Jon >>>> ________________________________ >>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < >>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kevin >>>> Boyd >>>> Sent: Thursday, April 23, 2020 9:08 PM >>>> To: gmx-users at gromacs.org >>>> Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node >>>> >>>> Hi, >>>> >>>> Can you post the full log for the Intel system? I typically find the >> real >>>> cycle and time accounting section a better place to start debugging >>>> performance issues. >>>> >>>> A couple quick notes, but need a side-by-side comparison for more useful >>>> analysis, and these points may apply to both systems so may not be your >>>> root cause: >>>> * At first glance, your Power system spends 1/3 of its time in >> constraint >>>> calculation, which is unusual. This can be reduced 2 ways - first, by >>>> adding more CPU cores. It doesn't make a ton of sense to benchmark on >> one >>>> core if your applications will use more. Second, if you upgrade to >> Gromacs >>>> 2020 you can probably put the constraint calculation on the GPU with >>>> -update GPU. >>>> * The Power system log has this line: >>>> >>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log#L304 >>>> indicating >>>> that threads perhaps were not actually pinned. Try adding -pinoffset 0 >> (or >>>> some other core) to specify where you want the process pinned. >>>> >>>> Kevin >>>> >>>> On Thu, Apr 23, 2020 at 9:40 AM Jonathan D. Halverson < >>>> halverson at princeton.edu> wrote: >>>> >>>>> *Message sent from a system outside of UConn.* >>>>> >>>>> >>>>> We are finding that GROMACS (2018.x, 2019.x, 2020.x) performs worse on >> an >>>>> IBM POWER9/V100 node versus an Intel Broadwell/P100. Both are running >>>> RHEL >>>>> 7.7 and Slurm 19.05.5. We have no concerns about GROMACS on our Intel >>>>> nodes. Everything below is about of the POWER9/V100 node. >>>>> >>>>> We ran the RNASE benchmark with 2019.6 with PME and cubic box using 1 >>>>> CPU-core and 1 GPU ( >>>>> ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz) and >>>>> found that the Broadwell/P100 gives 144 ns/day while POWER9/V100 gives >>>> 102 >>>>> ns/day. The difference in performance is roughly the same for the >> larger >>>>> ADH benchmark and when different numbers of CPU-cores are used. GROMACS >>>> is >>>>> always underperforming on our POWER9/V100 nodes. We have pinning turned >>>> on >>>>> (see Slurm script at bottom). >>>>> >>>>> Below is our build procedure on the POWER9/V100 node: >>>>> >>>>> version_gmx=2019.6 >>>>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version_gmx}.tar.gz >>>>> tar zxvf gromacs-${version_gmx}.tar.gz >>>>> cd gromacs-${version_gmx} >>>>> mkdir build && cd build >>>>> >>>>> module purge >>>>> module load rh/devtoolset/7 >>>>> module load cudatoolkit/10.2 >>>>> >>>>> OPTFLAGS="-Ofast -mcpu=power9 -mtune=power9 -mvsx -DNDEBUG" >>>>> >>>>> cmake3 .. -DCMAKE_BUILD_TYPE=Release \ >>>>> -DCMAKE_C_COMPILER=gcc -DCMAKE_C_FLAGS_RELEASE="$OPTFLAGS" \ >>>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CXX_FLAGS_RELEASE="$OPTFLAGS" \ >>>>> -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_MPI=OFF -DGMX_OPENMP=ON \ >>>>> -DGMX_SIMD=IBM_VSX -DGMX_DOUBLE=OFF \ >>>>> -DGMX_BUILD_OWN_FFTW=ON \ >>>>> -DGMX_GPU=ON -DGMX_CUDA_TARGET_SM=70 \ >>>>> -DGMX_OPENMP_MAX_THREADS=128 \ >>>>> -DCMAKE_INSTALL_PREFIX=$HOME/.local \ >>>>> -DGMX_COOL_QUOTES=OFF -DREGRESSIONTEST_DOWNLOAD=ON >>>>> >>>>> make -j 10 >>>>> make check >>>>> make install >>>>> >>>>> 45 of the 46 tests pass with the exception being HardwareUnitTests. >> There >>>>> are several posts about this and apparently it is not a concern. The >> full >>>>> build log is here: >>>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/build.log >>>>> >>>>> Here is more info about our POWER9/V100 node: >>>>> >>>>> $ lscpu >>>>> Architecture: ppc64le >>>>> Byte Order: Little Endian >>>>> CPU(s): 128 >>>>> On-line CPU(s) list: 0-127 >>>>> Thread(s) per core: 4 >>>>> Core(s) per socket: 16 >>>>> Socket(s): 2 >>>>> NUMA node(s): 6 >>>>> Model: 2.3 (pvr 004e 1203) >>>>> Model name: POWER9, altivec supported >>>>> CPU max MHz: 3800.0000 >>>>> CPU min MHz: 2300.0000 >>>>> >>>>> You see that we have 4 hardware threads per physical core. If we use 4 >>>>> hardware threads on the RNASE benchmark instead of 1 the performance >> goes >>>>> to 119 ns/day which is still about 20% less than the Broadwell/P100 >>>> value. >>>>> When using multiple CPU-cores on the POWER9/V100 there is significant >>>>> variation in the execution time of the code. >>>>> >>>>> There are four GPUs per POWER9/V100 node: >>>>> >>>>> $ nvidia-smi -q >>>>> Driver Version : 440.33.01 >>>>> CUDA Version : 10.2 >>>>> GPU 00000004:04:00.0 >>>>> Product Name : Tesla V100-SXM2-32GB >>>>> >>>>> The GPUs have been shown to perform as expected on other applications. >>>>> >>>>> >>>>> >>>>> >>>>> The following lines are found in md.log for the POWER9/V100 run: >>>>> >>>>> Overriding thread affinity set outside gmx mdrun >>>>> Pinning threads with an auto-selected logical core stride of 128 >>>>> NOTE: Thread affinity was not set. >>>>> >>>>> The full md.log is available here: >>>>> >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log >>>>> >>>>> >>>>> >>>>> Below are the MegaFlops Accounting for the POWER9/V100 versus >>>>> Broadwell/P100: >>>>> >>>>> ================ IBM POWER9 WITH NVIDIA V100 ================ >>>>> Computing: M-Number M-Flops % >>>> Flops >> ----------------------------------------------------------------------------- >>>>> Pair Search distance check 297.763872 2679.875 >>>> 0.0 >>>>> NxN Ewald Elec. + LJ [F] 244214.215808 16118138.243 >>>> 98.0 >>>>> NxN Ewald Elec. + LJ [V&F] 2483.565760 265741.536 >>>> 1.6 >>>>> 1,4 nonbonded interactions 53.415341 4807.381 >>>> 0.0 >>>>> Shift-X 3.029040 18.174 >>>> 0.0 >>>>> Angles 37.043704 6223.342 >>>> 0.0 >>>>> Propers 55.825582 12784.058 >>>> 0.1 >>>>> Impropers 4.220422 877.848 >>>> 0.0 >>>>> Virial 2.432585 43.787 >>>> 0.0 >>>>> Stop-CM 2.452080 24.521 >>>> 0.0 >>>>> Calc-Ekin 48.128080 1299.458 >>>> 0.0 >>>>> Lincs 20.536159 1232.170 >>>> 0.0 >>>>> Lincs-Mat 444.613344 1778.453 >>>> 0.0 >>>>> Constraint-V 261.192228 2089.538 >>>> 0.0 >>>>> Constraint-Vir 2.430161 58.324 >>>> 0.0 >>>>> Settle 73.382008 23702.389 >>>> 0.1 >> ----------------------------------------------------------------------------- >>>>> Total 16441499.096 >>>> 100.0 >> ----------------------------------------------------------------------------- >>>>> ================ INTEL BROADWELL WITH NVIDIA P100 ================ >>>>> Computing: M-Number M-Flops % >>>> Flops >> ----------------------------------------------------------------------------- >>>>> Pair Search distance check 271.334272 2442.008 >>>> 0.0 >>>>> NxN Ewald Elec. + LJ [F] 191599.850112 12645590.107 >>>> 98.0 >>>>> NxN Ewald Elec. + LJ [V&F] 1946.866432 208314.708 >>>> 1.6 >>>>> 1,4 nonbonded interactions 53.415341 4807.381 >>>> 0.0 >>>>> Shift-X 3.029040 18.174 >>>> 0.0 >>>>> Bonds 10.541054 621.922 >>>> 0.0 >>>>> Angles 37.043704 6223.342 >>>> 0.0 >>>>> Propers 55.825582 12784.058 >>>> 0.1 >>>>> Impropers 4.220422 877.848 >>>> 0.0 >>>>> Virial 2.432585 43.787 >>>> 0.0 >>>>> Stop-CM 2.452080 24.521 >>>> 0.0 >>>>> Calc-Ekin 48.128080 1299.458 >>>> 0.0 >>>>> Lincs 9.992997 599.580 >>>> 0.0 >>>>> Lincs-Mat 50.775228 203.101 >>>> 0.0 >>>>> Constraint-V 240.108012 1920.864 >>>> 0.0 >>>>> Constraint-Vir 2.323707 55.769 >>>> 0.0 >>>>> Settle 73.382008 23702.389 >>>> 0.2 >> ----------------------------------------------------------------------------- >>>>> Total 12909529.017 >>>> 100.0 >> ----------------------------------------------------------------------------- >>>>> Some of the rows are identical between the two tables above. The >> largest >>>>> difference >>>>> is observed for the "NxN Ewald Elec. + LJ [F]" row. >>>>> >>>>> >>>>> >>>>> Here is our Slurm script: >>>>> >>>>> #!/bin/bash >>>>> #SBATCH --job-name=gmx # create a short name for your job >>>>> #SBATCH --nodes=1 # node count >>>>> #SBATCH --ntasks=1 # total number of tasks across all >> nodes >>>>> #SBATCH --cpus-per-task=1 # cpu-cores per task (>1 if >>>>> multi-threaded tasks) >>>>> #SBATCH --mem=4G # memory per node (4G per cpu-core is >>>>> default) >>>>> #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) >>>>> #SBATCH --gres=gpu:1 # number of gpus per node >>>>> >>>>> module purge >>>>> module load cudatoolkit/10.2 >>>>> >>>>> BCH=../rnase_cubic >>>>> gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o >>>>> bench.tpr >>>>> gmx mdrun -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s >>>>> bench.tpr >>>>> >>>>> >>>>> >>>>> How do we get optimal performance out of GROMACS on our POWER9/V100 >>>> nodes? >>>>> Jon >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-request at gromacs.org. >>>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From tingguang.sun at gxust.edu.cn Sat Apr 25 18:19:02 2020 From: tingguang.sun at gxust.edu.cn (Tingguang.S) Date: Sat, 25 Apr 2020 16:19:02 -0000 Subject: [gmx-users] =?utf-8?q?Why_there_is_no_phosphorous_atom_in_the_=22?= =?utf-8?q?DA5=22_residue_in_dna=2Ertp?= Message-ID: Dear all, When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp. Can some one help me with this ? From jalemkul at vt.edu Sat Apr 25 18:20:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 25 Apr 2020 16:20:57 -0000 Subject: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp In-Reply-To: References: Message-ID: <3e1e17b5-4cf8-e1fa-7e94-c7e3bbfdc378@vt.edu> On 4/25/20 12:18 PM, Tingguang.S wrote: > Dear all, > > > When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp. > Can some one help me with this ? DNA is not typically phosphorylated on its 5'-hydroxyl. Synthetic nucleotides sometimes are, but the force field is designed for typical biologically relevant structures. If the 5'-phosphate is relevant (which it can be), you need to build your own .rtp entry or terminal database entry. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From tingguang.sun at gxust.edu.cn Sat Apr 25 18:48:13 2020 From: tingguang.sun at gxust.edu.cn (Tingguang.S) Date: Sat, 25 Apr 2020 16:48:13 -0000 Subject: [gmx-users] =?utf-8?q?Why_there_is_no_phosphorous_atom_in_the_=22?= =?utf-8?q?DA5=22_residue_in_dna=2Ertp?= In-Reply-To: <3e1e17b5-4cf8-e1fa-7e94-c7e3bbfdc378@vt.edu> Message-ID: Thank you Justin! I delete the phosphate group and the problem is resolved ! Best regards Sting From: Justin Lemkul Date: 2020-04-26 00:20:44 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp> > >On 4/25/20 12:18 PM, Tingguang.S wrote: >> Dear all, >> >> >> When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp. >> Can some one help me with this ? > >DNA is not typically phosphorylated on its 5'-hydroxyl. Synthetic >nucleotides sometimes are, but the force field is designed for typical >biologically relevant structures. If the 5'-phosphate is relevant (which >it can be), you need to build your own .rtp entry or terminal database >entry. > >-Justin > >-- >================================================== > >Justin A. Lemkul, Ph.D. >Assistant Professor >Office: 301 Fralin Hall >Lab: 303 Engel Hall > >Virginia Tech Department of Biochemistry >340 West Campus Dr. >Blacksburg, VA 24061 > >jalemkul at vt.edu | (540) 231-3129 >http://www.thelemkullab.com > >================================================== > >-- >Gromacs Users mailing list > >* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From afsane_farhadi at yahoo.com Sat Apr 25 19:48:30 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Sat, 25 Apr 2020 17:48:30 -0000 Subject: [gmx-users] lincs warning References: <944887700.136779.1587834974435.ref@mail.yahoo.com> Message-ID: <944887700.136779.1587834974435@mail.yahoo.com> Hi gromacs users?I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas ?is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right?Can any body help me please? Sent from Yahoo Mail on Android From netalyk at gmail.com Sun Apr 26 09:38:27 2020 From: netalyk at gmail.com (Netaly Khazanov) Date: Sun, 26 Apr 2020 07:38:27 -0000 Subject: [gmx-users] gromacs installation (2020&2019) Message-ID: Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=gromacs2020 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ I've used gcc 5 version (tried also 6 version) However, I am struggling through make execution : in gromacs 2019 - [ 37%] Built target libgromacs_generated [ 37%] Built target libgromacs_external Scanning dependencies of target gpu_utilstest_cuda [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so [ 37%] Built target gpu_utilstest_cuda in gromacs 2020- [ 27%] Built target linearalgebra [ 27%] Built target scanner [ 27%] Built target tng_io_obj [ 27%] Built target modularsimulator It just stuck on the line and doesn't continue to run. Any suggestions will be appreciated. Thanks in advance. -- Netaly From paolo.costa85 at gmail.com Sun Apr 26 11:15:27 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 26 Apr 2020 09:15:27 -0000 Subject: [gmx-users] Fatal error pdb2gmx Message-ID: Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got the following fatal error: "*Atom O10 in residue POM 0 was not found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea what the warning means, however I do not understand the fatal error since I am sure that the Atom O1 is present in the residue I created. In attachment you can find the .pdb and the .rtp files I created. Please, can somebody figure out what cause such errors? Thanks a lot. Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Sun Apr 26 13:32:48 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 26 Apr 2020 11:32:48 -0000 Subject: [gmx-users] Fatal error pdb2gmx In-Reply-To: References: Message-ID: On 4/26/20 5:15 AM, Paolo Costa wrote: > Dear Gromax users, > > I created a new residue of 118 atoms within Amber99 force field. However > when I run the "pdb2gmx" I got many times the following warning: "*WARNING: > Duplicate line found in or between hackblock and rtp entries" *and in the > end I got the following fatal error: "*Atom O10 in residue POM 0 was not > found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea > what the warning means, however I do not understand the fatal error since I > am sure that the Atom O1 is present in the residue I created. In attachment > you can find the .pdb and the .rtp files I created. The mailing list does not accept attachments. If you want to share files, upload them to a file-sharing service and provide a link. Note that the error mentions O10, not O1. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From ydu-sci at outlook.com Sun Apr 26 17:06:54 2020 From: ydu-sci at outlook.com (Yu Du) Date: Sun, 26 Apr 2020 15:06:54 -0000 Subject: [gmx-users] gromacs installation (2020&2019) In-Reply-To: References: Message-ID: Hi Netaly, Although I do not know the exact reason of the failure, after skimming through your command, I think that you probably need to assign absolute path to CMAKE_INSTALL_PREFIX and have access to the internet for downloading REGRESSIONTEST and FFTW package. If you are new to GROMACS, I recommend installation from simple case, such as only CPU no GPU. Only after successfully installing CPU only version GROMACS, run to the next level CPU+GPU. This step-by-step installation practice can give you a feeling of choosing CMake options. Cheers, Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Netaly Khazanov Sent: Sunday, April 26, 2020 15:38 To: Discussion list for GROMACS users Subject: [gmx-users] gromacs installation (2020&2019) Dear All, I am trying to install gromacs 2020 and 2019 versions on CentOS release 6.10 (Final) linux system. I passed throuht cmake compilation. Using command cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=gromacs2020 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ I've used gcc 5 version (tried also 6 version) However, I am struggling through make execution : in gromacs 2019 - [ 37%] Built target libgromacs_generated [ 37%] Built target libgromacs_external Scanning dependencies of target gpu_utilstest_cuda [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so [ 37%] Built target gpu_utilstest_cuda in gromacs 2020- [ 27%] Built target linearalgebra [ 27%] Built target scanner [ 27%] Built target tng_io_obj [ 27%] Built target modularsimulator It just stuck on the line and doesn't continue to run. Any suggestions will be appreciated. Thanks in advance. -- Netaly -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From ydu-sci at outlook.com Sun Apr 26 17:17:06 2020 From: ydu-sci at outlook.com (Yu Du) Date: Sun, 26 Apr 2020 15:17:06 -0000 Subject: [gmx-users] lincs warning In-Reply-To: <944887700.136779.1587834974435@mail.yahoo.com> References: <944887700.136779.1587834974435.ref@mail.yahoo.com>, <944887700.136779.1587834974435@mail.yahoo.com> Message-ID: Hi Afsane, You need to provide more details of the simulation, such as how you generated the configuration and topology, what force field you used and so on, or we can not give you any advice. Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Afsane Farhadi Sent: Sunday, April 26, 2020 01:16 To: Discussion List for GROMACS Users Subject: [gmx-users] lincs warning Hi gromacs users I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right Can any body help me please? Sent from Yahoo Mail on Android -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From lamonteserincastanedo at gmail.com Sun Apr 26 17:18:41 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 26 Apr 2020 15:18:41 -0000 Subject: [gmx-users] gromacs installation (2020&2019) In-Reply-To: References: Message-ID: Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same time? If not a couple of things to keep in mind. Be sure before installing Gromacs you have all the utilities that Gromacs use, compilers, etc and that their versions are supported. I saw you are trying to install it for GPU, for that you need to install first the cuda toolkit versi?n for your linux. Now if you are installing Gromacs in an Ubuntu virtual machine on windows this is going to be a big problem. So for this case my recommendation is install it without GPU. Follow the instructions for installation in the website. Should work perfectly. Kindly, Lazaro On Sun, Apr 26, 2020 at 12:07 PM Yu Du wrote: > Hi Netaly, > > Although I do not know the exact reason of the failure, after skimming > through your command, I think that you probably need to assign absolute > path to CMAKE_INSTALL_PREFIX and have access to the internet for > downloading REGRESSIONTEST and FFTW package. > > If you are new to GROMACS, I recommend installation from simple case, such > as only CPU no GPU. Only after successfully installing CPU only version > GROMACS, run to the next level CPU+GPU. This step-by-step installation > practice can give you a feeling of choosing CMake options. > > Cheers, > > Du, Yu > PhD Student, > Shanghai Institute of Organic Chemistry > 345 Ling Ling Rd., Shanghai, China. > Zip: 200032, Tel: (86) 021 5492 5275 > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Netaly > Khazanov > Sent: Sunday, April 26, 2020 15:38 > To: Discussion list for GROMACS users > Subject: [gmx-users] gromacs installation (2020&2019) > > Dear All, > I am trying to install gromacs 2020 and 2019 versions on CentOS release > 6.10 (Final) linux system. > I passed throuht cmake compilation. Using command > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on > -DCMAKE_INSTALL_PREFIX=gromacs2020 > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3 > -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc > -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ > -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ > I've used gcc 5 version (tried also 6 version) > > However, I am struggling through make execution : > in gromacs 2019 - > > [ 37%] Built target libgromacs_generated > [ 37%] Built target libgromacs_external > Scanning dependencies of target gpu_utilstest_cuda > [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so > [ 37%] Built target gpu_utilstest_cuda > > in gromacs 2020- > [ 27%] Built target linearalgebra > [ 27%] Built target scanner > [ 27%] Built target tng_io_obj > [ 27%] Built target modularsimulator > > It just stuck on the line and doesn't continue to run. > > Any suggestions will be appreciated. > Thanks in advance. > > > -- > Netaly > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From paolo.costa85 at gmail.com Sun Apr 26 19:57:46 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 26 Apr 2020 17:57:46 -0000 Subject: [gmx-users] Error No default Proper Dih. types Message-ID: Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known works, while the parameters for the bonding interactions I determined by Gaussian together with VFFDT software. I did not insert any parameters for the dihedral angles since the VFFTDT software does not calculated them. However as written in the related paper (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation related to metals can often be ignored".* Does somebody knows how to overcome such error in Gromacs? Thanks a lot. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Sun Apr 26 20:02:58 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 26 Apr 2020 18:02:58 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: References: Message-ID: On 4/26/20 1:57 PM, Paolo Costa wrote: > Dear Gromacs users, > > within Amber99 force field I created a new molecule, polyoxometallate, by > creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > from known works, while the parameters for the bonding interactions I > determined by Gaussian together with VFFDT software. > I did not insert any parameters for the dihedral angles since the VFFTDT > software does not calculated them. However as written in the related paper > (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation related > to metals can often be ignored".* > Does somebody knows how to overcome such error in Gromacs? pdb2gmx generates all possible angles and dihedrals, as determined by the bonds that are defined in the .rtp entry. Thus, you likely have dihedrals in the topology in which one of the participating atoms is the metal. You have to have parameters for all defined interactions, but it is true that dihedral terms are not typically used in this case. The simplest solution is to define dihedrals with zero force constants so they do not contribute to the forces in the system. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Sun Apr 26 20:08:26 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 26 Apr 2020 18:08:26 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: References: Message-ID: Dear Justin, thanks a lot for your quick reply and useful information. Thus, I will go through to all the dihedral terms and define zero the corresponding force constant as you suggested. In any case, I guess it will be too much work to calculate also the force constant for the torsion angle rotation. Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul ha scritto: > > > On 4/26/20 1:57 PM, Paolo Costa wrote: > > Dear Gromacs users, > > > > within Amber99 force field I created a new molecule, polyoxometallate, by > > creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp > > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > > from known works, while the parameters for the bonding interactions I > > determined by Gaussian together with VFFDT software. > > I did not insert any parameters for the dihedral angles since the VFFTDT > > software does not calculated them. However as written in the related > paper > > (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation > related > > to metals can often be ignored".* > > Does somebody knows how to overcome such error in Gromacs? > > pdb2gmx generates all possible angles and dihedrals, as determined by > the bonds that are defined in the .rtp entry. Thus, you likely have > dihedrals in the topology in which one of the participating atoms is the > metal. You have to have parameters for all defined interactions, but it > is true that dihedral terms are not typically used in this case. The > simplest solution is to define dihedrals with zero force constants so > they do not contribute to the forces in the system. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From alexanderwien2k at gmail.com Sun Apr 26 20:18:52 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 26 Apr 2020 18:18:52 -0000 Subject: [gmx-users] wham - Bootstraping Message-ID: Dear all, Each windows of a wham analysis is a 30 ns long simulation. And I choose 25 ns of them in gmx wham -b 5000 -nBootstrap 250 -bins 250 -bs-method b-hist ... . I noticed the below massages in the log file that only 395 , 1854, and around 2000 are being evaluated out of 24250 contributions. Updated rapid wham stuff. (evaluating only 395 of 24250 contributions) Updated rapid wham stuff. (evaluating only 1854 of 24250 contributions) Would you please let me know how 395, 1854 ... are being considered for evaluation? and what do they mean? Regards, Alex From jalemkul at vt.edu Sun Apr 26 20:32:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 26 Apr 2020 18:32:57 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: References: Message-ID: <16bb1386-fee1-b5c5-c8d6-eb53e1edb28b@vt.edu> On 4/26/20 2:08 PM, Paolo Costa wrote: > Dear Justin, > > thanks a lot for your quick reply and useful information. > Thus, I will go through to all the dihedral terms and define zero the > corresponding force constant as you suggested. In any case, I guess it will > be too much work to calculate also the force constant for the torsion angle > rotation. Metals are usually the bridge point between multiple groups and as such their dihedrals are all coupled and not generally considered "soft" (rotatable). So the conformational energetics of these molecules usually involves only bonds and angles in terms of internal parameters. -Justin > Thanks again. > > Paolo > > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul ha > scritto: > >> >> On 4/26/20 1:57 PM, Paolo Costa wrote: >>> Dear Gromacs users, >>> >>> within Amber99 force field I created a new molecule, polyoxometallate, by >>> creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp >>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters >>> from known works, while the parameters for the bonding interactions I >>> determined by Gaussian together with VFFDT software. >>> I did not insert any parameters for the dihedral angles since the VFFTDT >>> software does not calculated them. However as written in the related >> paper >>> (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation >> related >>> to metals can often be ignored".* >>> Does somebody knows how to overcome such error in Gromacs? >> pdb2gmx generates all possible angles and dihedrals, as determined by >> the bonds that are defined in the .rtp entry. Thus, you likely have >> dihedrals in the topology in which one of the participating atoms is the >> metal. You have to have parameters for all defined interactions, but it >> is true that dihedral terms are not typically used in this case. The >> simplest solution is to define dihedrals with zero force constants so >> they do not contribute to the forces in the system. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paolo.costa85 at gmail.com Sun Apr 26 21:55:15 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 26 Apr 2020 19:55:15 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: <16bb1386-fee1-b5c5-c8d6-eb53e1edb28b@vt.edu> References: <16bb1386-fee1-b5c5-c8d6-eb53e1edb28b@vt.edu> Message-ID: Dear Justin, thanks for your extra description. Very nice! Last doubt, which values of "phase" and "pn" should I use for [ dihedraltypes ]? Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul ha scritto: > > > On 4/26/20 2:08 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your quick reply and useful information. > > Thus, I will go through to all the dihedral terms and define zero the > > corresponding force constant as you suggested. In any case, I guess it > will > > be too much work to calculate also the force constant for the torsion > angle > > rotation. > > Metals are usually the bridge point between multiple groups and as such > their dihedrals are all coupled and not generally considered "soft" > (rotatable). So the conformational energetics of these molecules usually > involves only bonds and angles in terms of internal parameters. > > -Justin > > > Thanks again. > > > > Paolo > > > > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/26/20 1:57 PM, Paolo Costa wrote: > >>> Dear Gromacs users, > >>> > >>> within Amber99 force field I created a new molecule, polyoxometallate, > by > >>> creating a new .rtp file and modifying the atomtypes.atp, > ffnonbonded.itp > >>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > >>> from known works, while the parameters for the bonding interactions I > >>> determined by Gaussian together with VFFDT software. > >>> I did not insert any parameters for the dihedral angles since the > VFFTDT > >>> software does not calculated them. However as written in the related > >> paper > >>> (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation > >> related > >>> to metals can often be ignored".* > >>> Does somebody knows how to overcome such error in Gromacs? > >> pdb2gmx generates all possible angles and dihedrals, as determined by > >> the bonds that are defined in the .rtp entry. Thus, you likely have > >> dihedrals in the topology in which one of the participating atoms is the > >> metal. You have to have parameters for all defined interactions, but it > >> is true that dihedral terms are not typically used in this case. The > >> simplest solution is to define dihedrals with zero force constants so > >> they do not contribute to the forces in the system. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From jalemkul at vt.edu Sun Apr 26 22:32:45 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 26 Apr 2020 20:32:45 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: References: <16bb1386-fee1-b5c5-c8d6-eb53e1edb28b@vt.edu> Message-ID: On 4/26/20 3:53 PM, Paolo Costa wrote: > Dear Justin, > > thanks for your extra description. Very nice! > Last doubt, which values of "phase" and "pn" should I use for [ > dihedraltypes ]? If the force constant is zero, the remaining parameters are irrelevant. -Justin > Thanks again. > > Paolo > > Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul ha > scritto: > >> >> On 4/26/20 2:08 PM, Paolo Costa wrote: >>> Dear Justin, >>> >>> thanks a lot for your quick reply and useful information. >>> Thus, I will go through to all the dihedral terms and define zero the >>> corresponding force constant as you suggested. In any case, I guess it >> will >>> be too much work to calculate also the force constant for the torsion >> angle >>> rotation. >> Metals are usually the bridge point between multiple groups and as such >> their dihedrals are all coupled and not generally considered "soft" >> (rotatable). So the conformational energetics of these molecules usually >> involves only bonds and angles in terms of internal parameters. >> >> -Justin >> >>> Thanks again. >>> >>> Paolo >>> >>> Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul >> ha >>> scritto: >>> >>>> On 4/26/20 1:57 PM, Paolo Costa wrote: >>>>> Dear Gromacs users, >>>>> >>>>> within Amber99 force field I created a new molecule, polyoxometallate, >> by >>>>> creating a new .rtp file and modifying the atomtypes.atp, >> ffnonbonded.itp >>>>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters >>>>> from known works, while the parameters for the bonding interactions I >>>>> determined by Gaussian together with VFFDT software. >>>>> I did not insert any parameters for the dihedral angles since the >> VFFTDT >>>>> software does not calculated them. However as written in the related >>>> paper >>>>> (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation >>>> related >>>>> to metals can often be ignored".* >>>>> Does somebody knows how to overcome such error in Gromacs? >>>> pdb2gmx generates all possible angles and dihedrals, as determined by >>>> the bonds that are defined in the .rtp entry. Thus, you likely have >>>> dihedrals in the topology in which one of the participating atoms is the >>>> metal. You have to have parameters for all defined interactions, but it >>>> is true that dihedral terms are not typically used in this case. The >>>> simplest solution is to define dihedrals with zero force constants so >>>> they do not contribute to the forces in the system. >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Assistant Professor >>>> Office: 301 Fralin Hall >>>> Lab: 303 Engel Hall >>>> >>>> Virginia Tech Department of Biochemistry >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> >>>> jalemkul at vt.edu | (540) 231-3129 >>>> http://www.thelemkullab.com >>>> >>>> ================================================== >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From dburns at iastate.edu Sun Apr 26 22:45:22 2020 From: dburns at iastate.edu (Daniel Burns) Date: Sun, 26 Apr 2020 20:45:22 -0000 Subject: [gmx-users] Atom CA used in that entry is not found in the input file Message-ID: Hello, I edited a few selenomethionine residues, changing "S" to "SD" and removed the "SE" at the end of the line. I then ran pdb2gmx with Charmm36. I get the following error (not sure why the residue number doesn't match): Fatal error: Residue 324 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. My .pdb file section looks like this: ATOM 569 N MET A 324 87.364 46.446 53.851 1.00 3.42 N ATOM 570 CA MET A 324 86.617 45.972 52.679 1.00 6.50 C ATOM 571 C MET A 324 87.405 46.212 51.424 1.00 6.43 C ATOM 572 O MET A 324 86.987 45.830 50.332 1.00 8.80 O ATOM 573 CB MET A 324 85.203 46.573 52.584 1.00 5.66 C ATOM 574 CG MET A 324 84.258 46.053 53.663 1.00 5.50 C ATOM 575 CE MET A 324 83.200 44.225 51.772 1.00 3.19 C ATOM 576 SD MET A 324 83.876 44.132 53.563 1.00 14.27 S ATOM 577 N GLY A 325 88.553 46.854 51.604 1.00 9.51 N ATOM 578 CA GLY A 325 89.548 47.012 50.546 1.00 9.78 C ATOM 579 C GLY A 325 89.087 47.608 49.227 1.00 9.91 C ATOM 580 O GLY A 325 89.352 47.048 48.159 1.00 11.43 O ATOM 581 N GLY A 326 88.403 48.742 49.271 1.00 7.35 N ATOM 582 CA GLY A 326 87.942 49.290 48.005 1.00 6.34 C ATOM 583 C GLY A 326 86.542 48.875 47.602 1.00 3.91 C ATOM 584 O GLY A 326 85.947 49.547 46.765 1.00 4.00 O I don't see anything wrong with my GLY residues and none of the other Glycines are presenting an error. This does follow one of my edited MET residues. Thank you, Dan From lamonteserincastanedo at gmail.com Sun Apr 26 23:33:55 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Sun, 26 Apr 2020 21:33:55 -0000 Subject: [gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis Message-ID: Dear Gromacs users, I am trying to run a dPCA to select the best conformation from my trajectory. When I follow the steps in gromacs manual I have a question about one of the steps: 3. Make an index file , named as covar.ndx, which necessarily contains one group of atom 1 to integer(2*N/3), where N is the number of dihedral angles. For example, for a peptide of 5 dihedral angles How can I create the covar.ndx? How could I use gmx make_ndx for this? In my case I have 99 atoms and 66 cos/sin integrals. So I guess the covar.ndx should has one group with atoms numbers from 1 2 3 4 5... to 66? Should I have to do this in a text editor by hand? Kindly, Lazaro From paolo.costa85 at gmail.com Sun Apr 26 23:37:19 2020 From: paolo.costa85 at gmail.com (Paolo Costa) Date: Sun, 26 Apr 2020 21:37:19 -0000 Subject: [gmx-users] Error No default Proper Dih. types In-Reply-To: References: <16bb1386-fee1-b5c5-c8d6-eb53e1edb28b@vt.edu> Message-ID: Dear Justin, thanks a lot. Paolo Il giorno dom 26 apr 2020 alle ore 22:33 Justin Lemkul ha scritto: > > > On 4/26/20 3:53 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks for your extra description. Very nice! > > Last doubt, which values of "phase" and "pn" should I use for [ > > dihedraltypes ]? > > If the force constant is zero, the remaining parameters are irrelevant. > > -Justin > > > Thanks again. > > > > Paolo > > > > Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/26/20 2:08 PM, Paolo Costa wrote: > >>> Dear Justin, > >>> > >>> thanks a lot for your quick reply and useful information. > >>> Thus, I will go through to all the dihedral terms and define zero the > >>> corresponding force constant as you suggested. In any case, I guess it > >> will > >>> be too much work to calculate also the force constant for the torsion > >> angle > >>> rotation. > >> Metals are usually the bridge point between multiple groups and as such > >> their dihedrals are all coupled and not generally considered "soft" > >> (rotatable). So the conformational energetics of these molecules usually > >> involves only bonds and angles in terms of internal parameters. > >> > >> -Justin > >> > >>> Thanks again. > >>> > >>> Paolo > >>> > >>> Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul < > jalemkul at vt.edu> > >> ha > >>> scritto: > >>> > >>>> On 4/26/20 1:57 PM, Paolo Costa wrote: > >>>>> Dear Gromacs users, > >>>>> > >>>>> within Amber99 force field I created a new molecule, > polyoxometallate, > >> by > >>>>> creating a new .rtp file and modifying the atomtypes.atp, > >> ffnonbonded.itp > >>>>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ > parameters > >>>>> from known works, while the parameters for the bonding interactions I > >>>>> determined by Gaussian together with VFFDT software. > >>>>> I did not insert any parameters for the dihedral angles since the > >> VFFTDT > >>>>> software does not calculated them. However as written in the related > >>>> paper > >>>>> (J. Chem. Inf. Model. 2016, 56, 811?818), *"Torsion angle rotation > >>>> related > >>>>> to metals can often be ignored".* > >>>>> Does somebody knows how to overcome such error in Gromacs? > >>>> pdb2gmx generates all possible angles and dihedrals, as determined by > >>>> the bonds that are defined in the .rtp entry. Thus, you likely have > >>>> dihedrals in the topology in which one of the participating atoms is > the > >>>> metal. You have to have parameters for all defined interactions, but > it > >>>> is true that dihedral terms are not typically used in this case. The > >>>> simplest solution is to define dihedrals with zero force constants so > >>>> they do not contribute to the forces in the system. > >>>> > >>>> -Justin > >>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalemkul at vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) From n.gandhiau at gmail.com Mon Apr 27 09:38:58 2020 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Mon, 27 Apr 2020 07:38:58 -0000 Subject: [gmx-users] multiple nodes Message-ID: Dear List, Below is the job script for running gromacs on our HPC (single node) #!/bin/bash -l #PBS -N gro1 #PBS -l walltime=300:00:00 #PBS -l select=3:ncpus=12:mpiprocs=12:mem=32gb #PBS -j oe cd $PBS_O_WORKDIR module purge module load gromacs/2019.3-foss-2019a export OMP_NUM_THREADS=12 gmx_mpi mdrun -v -deffnm step4.1_equilibration Could you help with the job script for multiple nodes? Do I need mpirun -np 24 gmx_mpi... in the syntax? Thanks for your help in advance. Regards, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate From netalyk at gmail.com Mon Apr 27 11:24:15 2020 From: netalyk at gmail.com (Netaly Khazanov) Date: Mon, 27 Apr 2020 09:24:15 -0000 Subject: [gmx-users] gromacs installation (2020&2019) In-Reply-To: References: Message-ID: Thank you for trying to help me. I will take into account all your comments. On Sun, Apr 26, 2020 at 6:18 PM lazaro monteserin < lamonteserincastanedo at gmail.com> wrote: > Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same > time? If not a couple of things to keep in mind. Be sure before installing > Gromacs you have all the utilities that Gromacs use, compilers, etc and > that their versions are supported. I saw you are trying to install it for > GPU, for that you need to install first the cuda toolkit versi?n for your > linux. Now if you are installing Gromacs in an Ubuntu virtual machine on > windows this is going to be a big problem. So for this case my > recommendation is install it without GPU. Follow the instructions for > installation in the website. Should work perfectly. Kindly, Lazaro > > On Sun, Apr 26, 2020 at 12:07 PM Yu Du wrote: > > > Hi Netaly, > > > > Although I do not know the exact reason of the failure, after skimming > > through your command, I think that you probably need to assign absolute > > path to CMAKE_INSTALL_PREFIX and have access to the internet for > > downloading REGRESSIONTEST and FFTW package. > > > > If you are new to GROMACS, I recommend installation from simple case, > such > > as only CPU no GPU. Only after successfully installing CPU only version > > GROMACS, run to the next level CPU+GPU. This step-by-step installation > > practice can give you a feeling of choosing CMake options. > > > > Cheers, > > > > Du, Yu > > PhD Student, > > Shanghai Institute of Organic Chemistry > > 345 Ling Ling Rd., Shanghai, China. > > Zip: 200032, Tel: (86) 021 5492 5275 > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Netaly > > Khazanov > > Sent: Sunday, April 26, 2020 15:38 > > To: Discussion list for GROMACS users > > Subject: [gmx-users] gromacs installation (2020&2019) > > > > Dear All, > > I am trying to install gromacs 2020 and 2019 versions on CentOS release > > 6.10 (Final) linux system. > > I passed throuht cmake compilation. Using command > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > -DGMX_GPU=on > > -DCMAKE_INSTALL_PREFIX=gromacs2020 > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3 > > -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc > > -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ > > -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++ > > I've used gcc 5 version (tried also 6 version) > > > > However, I am struggling through make execution : > > in gromacs 2019 - > > > > [ 37%] Built target libgromacs_generated > > [ 37%] Built target libgromacs_external > > Scanning dependencies of target gpu_utilstest_cuda > > [ 37%] Linking CXX shared library > ../../../../lib/libgpu_utilstest_cuda.so > > [ 37%] Built target gpu_utilstest_cuda > > > > in gromacs 2020- > > [ 27%] Built target linearalgebra > > [ 27%] Built target scanner > > [ 27%] Built target tng_io_obj > > [ 27%] Built target modularsimulator > > > > It just stuck on the line and doesn't continue to run. > > > > Any suggestions will be appreciated. > > Thanks in advance. > > > > > > -- > > Netaly > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. -- Netaly From magnus.lundborg at scilifelab.se Mon Apr 27 13:22:25 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 27 Apr 2020 11:22:25 -0000 Subject: [gmx-users] Artifact in pull-pbc-ref-prev-step-com In-Reply-To: References: <1202674d-07dc-dea0-5e76-16baf6efe06f@scilifelab.se> Message-ID: Hi, On 2020-04-24 20:32, Alex wrote: > Hi Magnus, > I see, many thanks for the insights. > > > On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < > magnus.lundborg at scilifelab.se> wrote: > >> Hi Alex, >> >> pull-group1-pbcatom lets you specify the exact atom used as the PBC >> reference. Both 0 and -1 are special cases. For small molecules 0 is >> (almost?) always OK. Find one in the center of you membrane (in the pull >> direction). I'll actually have to check if -1 is even compatible with >> pull-pbc-ref-prev-step-com. It's possible that that combination should >> not be allowed even. >> > So, the pull-group1-pbcatm could be any other number as atom number rather > than 0 and -1. Yes, pick an atom located centrally in the structure. > >> As you say, you can define a subgroup within the larger membrane group, >> but that is mainly of use if you know that some atoms consistently in >> the center of the whole group and others are more flexible. >> > In this case where the subgroup defined in index.ndx file has more than one > atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to > the pull-group1-pbcatom? > If I am not mistaken, here, the entry number in index.ndx file belong to > the subgroup should be assigned to the pull-group1-pbcatom. > > [ system ] > [ Other ] > .... > [ non-water ] > [ subgroup ] > > Would you please confirm if I am correct? Yes, pick one atom from that subgroup, the atom should be centrally placed (at least not so far away that the COM of the pull group could be wrongly calculated). In almost all cases any atom should work (and in those cases using '0' should work as well, but makes it less transparent regarding what atom is used). With "pull-pbc-ref-prev-step-com" the specified atom is only used to set the PBC initially. After that the COM of the previous step is used, making it less sensitive if the chosen atom is very mobile. Cheers, Magnus > > Thank you > Alex > > >> Regards, >> >> Magnus >> >> On 2020-04-21 16:24, Alex wrote: >>> Hi Magnus, >>> Actually I am confused with the available options for the >>> "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom". >>> For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when >>> one of the group is large, even the 2020.1 version of grmacs would give a >>> warning if one used No in a case of presence of a large group. >>> Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0 >>> the middle atom (number wise) of the large group is used automatically >>> which is safe only for small groups as manual states. So, only >>> remaining option is -1. >>> So, what I understood for a layered-large group similar to what I have >> one >>> should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1 >>> which would cause moving the system along -Z during the pulling. >>> >>> Using gmx select, can I manually define a sub-group around the COM of the >>> large group, and consider it as one of the pulling groups instead of the >>> large group? >>> >>> Thank you >>> Alex >>> >>> On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < >>> magnus.lundborg at scilifelab.se> wrote: >>> >>>> Hi Alex, >>>> >>>> I don't see why it would need pull-group1-pbcatom = -1. Why not pick a >>>> central atom? >>>> >>>> Regards, >>>> >>>> Magnus >>>> >>>> On 2020-04-20 13:40, Alex wrote: >>>>> Hi Magnus, >>>>> Thanks. >>>>> The problem raises only because of using the pull-pbc-ref-prev-step-com >>>>> which needs the pull-group1-pbcatom to be -1 to be meaningful. >>>>> For an identical system and mdp parameters using 2018 version of >> gromacs >>>>> which is independent to the pull-pbc-ref-prev-step-com, I see no issue. >>>>> >>>>> Regards, >>>>> Alex >>>>> >>>>> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < >>>>> magnus.lundborg at scilifelab.se> wrote: >>>>> >>>>>> Sorry, about the statement about pbcatom -1. I was thinking about 0. I >>>>>> don't know if pbcatom -1 is good or not in this case. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Magnus >>>>>> >>>>>> On 2020-04-20 09:24, Magnus Lundborg wrote: >>>>>>> Hi Alex, >>>>>>> >>>>>>> I don't think this is related to using pull-pbc-ref-prev-step-com. >>>>>>> Have you tried without it? However, it is risky using pbcatom -1, >>>>>>> since you don't know what atom you are using as the initial >> reference. >>>>>>> I would suggest picking an atom you know is located at the centre of >>>>>>> the structure. >>>>>>> >>>>>>> I would think that the problem has to do with the comm removal. What >>>>>>> are your parameters for comm-mode, nstcomm and comm-grps? It is >>>>>>> possible that you need to lower your nstcomm. It is also possible, >> but >>>>>>> not certain, the comm-mode Linear-acceleration-correction might help >>>>>>> you. For some reason, it seems like I have sometimes avoided similar >>>>>>> problems by using the sd integrator instead, but I haven't evaluated >>>>>>> that properly - it might just have been coincidences. If you see a >>>>>>> clear difference using the sd integrator it might be good if you'd >>>>>>> file an issue about it on gitlab so that someone can look into if >>>>>>> there is something wrong. >>>>>>> >>>>>>> Regards, >>>>>>> Magnus >>>>>>> >>>>>>> On 2020-04-18 20:12, Alex wrote: >>>>>>>> Dear all, >>>>>>>> To generate the initial configurations for umbrella sampling, I >>>>>>>> conducted a >>>>>>>> simple pulling simulation by which a single-small molecule (mol_A) >> is >>>>>>>> being >>>>>>>> dragged along -Z from water into the body of a thin film. >>>>>>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com = >>>>>>>> yes" and >>>>>>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the >>>>>>>> system >>>>>>>> along the pulling direction as soon as the mol_A reach to the thin >>>> film, >>>>>>>> please find below the pulling flags movie and plot in below links. >>>>>>>> >>>>>>>> Centering the thin film and mol_A could solve the issue, (echo 1 0 >> | >>>>>>>> trjconv -center yes) to some extent but still COM changes in the >> early >>>>>>>> stage below 2ns. , >>>>>>>> COM: >>>>>>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 >>>>>>>> >>>>>>>> Movie in which the water molecules are hidden: >>>>>>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv >>>>>>>> >>>>>>>> - >>>>>>>> gmx version 2020.1 >>>>>>>> ----- >>>>>>>> pull = yes >>>>>>>> pull-print-com = no >>>>>>>> pull-print-ref-value = yes >>>>>>>> pull-print-components = Yes >>>>>>>> pull-nstxout = 1000 >>>>>>>> pull-nstfout = 1000 >>>>>>>> pull-pbc-ref-prev-step-com = yes >>>>>>>> pull-ngroups = 2 >>>>>>>> pull-ncoords = 1 >>>>>>>> pull-group1-name = Thin-film >>>>>>>> pull-group1-pbcatom = -1 >>>>>>>> pull-group2-name = mol_A >>>>>>>> pull-group2-pbcatom = 0 >>>>>>>> pull-coord1-type = umbrella >>>>>>>> pull-coord1-geometry = direction >>>>>>>> pull-coord1-groups = 1 2 >>>>>>>> pull-coord1-dim = N N Y >>>>>>>> pull-coord1-origin = 0.0 0.0 0.0 >>>>>>>> pull-coord1-vec = 0.0 0.0 -1.0 >>>>>>>> pull-coord1-start = yes >>>>>>>> pull-coord1-init = 0 >>>>>>>> pull-coord1-rate = 0.0005 >>>>>>>> pull-coord1-k = 5000 >>>>>>>> ----- >>>>>>>> I wonder if I could extract correct initial configuration from this >>>>>>>> trajectory? With correct initial configuration, I mean a set of gro >>>>>>>> file in >>>>>>>> which change from one from to another is the distance between the >> COM >>>> of >>>>>>>> the thin-film and mol_A? >>>>>>>> >>>>>>>> Thank you >>>>>>>> Alex >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-request at gromacs.org. >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> From ask.archana at gmail.com Mon Apr 27 14:27:31 2020 From: ask.archana at gmail.com (Archana Sonawani-Jagtap) Date: Mon, 27 Apr 2020 12:27:31 -0000 Subject: [gmx-users] gmx sasa for protein-ligand complex(problem with command usage) Message-ID: Dear Gromacs Users, I have GPCR-protein complex simulation and want to calculate buried surface area of the complex. I am using gmx sasa but facing problem in using the command especially the -output part. I need to calculate SASA for unbound receptor,unbound ligand and of complex. I have made index file where complex is ofcourse group 1 Protein and receptor is group 24 and ligand is group 25 when I provide the following command I gt TOTAL SASA gmx sasa -f .xtc -s .tpr -o bound-sasa.xvg -tu ns -n .ndx -surface 'group "1"' but when I add the output part -output '"hydrophobic" group "1" and charge {-0.2 to 02}; "hydrophilic" group "1" and not charge {-0.2 to 0.2}; Error in user input: Selection '"hydrophilic" group "1" and not charge {-0.2 to 0.2}' never matches any atoms. Can anyone tell me how to get SASA for receptor, ligand and compex. Thanks Archana From halverson at Princeton.EDU Mon Apr 27 16:26:25 2020 From: halverson at Princeton.EDU (Jonathan D. Halverson) Date: Mon, 27 Apr 2020 14:26:25 -0000 Subject: [gmx-users] GROMACS performance issues on POWER9/V100 node In-Reply-To: References: , Message-ID: Hi Szil?rd, Our OS is RHEL 7.6. Thank you for your test results. It's nice to see consistent results on a POWER9 system. Your suggestion of allocating the whole node was a good one. I did this in two ways. The first was to bypass the Slurm scheduler by ssh-ing to an empty node and running the benchmark. The second way was through Slurm using the --exclusive directive (which allocates the entire node indepedent of job size). In both cases, which used 32 hardware threads and one V100 GPU for ADH (PME, cubic, 40k steps), the performance was about 132 ns/day which is significantly better than the 90 ns/day from before (without --exclusive). Links to the md.log files are below. Here is the Slurm script with --exclusive: -------------------------------------------------------------------------------------------------- #!/bin/bash #SBATCH --job-name=gmx # create a short name for your job #SBATCH --nodes=1 # node count #SBATCH --ntasks=1 # total number of tasks across all nodes #SBATCH --cpus-per-task=32 # cpu-cores per task (>1 if multi-threaded tasks) #SBATCH --mem=8G # memory per node (4G per cpu-core is default) #SBATCH --time=00:10:00 # total run time limit (HH:MM:SS) #SBATCH --gres=gpu:1 # number of gpus per node #SBATCH --exclusive # TASK AFFINITIES SET CORRECTLY BUT ENTIRE NODE ALLOCATED TO JOB module purge module load cudatoolkit/10.2 BCH=../adh_cubic gmx grompp -f $BCH/pme_verlet.mdp -c $BCH/conf.gro -p $BCH/topol.top -o bench.tpr srun gmx mdrun -nsteps 40000 -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s bench.tpr -------------------------------------------------------------------------------------------------- Here are the log files: md.log with --exclusive: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.with-exclusive md.log without --exclusive: https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log.without-exclusive Szil?rd, what is your reading of these two files? This is a shared cluster so I can't use --exclusive for all jobs. Our nodes have four GPUs and 128 hardware threads (SMT4 so 32 cores over 2 sockets). Any thoughts on how to make a job behave like it is being run with --exclusive? The task affinities are apparently not being set properly in that case. To solve this I tried experimenting with the --cpu-bind settings. When --exclusive is not used, I find a slight performance gain by using --cpu-bind=cores: srun --cpu-bind=cores gmx mdrun -nsteps 40000 -pin on -ntmpi $SLURM_NTASKS -ntomp $SLURM_CPUS_PER_TASK -s bench.tpr In this case it still gives "NOTE: Thread affinity was not set" and performance is still poor. The --exclusive result suggests that the failed hardware unit test can be ignored, I believe. Here's a bit about our Slurm configuration: $ grep -i affinity /etc/slurm/slurm.conf TaskPlugin=affinity,cgroup ldd shows that gmx is linked against libhwloc.so.5. I have not heard from my contact at ORNL. All I can find online is that they offer GROMACS 5.1 (https://www.olcf.ornl.gov/software_package/gromacs/) and apparently nothing special is done about thread affinities. Jon ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Szil?rd P?ll Sent: Friday, April 24, 2020 6:06 PM To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 node Hi, Affinity settings on the Talos II with Ubuntu 18.04 kernel 5.0 works fine. I get threads pinned where they should be (hwloc confirmed) and consistent results. I also get reasonable thread placement even without pinning (i.e. the kernel scatters first until #threads <= #hwthreads). I see only a minor penalty to not pinning -- not too surprising given that I have a single NUMA node and the kernel is doing its job. Here are my quick the test results run on an 8-core Talos II Power9 + a GPU, using the adh_cubic input: $ grep Perf *.log test_1x1_rep1.log:Performance: 16.617 test_1x1_rep2.log:Performance: 16.479 test_1x1_rep3.log:Performance: 16.520 test_1x2_rep1.log:Performance: 32.034 test_1x2_rep2.log:Performance: 32.389 test_1x2_rep3.log:Performance: 32.340 test_1x4_rep1.log:Performance: 62.341 test_1x4_rep2.log:Performance: 62.569 test_1x4_rep3.log:Performance: 62.476 test_1x8_rep1.log:Performance: 97.049 test_1x8_rep2.log:Performance: 96.653 test_1x8_rep3.log:Performance: 96.889 This seems to point towards some issue with the OS or setup on the IBM machines you have -- and the unit test error may be one of the symptoms of it (as it suggests something is off with the hardware topology and a NUMA node is missing from it). I'd still suggest checking if a full not allocation with all threads, memory, etc passed to the job results in successful affinity settings i) in mdrun ii) in some other tool. Please update this thread if you have further findings. Cheers, -- Szil?rd On Fri, Apr 24, 2020 at 10:52 PM Szil?rd P?ll wrote: > > The following lines are found in md.log for the POWER9/V100 run: >> >> Overriding thread affinity set outside gmx mdrun >> Pinning threads with an auto-selected logical core stride of 128 >> NOTE: Thread affinity was not set. >> >> The full md.log is available here: >> https://github.com/jdh4/running_gromacs/blob/master/03_benchmarks/md.log > > > I glanced over that at first, will see if I can reproduce it, though I > only have access to a Raptor Talos, not an IBM machine with Ubuntu. > > What OS are you using? > > > -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From blau at kth.se Mon Apr 27 17:19:18 2020 From: blau at kth.se (Christian Blau) Date: Mon, 27 Apr 2020 15:19:18 -0000 Subject: [gmx-users] lincs warning In-Reply-To: <944887700.136779.1587834974435@mail.yahoo.com> References: <944887700.136779.1587834974435.ref@mail.yahoo.com> <944887700.136779.1587834974435@mail.yahoo.com> Message-ID: Hi Afsane, This might be an issue with the pressure coupling, depending on the compressibility you give for your system and the algorithm that you use for pressure coupling you might see quite large fluctuations in pressure. One idea might be to use temperature coupling to quickly dissipate large energies due to large fluctuations in box size. If you're not already using it you could try a robust temperature coupling with? v-rescale with tau-t = 0.1, which is usually recommendable. Using some steps to carefully anneal your system might help as well. To carefully heat your system from 0 to 300K in the first 100ps of the simulation you might use "annealing = single annealing-npoints = 2 annealing-time = 0 100 annealing-temp = 0 300". Then pressure-pre-equlibrating your system with the Berendsen barostat might be helpful, just don't use it for your production run. Best, Christian On 2020-04-25 19:16, Afsane Farhadi wrote: > Hi gromacs users?I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas ?is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right?Can any body help me please? > > Sent from Yahoo Mail on Android From afsane_farhadi at yahoo.com Mon Apr 27 17:32:12 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Mon, 27 Apr 2020 15:32:12 -0000 Subject: [gmx-users] lincs warning In-Reply-To: <885237322.546958.1587986529061@mail.yahoo.com> References: <885237322.546958.1587986529061.ref@mail.yahoo.com> <885237322.546958.1587986529061@mail.yahoo.com> Message-ID: <115006941.620788.1588000199418@mail.yahoo.com> Sent from Yahoo Mail on Android ----- Forwarded Message ----- From: "Afsane Farhadi" To: "gromacs.org_gmx-users at maillist.sys.kth.se" Cc: Sent: Mon, Apr 27, 2020 at 3:52 PM Subject: lincs warning Hi users?I have two types of molecules ,methane and carbondioxide. i optimized them by gaussian calculation and i edited the atom name and residue by vim. ?I extracted the epsilon and sigma parameter from the articles . i generated a box of 500 methane molecules and 62 carbondioxide by insert-molecules. I have done energy minimization and its ok (potential energy is ?-2e+03).when i was running npt.mdp the lincs warning was showed( bond rotate more than 30 degree)I need help thanks alot for your quick answers .the topology and npt.mdp is:#include "oplsaa.ff/forcefield.itp" [ atomtypes ] ??? CO????? C01????? 12.0110??? 0.775??? A??? 2.75700E-01?? 2.33790E-01 ??? OC????? O01????? 15.99940? -0.388??? A??? 3.03300E-01?? 6.69120E-01 ? opls_801? H801???? 1.0080???? 0.125??? A??? 1.48720E-01?? 0.65688E-01 ? opls_803? H803???? 1.0080???? 0.125??? A??? 1.48720E-01?? 0.65688E-01 ? opls_804? H804???? 1.0080???? 0.125??? A??? 1.48720E-01?? 0.65688E-01 ? opls_800? C800??? 12.0110??? -0.502??? A??? 1.90820E-01?? 4.57729E-01 ? opls_802? H802???? 1.0080???? 0.125??? A??? 1.48720E-01?? 0.65688E-01 [ moleculetype ] ; Name?????????????? nrexcl CH4?????????????????? 3 [ atoms ] ;?? nr?????? type? resnr residue? atom?? cgnr???? charge?????? mass ? ???? 1?? opls_800????? 1????? H?? C????? 1??? -0.5020??? 12.0110? ???? 2?? opls_801????? 1????? H?? H????? 1???? 0.1250???? 1.0080? ???? 3?? opls_802????? 1????? H?? H????? 1???? 0.1250???? 1.0080? ???? 4?? opls_803????? 1????? H?? H????? 1???? 0.1250???? 1.0080? ???? 5?? opls_804????? 1????? H?? H????? 1???? 0.1250???? 1.0080? [ bonds ] ??? 2???? 1???? 1????? 0.1090 138490.400 ??? 3???? 1???? 1????? 0.1090 138490.400 ??? 4???? 1???? 1????? 0.1090 138490.400 ??? 5???? 1???? 1????? 0.1090 138490.400 [ angles ] ;? ai??? aj??? ak funct??????????? c0??????????? c1??????????? c2??????????? c3? ??? 2???? 1???? 3???? 1??? 109.500??? 146.440 ??? 2???? 1???? 4???? 1??? 109.500??? 146.440 ??? 2???? 1???? 5???? 1??? 109.500??? 146.440 ??? 3???? 1???? 4???? 1??? 109.500??? 146.440 ??? 4???? 1???? 5???? 1??? 109.500??? 146.440 ??? 3???? 1???? 5???? 1??? 109.500??? 146.440 [ moleculetype ] ; Name?????????????? nrexcl CAR?? 3 [atoms] ; nr? type resnr residue atom cgnr charge mass ? 1?? CO??? 1???? CAR??? CO?? 1??? 0.775? 12.0110 ? 2?? OC??? 1???? CAR??? OC?? 1?? -0.388? 15.9994 ? 3?? OC??? 1???? CAR??? OC?? 1?? -0.388? 15.9994 ? [ bonds ] ? 1??? 2??? 1?? 0.11620? 844300 ? 1??? 3??? 1?? 0.11620? 844300 ?? ?? ? [angles] ;? ai??? aj??? ak?? funct??????????? c0??????????? c1??????????? c2??????????? c3? ? ?? 2???? 1???? 3???? 1?????????? 180???????? 451.9 ?? ? [system]: co2 in methane ?[molecules] ? CH4???? 500 ? CAR???? 62################ Sent from Yahoo Mail on Android From Weitse.Hsu at colorado.edu Tue Apr 28 00:59:37 2020 From: Weitse.Hsu at colorado.edu (Wei-Tse Hsu) Date: Mon, 27 Apr 2020 22:59:37 -0000 Subject: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field? Message-ID: Dear gmx users, I prepared a topology using Open Forcefiled for my system. To make GROMACS able to recognize the water molecules and the ions to be added, I need to include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my topology file (.top file). I was planning to use GROMOS54a7 with TIP3P water model, so I add the following lines to my topology file: ; Include water topology #include "gromos54a7.ff/tip3p.itp" In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the error of " Atomtype OWT3 not found", I later found that OWT3 was not defined in ffnonbonded.itp. I also tried pdb2gmx command using other system and chose gromos54a7 force field, but there is no option for selecting TIP3P water model. Therefore, I wonder if TIP3P water model is actually not available in GROMOS54a7 force field even if there is a tip3p.itp in gromos54a7.ff. I might just use SPC water model instead, but I want to make sure that my understanding is correct. Thank you! Best, Wei-Tse From shakirashukoor1993 at gmail.com Tue Apr 28 01:44:04 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Mon, 27 Apr 2020 23:44:04 -0000 Subject: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field? In-Reply-To: References: Message-ID: Hi As far as I know tip3p water model is modelled to use in combination with CHARMM force field. However there is nothing wrong in using TIP3P in combination with GROMOS force field. And u will have both the bonded and non bonded parameters of that specific water model in tip3p,itp file itself. You don't have to get it from the force field. Instead you have to add this itp file to the defined topology file you are giving. On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu wrote: > Dear gmx users, > I prepared a topology using Open Forcefiled for my system. To make GROMACS > able to recognize the water molecules and the ions to be added, I need to > include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my > topology file (.top file). I was planning to use GROMOS54a7 with TIP3P > water model, so I add the following lines to my topology file: > > ; Include water topology > #include "gromos54a7.ff/tip3p.itp" > > In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the > error of " Atomtype OWT3 not found", I later found that OWT3 was not > defined in ffnonbonded.itp. I also tried pdb2gmx command using other system > and chose gromos54a7 force field, but there is no option for selecting > TIP3P water model. Therefore, I wonder if TIP3P water model is actually not > available in GROMOS54a7 force field even if there is a tip3p.itp in > gromos54a7.ff. I might just use SPC water model instead, but I want to make > sure that my understanding is correct. Thank you! > > Best, > Wei-Tse > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From jalemkul at vt.edu Tue Apr 28 03:32:18 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 28 Apr 2020 01:32:18 -0000 Subject: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field? In-Reply-To: References: Message-ID: <681eb59d-697e-7afa-0e3a-860b801e124f@vt.edu> On 4/27/20 7:43 PM, shakira shukoor wrote: > Hi > As far as I know tip3p water model is modelled to use in combination with > CHARMM force field. However there is nothing wrong in using TIP3P in > combination with GROMOS force field. And u will have both the bonded and > non bonded parameters of that specific water model in tip3p,itp file > itself. You don't have to get it from the force field. Instead you have to > add this itp file to the defined topology file you are giving. GROMOS force fields were parametrized for use with SPC. As far as I know, no one has demonstrated that the use of TIP3P with GROMOS is valid. -Justin > On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu wrote: > >> Dear gmx users, >> I prepared a topology using Open Forcefiled for my system. To make GROMACS >> able to recognize the water molecules and the ions to be added, I need to >> include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my >> topology file (.top file). I was planning to use GROMOS54a7 with TIP3P >> water model, so I add the following lines to my topology file: >> >> ; Include water topology >> #include "gromos54a7.ff/tip3p.itp" >> >> In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the >> error of " Atomtype OWT3 not found", I later found that OWT3 was not >> defined in ffnonbonded.itp. I also tried pdb2gmx command using other system >> and chose gromos54a7 force field, but there is no option for selecting >> TIP3P water model. Therefore, I wonder if TIP3P water model is actually not >> available in GROMOS54a7 force field even if there is a tip3p.itp in >> gromos54a7.ff. I might just use SPC water model instead, but I want to make >> sure that my understanding is correct. Thank you! >> >> Best, >> Wei-Tse >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Tue Apr 28 03:33:34 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 28 Apr 2020 01:33:34 -0000 Subject: [gmx-users] Atom CA used in that entry is not found in the input file In-Reply-To: References: Message-ID: <0c6b6064-5320-dc90-a17b-dec14c7df02a@vt.edu> On 4/26/20 4:45 PM, Daniel Burns wrote: > Hello, > > I edited a few selenomethionine residues, changing "S" to "SD" and removed > the "SE" at the end of the line. I then ran pdb2gmx with Charmm36. I get > the following error (not sure why the residue number doesn't match): > > Fatal error: > Residue 324 named GLY of a molecule in the input file was mapped > to an entry in the topology database, but the atom CA used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. > > My .pdb file section looks like this: > ATOM 569 N MET A 324 87.364 46.446 53.851 1.00 3.42 > N > ATOM 570 CA MET A 324 86.617 45.972 52.679 1.00 6.50 > C > ATOM 571 C MET A 324 87.405 46.212 51.424 1.00 6.43 > C > ATOM 572 O MET A 324 86.987 45.830 50.332 1.00 8.80 > O > ATOM 573 CB MET A 324 85.203 46.573 52.584 1.00 5.66 > C > ATOM 574 CG MET A 324 84.258 46.053 53.663 1.00 5.50 > C > ATOM 575 CE MET A 324 83.200 44.225 51.772 1.00 3.19 > C > ATOM 576 SD MET A 324 83.876 44.132 53.563 1.00 14.27 > S > ATOM 577 N GLY A 325 88.553 46.854 51.604 1.00 9.51 > N > ATOM 578 CA GLY A 325 89.548 47.012 50.546 1.00 9.78 > C > ATOM 579 C GLY A 325 89.087 47.608 49.227 1.00 9.91 > C > ATOM 580 O GLY A 325 89.352 47.048 48.159 1.00 11.43 > O > ATOM 581 N GLY A 326 88.403 48.742 49.271 1.00 7.35 > N > ATOM 582 CA GLY A 326 87.942 49.290 48.005 1.00 6.34 > C > ATOM 583 C GLY A 326 86.542 48.875 47.602 1.00 3.91 > C > ATOM 584 O GLY A 326 85.947 49.547 46.765 1.00 4.00 > O > > I don't see anything wrong with my GLY residues and none of the other > Glycines are presenting an error. This does follow one of my edited MET > residues. Please provide the full screen output from pdb2gmx. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From neena.susaneappen at mail.utoronto.ca Tue Apr 28 03:50:05 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Tue, 28 Apr 2020 01:50:05 -0000 Subject: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis Message-ID: Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena From elham802011 at yahoo.com Tue Apr 28 11:08:31 2020 From: elham802011 at yahoo.com (Elham Taghikhani) Date: Tue, 28 Apr 2020 09:08:31 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization In-Reply-To: <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> References: <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> Message-ID: Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom which errored during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? > On Apr 20, 2020, at 1:08 AM, Elham Taghikhani wrote: > > ?Thank you > I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. > Could you explain how can I observe bad contacts in the structure? > I even tried the different box size but it didn't work. > Both ligand and protein are ok with minimization separately. > > >>> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: >>> >> ? >> Hi >> >> I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+03 >> Number of steps = 50000 >> Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 >> Segmentation fault (core dumped) >> >> and this is my mpd file: >> ; LINES STARTING WITH ';' ARE COMMENTS >> title = Minimization ; Title of run >> >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent minimization) >> emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol >> emstep = 0.01 ; Energy step size >> nsteps = 50000 ; Maximum number of (minimization) steps to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor list (simple, grid) >> rlist = 1.2 ; Cut-off for making neighbor list (short range forces) >> coulombtype = PME ; Treatment of long range electrostatic interactions >> rcoulomb = 1.2 ; long range electrostatic cut-off >> vdwtype = cutoff >> vdw-modifier = force-switch >> rvdw-switch = 1.0 >> rvdw = 1.2 ; long range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions >> DispCorr = no >> Can anyone suggest how to troubleshoot this error? >> The system is nuetralized. >> >> Thank you in advance. >> From miro.astore at gmail.com Tue Apr 28 12:17:11 2020 From: miro.astore at gmail.com (Miro Astore) Date: Tue, 28 Apr 2020 10:17:11 -0000 Subject: [gmx-users] debugging Message-ID: Hi all, I am interested in how Gromacs works at the back end but I don't have much C experience so this might be silly. I have noticed that one of my systems that includes virtual sites parses fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a segmentation fault. 21169 Segmentation fault (core dumped) I'd like to try and debug this further. Should I try and go after this myself? -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From slall at ncbs.res.in Tue Apr 28 12:26:47 2020 From: slall at ncbs.res.in (Sahil Lall) Date: Tue, 28 Apr 2020 10:26:47 -0000 Subject: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis In-Reply-To: References: Message-ID: Hello, Though I don't know the answer to your question, I can offer a workaround for the task. I have simulated such C-terminally amidated peptides in vacuum before and I performed the same analysis using the Hydrogen bonds plugin in VMD. Hope this helps. Cheers, Sahil On 2020-04-28 07:20, Neena Susan Eappen wrote: > Hello gromacs users, > > My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? > > Many thanks, > Neena From blau at kth.se Tue Apr 28 12:45:07 2020 From: blau at kth.se (Christian Blau) Date: Tue, 28 Apr 2020 10:45:07 -0000 Subject: [gmx-users] debugging In-Reply-To: References: Message-ID: <70c06ebc-dd09-a872-650a-b5476bd189f2@kth.se> Hi Miro, This can be of great help and a wonderful learning experience; at the same time also an enormous time-sink. First, you did already do a bunch of very helpful work in trying to find the latest version, where things still work,? have the error be reproducible on a test system. If you were to file an issue on gitlab here: https://gitlab.com/gromacs/gromacs/-/issues - note that we moved from redmine - with the test sytem attached, this would help tremendously in fixing the bug. If you are up for the joy of debugging yourself and possibly provide your solution to gromacs, here are the steps that I would take: 0. check that this issue has not been already reported and solved (try the latest patch release (you did that), check in gitlab issues) 1. identify the smallest system where the issue occurs (or at least reasonably small, so that you can test quickly) 2. have a debug built of gromacs, using -DCMAKE_BUILD_TYPE=Debug 3. Set up a good build and debug environment. This in itself can take some time to find something that works well for the system that you're on. For a quick start gdb might work as well, more visual aids via IDEs like vscode and clion, ... are very useful. 4. Find the line where the error occurs (segfaults are kind of nice because they are very clear errors, often in a specific line and often a result of overlooked memory management (we're working our way through removing this via modernisation to modern C++ standards, but not there yet)) 5. Look at the call hierarchy, try to understand the larger context that you're in. 6. Try to identify the smallest surrounding context in which the bug occurs, try to figure which function/class allocates the memory for the object that causes the segfault If there are tests and the context is not too large: ? 7. See if there are some tests written for this context. (usually there are corresponding .cpp files in the test folder where bugs occur), add a test that reproduces the buggy behaviour. ? 8. Compile the tests, change code, then recompile tests until your test passes. ? 9. Check that your intial case works, otherwise add more tests that catch the failing behaviour, fix, repeat Otherwise: Follow memory allocations, resizes, etc of the offending object, see if you can trigger the segfault earlier by trying to access memory that you know should be accessible. Finally open a new merge-request on gitlab (see under https://gitlab.com/gromacs/gromacs/-/merge_requests), or create a merge request from the issue you had opened. Wait for comments and code-review. Hope that gives you a feeling for the task on hand - I would personally definitely recommend at least looking *at* the source code and giving it a shot, also for the sake of getting a feel for the internal gears of GROMACS and just taking it as far as you can and have time. Happy coding, Christian On 2020-04-28 12:16, Miro Astore wrote: > Hi all, > > I am interested in how Gromacs works at the back end but I don't have much > C experience so this might be silly. > > I have noticed that one of my systems that includes virtual sites parses > fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a > segmentation fault. > 21169 Segmentation fault (core dumped) > I'd like to try and debug this further. Should I try and go after this > myself? > From sadafrani6 at gmail.com Tue Apr 28 17:52:52 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Tue, 28 Apr 2020 15:52:52 -0000 Subject: [gmx-users] Invalid atomtype format Message-ID: Dear Gromacs users I am facing a problem between different versions of gromacs for gmx pdb2gmx. I have a protein-ligand system, I did all the necessary steps mentioned in gromacs manual for adding new residue to force field. When I run this in gromacs 2019 it gives me a warning as below:- Fatal error: Invalid atomtype format: '' But it still generates a gro file and topology. But When I am using gromacs 2020, I get the same message of invalid atomtype format as below:- Reading 78I-T.pdb... WARNING: all CONECT records are ignored Read '', 4083 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. WARNING: Chain identifier 'A' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. There are 2 chains and 0 blocks of water and 492 residues with 4083 atoms chain #res #atoms 1 'A' 489 3971 2 'A' 3 112 All occupancies are one Opening force field file ./amber99sb-ildn.ff/atomtypes.atp ------------------------------------------------------- Program: gmx pdb2gmx, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) Fatal error: *Invalid atomtype format: ''* I am unable to sort out this problem. I have added the atom types of my molecule as mentioned:- ;[ atomtypes ] ; name bond_type mass charge ptype sigma eps nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 na 14.01000 0.000 A 3.25000e-1 7.11280e-1 c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 os 16.00000 0.000 A 3.00001e-1 7.11280e-1 h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 o 16.00000 0.000 A 2.95992e-1 8.78640e-1 oh 16.00000 0.000 A 3.06647e-1 8.80314e-1 ho 1.00800 0.000 A 0.00000e+0 0.00000e+0 h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 c 12.01000 0.000 A 3.39967e-1 3.59824e-1 n 14.01000 0.000 A 3.25000e-1 7.11280e-1 ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 Could you please help me to sort out this problem. Even when the format is incorrect does it mean that gromacs 2019 is generating a wrong topology? Thanks in advance. Sadaf From Weitse.Hsu at colorado.edu Wed Apr 29 05:16:21 2020 From: Weitse.Hsu at colorado.edu (Wei-Tse Hsu) Date: Wed, 29 Apr 2020 03:16:21 -0000 Subject: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field? In-Reply-To: <681eb59d-697e-7afa-0e3a-860b801e124f@vt.edu> References: <681eb59d-697e-7afa-0e3a-860b801e124f@vt.edu> Message-ID: Hi Shakira and Dr. Lemkul, Thank you so much for your reply! I ended up using an AMBER force field. Best, Wei-Tse On Mon, Apr 27, 2020 at 7:32 PM Justin Lemkul wrote: > > > On 4/27/20 7:43 PM, shakira shukoor wrote: > > Hi > > As far as I know tip3p water model is modelled to use in combination with > > CHARMM force field. However there is nothing wrong in using TIP3P in > > combination with GROMOS force field. And u will have both the bonded and > > non bonded parameters of that specific water model in tip3p,itp file > > itself. You don't have to get it from the force field. Instead you have > to > > add this itp file to the defined topology file you are giving. > > GROMOS force fields were parametrized for use with SPC. As far as I > know, no one has demonstrated that the use of TIP3P with GROMOS is valid. > > -Justin > > > On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu > wrote: > > > >> Dear gmx users, > >> I prepared a topology using Open Forcefiled for my system. To make > GROMACS > >> able to recognize the water molecules and the ions to be added, I need > to > >> include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my > >> topology file (.top file). I was planning to use GROMOS54a7 with TIP3P > >> water model, so I add the following lines to my topology file: > >> > >> ; Include water topology > >> #include "gromos54a7.ff/tip3p.itp" > >> > >> In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the > >> error of " Atomtype OWT3 not found", I later found that OWT3 was not > >> defined in ffnonbonded.itp. I also tried pdb2gmx command using other > system > >> and chose gromos54a7 force field, but there is no option for selecting > >> TIP3P water model. Therefore, I wonder if TIP3P water model is actually > not > >> available in GROMOS54a7 force field even if there is a tip3p.itp in > >> gromos54a7.ff. I might just use SPC water model instead, but I want to > make > >> sure that my understanding is correct. Thank you! > >> > >> Best, > >> Wei-Tse > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > > http://secure-web.cisco.com/1jiuLNgPYje4gVKYOwViv436SLC3KS0A2GQwla3f8JpjGb7IV9SzlFLXlLGZA5gp1w5hZnD71uDp7nseGks0eUee-C_sO3BnHnkKJb1RTW8pA3R4KJKyttkgJE4rApHLqTNRTmyfwLL4LwDMRo7tFjQiwv-Lz1uuAeT3YP3I2wQmHIkzyvdt5DI0J8yjnzYn2fXHdb17TED8np43r3As0cbEwVyhXW_dsYWauCdHP8zD9B7S8ns0sswKvrUpQFmIP16R2mJqEPbG2m5PvhLjPlrVfY1f2JRkpewMmkKabaZxGO0y-Pd8Ml7Vfs_7xuRzpYcyFu36gV2-gs2Qk_kaD51H40RlnXzy_0PIF-z3bdpMVVB3olCx6kZdhF7q6lwSFsc5_8msPUlLROg-REP9rnvj2IGi8HgoHdRE0pBMavNkcCwmQOEqMIlg9_mcsJOwFzCa2TWBKjaLZB0QSjwjxQg/http%3A%2F%2Fwww.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > From mwinokan at me.com Wed Apr 29 12:41:30 2020 From: mwinokan at me.com (Max Winokan) Date: Wed, 29 Apr 2020 10:41:30 -0000 Subject: [gmx-users] Atom positions change between topology generation and NVT mdrun In-Reply-To: References: Message-ID: Dear GMX-Users, I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. Thank you and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey GU2 7XH Guildford United Kingdom Office: 03AZ04 Email: m.winokan at surrey.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From mwinokan at me.com Wed Apr 29 13:35:41 2020 From: mwinokan at me.com (Max Winokan) Date: Wed, 29 Apr 2020 11:35:41 -0000 Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration Message-ID: Dear GMX-Users, I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. Thank you and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey GU2 7XH Guildford United Kingdom Office: 03AZ04 Email: m.winokan at surrey.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From mwinokan at me.com Wed Apr 29 13:49:32 2020 From: mwinokan at me.com (Max Winokan) Date: Wed, 29 Apr 2020 11:49:32 -0000 Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration In-Reply-To: <7C59FF17-D1C2-4E1D-B4A5-A1F1E61AACCF@me.com> References: <7C59FF17-D1C2-4E1D-B4A5-A1F1E61AACCF@me.com> Message-ID: My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. Best, Max From: on behalf of Max Winokan Reply to: Date: Wednesday, 29 April 2020 at 1:36 PM To: Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration Dear GMX-Users, I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. Thank you and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey GU2 7XH Guildford United Kingdom Office: 03AZ04 Email: m.winokan at surrey.ac.uk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From blau at kth.se Wed Apr 29 14:43:49 2020 From: blau at kth.se (Christian Blau) Date: Wed, 29 Apr 2020 12:43:49 -0000 Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration In-Reply-To: References: <7C59FF17-D1C2-4E1D-B4A5-A1F1E61AACCF@me.com> Message-ID: <54e4c564-7f17-b0d5-d219-eafe76b58ae9@kth.se> Hi Max, In the .mdp file that you uploaded you are using constraints???????????? = h-bonds?? ; bonds involving H are constrained Is that the right file? Otherwise running without these constraints might help. On the off-chance that happened: not using -ignh in grompp avoids re-placement of hydrogens. Best, Christian On 2020-04-29 13:49, Max Winokan wrote: > My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 > > > > If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. > > > > Best, > > > > Max > > > > From: on behalf of Max Winokan > Reply to: > Date: Wednesday, 29 April 2020 at 1:36 PM > To: > Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration > > > > Dear GMX-Users, > > > > I am running some simulations of unsolvated DNA base pair dimers, with a topology generated from a structure previously optimised with quantum mechanical models. Because these structures have been highly-optimised it is important that Gromacs begins the MD with these atom positions. > > > > After generating the topology with pdb2gmx I get the structure file (gc.gro) with the configuration seen below (after_pdb2gmx.jpg): > > > > > > This configuration matches the optimised input structure. However, when I examine the trajectory (.trr) produced by running my NVT simulation (the MDP file for which is attached), the first timestep is very different from the input gc.gro structure, as seen below (first_nvt_frame.jpg): > > > > > > The discrepancy is largest with the hydrogen atoms (which are not constrained of course), but all the atoms have been slightly shifted from the input configuration. Please could someone fill me in on the source of these position changes, and how I can modify my methods to avoid these. > > > > Thank you and best regards, > > > > Max Winokan > > > > PhD Candidate in Theoretical Physics > > Leverhulme Quantum Biology Doctoral Training Centre University of Surrey > > GU2 7XH Guildford > > United Kingdom > > Office: 03AZ04 > > Email: m.winokan at surrey.ac.uk > > > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > From mamapcr at gmail.com Wed Apr 29 14:50:30 2020 From: mamapcr at gmail.com (Dutta, Kunal) Date: Wed, 29 Apr 2020 12:50:30 -0000 Subject: [gmx-users] POPC: Fatal error: Message-ID: Dear Friends, I'm trying to learn Tutorial 2: KALP15 in DPPC The FOLLOWING PROBLEM APPEARS: " GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/kunal/Documents/MD_Simulation/B2AR in POPC Command line: gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -2044757183 Generated 837 of the 2346 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) *Fatal error:number of coordinates in coordinate file (popc128a.pdb, 14036) does not match topology (topol_popc.top, 17621)* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- " Thank you for your kind help. Sincerely, Kunal -- *--------------Every life is precious------------* From shakirashukoor1993 at gmail.com Wed Apr 29 14:54:45 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Wed, 29 Apr 2020 12:54:45 -0000 Subject: [gmx-users] POPC: Fatal error: In-Reply-To: References: Message-ID: Hi The error states that the number of POPC molecules in your configuration file and that mentioned in your topology files are not same. The number refers to the total number of atoms. On Wed, Apr 29, 2020 at 6:20 PM Dutta, Kunal wrote: > Dear Friends, > I'm trying to learn Tutorial 2: KALP15 in DPPC > > The FOLLOWING PROBLEM APPEARS: > > " > GROMACS: gmx grompp, version 2018.1 > Executable: /usr/bin/gmx > Data prefix: /usr > Working dir: /home/kunal/Documents/MD_Simulation/B2AR in POPC > Command line: > gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr > > > NOTE 1 [file minim.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to -2044757183 > Generated 837 of the 2346 non-bonded parameter combinations > Excluding 3 bonded neighbours molecule type 'POPC' > Excluding 2 bonded neighbours molecule type 'SOL' > > ------------------------------------------------------- > Program: gmx grompp, version 2018.1 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) > > > > *Fatal error:number of coordinates in coordinate file (popc128a.pdb, > 14036) does not match topology (topol_popc.top, 17621)* > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > " > > Thank you for your kind help. > Sincerely, > Kunal > > -- > *--------------Every life is precious------------* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From jalemkul at vt.edu Wed Apr 29 18:28:49 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 16:28:49 -0000 Subject: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis In-Reply-To: References: Message-ID: <4a347b6a-6571-45d0-ff22-419647de3f37@vt.edu> On 4/27/20 9:50 PM, Neena Susan Eappen wrote: > Hello gromacs users, > > My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? How do you know this group isn't being factored into the analysis? The NH2 residue is recognized as a protein residue by default and the analysis should consider all N-H pairs as H-bond donors. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 29 18:29:56 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 16:29:56 -0000 Subject: [gmx-users] Segmentation fault (core dumped) error during minimization In-Reply-To: References: <12A0D3EF-814A-4DB7-A904-DBB66C31BAD0@yahoo.com> Message-ID: <401bf4a4-b161-f5aa-1d8b-43f4a1f879f6@vt.edu> On 4/28/20 5:08 AM, Elham Taghikhani wrote: > Hi > As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. > And the atom which errored during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? > You'll have to provide more information about how you parametrized this covalent ligand. This is a far different case from a "normal" protein-ligand complex and requires very careful force field parametrization, including the linkage itself and any impacts that may have on associated protein terms. In this case, I don't see how you can assess the stability of the ligand topology by itself, as you said you had. Please explain in greater detail. -Justin >> On Apr 20, 2020, at 1:08 AM, Elham Taghikhani wrote: >> >> ?Thank you >> I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. >> Could you explain how can I observe bad contacts in the structure? >> I even tried the different box size but it didn't work. >> Both ligand and protein are ok with minimization separately. >> >> >>>> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: >>>> >>> ? >>> Hi >>> >>> I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. >>> >>> Steepest Descents: >>> Tolerance (Fmax) = 1.00000e+03 >>> Number of steps = 50000 >>> Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 >>> Segmentation fault (core dumped) >>> >>> and this is my mpd file: >>> ; LINES STARTING WITH ';' ARE COMMENTS >>> title = Minimization ; Title of run >>> >>> ; Parameters describing what to do, when to stop and what to save >>> integrator = steep ; Algorithm (steep = steepest descent minimization) >>> emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol >>> emstep = 0.01 ; Energy step size >>> nsteps = 50000 ; Maximum number of (minimization) steps to perform >>> >>> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions >>> nstlist = 1 ; Frequency to update the neighbor list and long range forces >>> cutoff-scheme = Verlet >>> ns_type = grid ; Method to determine neighbor list (simple, grid) >>> rlist = 1.2 ; Cut-off for making neighbor list (short range forces) >>> coulombtype = PME ; Treatment of long range electrostatic interactions >>> rcoulomb = 1.2 ; long range electrostatic cut-off >>> vdwtype = cutoff >>> vdw-modifier = force-switch >>> rvdw-switch = 1.0 >>> rvdw = 1.2 ; long range Van der Waals cut-off >>> pbc = xyz ; Periodic Boundary Conditions >>> DispCorr = no >>> Can anyone suggest how to troubleshoot this error? >>> The system is nuetralized. >>> >>> Thank you in advance. >>> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 29 18:30:59 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 16:30:59 -0000 Subject: [gmx-users] Invalid atomtype format In-Reply-To: References: Message-ID: On 4/28/20 11:52 AM, Sadaf Rani wrote: > Dear Gromacs users > I am facing a problem between different versions of gromacs for gmx > pdb2gmx. I have a protein-ligand system, I did all the necessary steps > mentioned in gromacs manual for adding new residue to force field. When I > run this in gromacs 2019 it gives me a warning as below:- > Fatal error: > Invalid atomtype format: '' > But it still generates a gro file and topology. But When I am using gromacs > 2020, I get the same message of invalid atomtype format as below:- > > Reading 78I-T.pdb... > WARNING: all CONECT records are ignored > Read '', 4083 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > WARNING: Chain identifier 'A' is used in two non-sequential blocks. > They will be treated as separate chains unless you reorder your file. > There are 2 chains and 0 blocks of water and 492 residues with 4083 atoms > > chain #res #atoms > 1 'A' 489 3971 > 2 'A' 3 112 > > All occupancies are one > Opening force field file ./amber99sb-ildn.ff/atomtypes.atp > > ------------------------------------------------------- > Program: gmx pdb2gmx, version 2020-UNCHECKED > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98) > > Fatal error: > *Invalid atomtype format: ''* > > I am unable to sort out this problem. > I have added the atom types of my molecule as mentioned:- > > ;[ atomtypes ] > ; name bond_type mass charge ptype sigma eps > nh 14.01000 0.000 A 3.25000e-1 7.11280e-1 > hn 1.00800 0.000 A 1.06908e-1 6.56888e-2 > ca 12.01000 0.000 A 3.39967e-1 3.59824e-1 > nb 14.01000 0.000 A 3.25000e-1 7.11280e-1 > h5 1.00800 0.000 A 2.42146e-1 6.27600e-2 > nc 14.01000 0.000 A 3.25000e-1 7.11280e-1 > cd 12.01000 0.000 A 3.39967e-1 3.59824e-1 > na 14.01000 0.000 A 3.25000e-1 7.11280e-1 > c3 12.01000 0.000 A 3.39967e-1 4.57730e-1 > h2 1.00800 0.000 A 2.29317e-1 6.56888e-2 > os 16.00000 0.000 A 3.00001e-1 7.11280e-1 > h1 1.00800 0.000 A 2.47135e-1 6.56888e-2 > p5 30.97000 0.000 A 3.74177e-1 8.36800e-1 > o 16.00000 0.000 A 2.95992e-1 8.78640e-1 > oh 16.00000 0.000 A 3.06647e-1 8.80314e-1 > ho 1.00800 0.000 A 0.00000e+0 0.00000e+0 > h4 1.00800 0.000 A 2.51055e-1 6.27600e-2 > c 12.01000 0.000 A 3.39967e-1 3.59824e-1 > n 14.01000 0.000 A 3.25000e-1 7.11280e-1 > ha 1.00800 0.000 A 2.59964e-1 6.27600e-2 > > Could you please help me to sort out this problem. Even when the format is > incorrect does it mean that gromacs 2019 is generating a wrong topology? You should upload a complete test case (including all force field files and your PDB structure) somewhere so that we can take a look at it. This is a weird error to try to debug. Make sure you're only ever using a plain-text editor like VIM or Emacs to avoid inclusion of inappropriate characters. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 29 18:33:02 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 16:33:02 -0000 Subject: [gmx-users] Atom positions change between topology generation and NVT equilibration In-Reply-To: References: <7C59FF17-D1C2-4E1D-B4A5-A1F1E61AACCF@me.com> Message-ID: On 4/29/20 7:49 AM, Max Winokan wrote: > My apologies for the missing images. Hopefully they are available along with the MDP in the following link: https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0 > > > > If anyone knows what could be going on, please let me know. Essentially the atom positions in the first NVT step are very different to the input topology, see my original email below. > > Was there an intervening energy minimization step? The output of pdb2gmx looks fine, though providing the actual coordinate files and topologies themselves would be more useful for diagnosing the issue. Note that if you are applying constraints, that operation is done before the first step so the coordinates can change. The distortion in the coordinates suggests and incorrect bonded topology. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Wed Apr 29 18:34:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 16:34:39 -0000 Subject: [gmx-users] POPC: Fatal error: In-Reply-To: References: Message-ID: <41715514-cb54-fd4a-0e50-4e179b605745@vt.edu> On 4/29/20 8:50 AM, Dutta, Kunal wrote: > Dear Friends, > I'm trying to learn Tutorial 2: KALP15 in DPPC > > The FOLLOWING PROBLEM APPEARS: > > " > GROMACS: gmx grompp, version 2018.1 > Executable: /usr/bin/gmx > Data prefix: /usr > Working dir: /home/kunal/Documents/MD_Simulation/B2AR in POPC > Command line: > gmx grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o popc.tpr > > > NOTE 1 [file minim.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to -2044757183 > Generated 837 of the 2346 non-bonded parameter combinations > Excluding 3 bonded neighbours molecule type 'POPC' > Excluding 2 bonded neighbours molecule type 'SOL' > > ------------------------------------------------------- > Program: gmx grompp, version 2018.1 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) > > > > *Fatal error:number of coordinates in coordinate file (popc128a.pdb, > 14036) does not match topology (topol_popc.top, 17621)* > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > " Likely you have specified the wrong number of water molecules in the topology. Don't adhere too closely to the tutorial when using different coordinate files (and lipids). There are probably a different number of waters in the POPC system so you will have to make more adjustments to the topology than might be immediately apparent. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Wed Apr 29 18:55:08 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Wed, 29 Apr 2020 16:55:08 -0000 Subject: [gmx-users] about segmentation fault related with gmx trjconv Message-ID: Dear gromacs users, Dear Mathias I have a problem when I try to generate the reference file .gro to run gmx covar doing the dPCA in gromacs: Note: first of all my system has 32 atoms. 1) $GMX/gmx angle -f md_0_100.xtc -n angle.ndx -or angle.trr -type dihedral 2) I modified the angle.ndx in order to only have one group: ------------------------------------------------ *Head of file:* [Phi and Psi] 1 2 4 5 ?..(all the dihedral angles) ------------------------------------------------ It says a note: "There are 99 dihedrals. Will fill 66 atom positions with cos/sin" 3) So I created my covar.ndx with 66 elements. 4) Then I run: gmx trjconv -f angle.trr -s md_0_100.tpr -o resized.gro -n covar.ndx -fit none -e 10000, where 10000 is in ps (my simulation was 10ns). But then I get the following error: *" line 31: 56948 Segmentation fault (core dumped) $GMX/gmx trjconv -f angle.trr -s md_0_100.tpr -o resized.gro -n covar.ndx -e 10000" * Any idea why is doing segmentation fault? Also notice that my molecule has 32 atoms and is not a typical protein or aminoacid. It is a nucleotide. Kindly, Lazaro From mjsubach at ncsu.edu Wed Apr 29 21:02:57 2020 From: mjsubach at ncsu.edu (Joel Subach) Date: Wed, 29 Apr 2020 19:02:57 -0000 Subject: [gmx-users] GROMACS TUTOR WANTED Message-ID: Hello I am in search of a gromacs tutor to assist me with protein ion channel dynamic simulations towards drug discovery, accordingly interested parties please email for more details, thanks:) From lamonteserincastanedo at gmail.com Wed Apr 29 23:01:13 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Wed, 29 Apr 2020 21:01:13 -0000 Subject: [gmx-users] about how to create angle.index with specific angles Message-ID: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? Any help would be very appreciate it. Kindly, Lazaro From jalemkul at vt.edu Thu Apr 30 00:23:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 22:23:47 -0000 Subject: [gmx-users] about how to create angle.index with specific angles In-Reply-To: References: Message-ID: On 4/29/20 5:01 PM, lazaro monteserin wrote: > Dear gromacs users, > > Is there any way to tell gmx mk_angndx to create the index file with > dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, > 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From lamonteserincastanedo at gmail.com Thu Apr 30 01:12:05 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Wed, 29 Apr 2020 23:12:05 -0000 Subject: [gmx-users] about how to create angle.index with specific angles In-Reply-To: References: Message-ID: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g > 1, > > 2, 3) from my molecule? > > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From no-reply at dropbox.com Thu Apr 30 01:35:13 2020 From: no-reply at dropbox.com (sadaf rani (via Dropbox)) Date: Wed, 29 Apr 2020 23:35:13 -0000 Subject: [gmx-users] =?utf-8?q?sadaf_rani_shared_=22Atom=5Ftype=5Ferror_fi?= =?utf-8?q?les=2Ezip=22_with_you?= Message-ID: <01010171c84b44a2-90704f62-6af2-4786-805e-24fff9f517e4-000000@us-west-2.amazonses.com> Hi there, sadaf rani (sadafrani6 at gmail.com) invited you to view the file " Atom_type_error files.zip " on Dropbox. View file[1] Enjoy! The Dropbox team sadaf and others will be able to see when you view this file. Other files shared with you through Dropbox may also show this info. Learn more[2] in our help center. [1]: https://www.dropbox.com/l/scl/AABOBBmk1NDOOW-YNWw7dM8VFd3Th70EUGI [2]: https://www.dropbox.com/l/AABD9Hnv_6jbvifK8cnQDesl6oKoUT8_qsc From sadafrani6 at gmail.com Thu Apr 30 01:41:17 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Wed, 29 Apr 2020 23:41:17 -0000 Subject: [gmx-users] Invalid atomtype format (Justin Lemkul) Message-ID: Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Thanks and Regards. Sadaf From jalemkul at vt.edu Thu Apr 30 01:57:11 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 29 Apr 2020 23:57:11 -0000 Subject: [gmx-users] about how to create angle.index with specific angles In-Reply-To: References: Message-ID: <55b50eff-d7a6-e899-09a7-3d8c296fec7b@vt.edu> On 4/29/20 7:11 PM, lazaro monteserin wrote: > Dear Dr. Lemkul it could be possible use that angle.index with the selected > dihedrals written by hand as index file for gmx angle for dihedral > Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin > Kindly, > Lazaro > > On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > >> >> On 4/29/20 5:01 PM, lazaro monteserin wrote: >>> Dear gromacs users, >>> >>> Is there any way to tell gmx mk_angndx to create the index file with >>> dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g >> 1, >>> 2, 3) from my molecule? >> mk_angndx is designed for distributions of similar angles (e.g. >> evaluating force field sampling). If you want to compute specific >> angles, use make_ndx or simply write the index groups by hand. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalemkul at vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Thu Apr 30 02:03:14 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 30 Apr 2020 00:03:14 -0000 Subject: [gmx-users] Invalid atomtype format (Justin Lemkul) In-Reply-To: References: Message-ID: <97a61f3c-3ac4-1cfd-72a7-6c61e61f199f@vt.edu> On 4/29/20 7:41 PM, Sadaf Rani wrote: > Dear Justin > I have shared the files for the users mailing list on the following link. > > https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Remove the blank lines from the end of atomtypes.atp and it works fine. Note that you should not be including LJ parameters in atomtypes.atp. Those are for ffnonbonded.itp. The atomtypes.atp file needs only the atom type and its mass as it is only used by pdb2gmx. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From no-reply at dropbox.com Thu Apr 30 12:47:43 2020 From: no-reply at dropbox.com (sadaf rani (via Dropbox)) Date: Thu, 30 Apr 2020 10:47:43 -0000 Subject: [gmx-users] =?utf-8?q?sadaf_rani_shared_=22atomtypes=2Eatp=22_wit?= =?utf-8?q?h_you?= Message-ID: <01010171cab2f95c-a6267c8a-f5f7-4b18-870a-847cc410137c-000000@us-west-2.amazonses.com> Hi there, sadaf rani (sadafrani6 at gmail.com) invited you to view the file " atomtypes.atp " on Dropbox. View file[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AAAIBx-k4_EsQMbDJFMeRpw1_H3zSXzzlgk From sadafrani6 at gmail.com Thu Apr 30 13:10:53 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 30 Apr 2020 11:10:53 -0000 Subject: [gmx-users] Invalid atomtype format (Justin Lemkul Message-ID: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 Thanks. Sadaf From jalemkul at vt.edu Thu Apr 30 16:17:08 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 30 Apr 2020 14:17:08 -0000 Subject: [gmx-users] Invalid atomtype format (Justin Lemkul In-Reply-To: References: Message-ID: <15169971-8b42-e743-1874-88720ba5b195@vt.edu> On 4/30/20 7:10 AM, Sadaf Rani wrote: > Dear Justin > > I have removed the blank lines but getting a new warning while doing gmx > pdb2gmx:- > > WARNING: Duplicate line found in or between hackblock and rtp entries > > I am not getting what else is wrong. Could you please help me to figure out. > I have shared the file on the following link:- > https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 There's a lot to go through here with multiple ligands so I'm not going to be able to go through your files line-by-line. You have duplicate bond entries somewhere. Make your system simpler. Run *only* one ligand at a time through pdb2gmx to figure out which one is triggering the problem. Also note that you should remove the extraneous number 1 from all your [ bonds ] lines in your .rtp entries. They're going to lead to incorrect format in the resulting topology. Just specify the pairs of atoms that are bonded. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From paul.bauer.q at gmail.com Thu Apr 30 19:02:20 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Thu, 30 Apr 2020 17:02:20 -0000 Subject: [gmx-users] GROMACS 2020.2 patch release available Message-ID: Hi GROMACS users, The official release of GROMACS 2020.2 is available! This second patch release again fixes issues found since the initial release of GROMACS 2020 and the release of 2020.1. We encourage all users of the 2020 series to update to 2020.2. Please see the link to the release notes below for more details. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz Documentation: http://manual.gromacs.org/2020.2/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.2.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From lamonteserincastanedo at gmail.com Thu Apr 30 20:07:50 2020 From: lamonteserincastanedo at gmail.com (lazaro monteserin) Date: Thu, 30 Apr 2020 18:07:50 -0000 Subject: [gmx-users] about how to create angle.index with specific angles In-Reply-To: <55b50eff-d7a6-e899-09a7-3d8c296fec7b@vt.edu> References: <55b50eff-d7a6-e899-09a7-3d8c296fec7b@vt.edu> Message-ID: Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > On 4/29/20 7:11 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul it could be possible use that angle.index with the > selected > > dihedrals written by hand as index file for gmx angle for dihedral > > Principal Component Analysis? > > You can create index groups however you like for whatever analysis you > want to perform. > > -Justin > > > Kindly, > > Lazaro > > > > On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 5:01 PM, lazaro monteserin wrote: > >>> Dear gromacs users, > >>> > >>> Is there any way to tell gmx mk_angndx to create the index file with > >>> dihedral angles from a (.tpr) for specific atom numbers (atom level, > e.g > >> 1, > >>> 2, 3) from my molecule? > >> mk_angndx is designed for distributions of similar angles (e.g. > >> evaluating force field sampling). If you want to compute specific > >> angles, use make_ndx or simply write the index groups by hand. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. >