From dburns at iastate.edu Sat Feb 1 00:23:35 2020 From: dburns at iastate.edu (Daniel Burns) Date: Fri, 31 Jan 2020 23:23:35 -0000 Subject: [gmx-users] Energy plots for specific atoms/selections Message-ID: Hi, I want to get an xvg file that will show me the LJ, Coulomb, and dihedral energies on a specific set of atoms. I've tried passing a .dat file with the groups of atoms from gmx select to gmx enemat but I get an error message saying that I must not have included those groups in my mdp file. How do I incorporate them into my mdp file if I don't want specific mdp options to work on them? I cannot figure out how to retrieve the data on my groups of interest. I've tried -rerun and included an index of the atoms of interest as well If anybody has a detailed explanation, I would be grateful. Thank you, Dan From atbfiles at zoho.com Sat Feb 1 05:01:43 2020 From: atbfiles at zoho.com (atb files) Date: Sat, 01 Feb 2020 04:01:43 -0000 Subject: [gmx-users] Charmm to Gromacs itps In-Reply-To: References: <16fe66a04c4.ad66ab4a133765.8415873409923566678@zoho.com> <4f014a17-e2ff-e32a-2228-1e44003ab325@vt.edu> <16feb4a73eb.c6617426182519.3166466143215009082@zoho.com> <16ffbc72a17.111f0d4f9117465.6369411725928786093@zoho.com> Message-ID: <16ffee92d79.b17dd925145762.697791105836382434@zoho.com> @Justin, thank you Justin. I will give it a try then.?@Miro, sure, I will look into it, thank you.?- Yogesh---- On Fri, 31 Jan 2020 20:24:36 +0530 Miro Astore wrote ----Would topotools in vmd not work in this context? I haven't used it but readabout it recently and it would seem this is the use case. Of course youalso need parameters. Wondering.Best, MiroLe sam. 1 f?vr. 2020 ? 00:55, Justin Lemkul a ?crit :>>> On 1/31/20 8:25 AM, atb files wrote:> >> >> >> > The files are given on the following server:> https://terpconnect.umd.edu/~jbklauda/memb.htmlThey have simulated> systems using NAMD.>> If the individual topologies are not available anywhere, just a PSF,> then you will have to write your own converter program to transform the> PSF into GROMACS .top format. PSF is very verbose so this should be> straightforward.>> -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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From yogesh.rma13 at gmail.com Sat Feb 1 11:05:34 2020 From: yogesh.rma13 at gmail.com (Yogesh Sharma) Date: Sat, 01 Feb 2020 10:05:34 -0000 Subject: [gmx-users] Protein pore collapse during simulation. Message-ID: sir, in efforts to find out the differences in the density of bilayers generated by charmm and gromac(berger lipids) i used grid-mat. there are significant differences in area per lipid. with these settings for both systems: override_vectors 5.2,10.0,6.9 grid 20 conserve_ratio yes protein yes precision 1.3 P_value 5.0 #Lower Z limit: 3.036 Upper Z limit: 7.784 charmm with hydrogen (sq. A) area per lipid upper leaflet: 10.5 area per lipid bottom leaflet 5.45 charmm (bilayer saved without hydrogen) (sq. A) area per lipid upper leaflet: 13 area per lipid bottom leaflet 7 gromac (sq. A) area per lipid upper leaflet: 70 area per lipid bottom leaflet 68 Are charmm values below experimental observation for POPC i.e gelation of bilayer? From shradheyagupta at gmail.com Sat Feb 1 19:36:13 2020 From: shradheyagupta at gmail.com (Shradheya R.R. Gupta) Date: Sat, 01 Feb 2020 18:36:13 -0000 Subject: [gmx-users] All atom force filed v/s united atom force filed. Message-ID: Dear researchers, What are the differences, merits and demerits of all atom force field and united atom force field over each other? Which force field is more relevant today? Thank you Shradheya R.R. Gupta DBT-BIF Researcher University of Rajasthan India From shradheyagupta at gmail.com Sat Feb 1 19:36:13 2020 From: shradheyagupta at gmail.com (Shradheya R.R. Gupta) Date: Sat, 01 Feb 2020 18:36:13 -0000 Subject: [gmx-users] All atom force filed v/s united atom force filed. Message-ID: Dear researchers, What are the differences, merits and demerits of all atom force field and united atom force field over each other? Which force field is more relevant today? Thank you Shradheya R.R. Gupta DBT-BIF Researcher University of Rajasthan India From tuk04130 at temple.edu Sat Feb 1 22:20:53 2020 From: tuk04130 at temple.edu (Lei Qian) Date: Sat, 01 Feb 2020 21:20:53 -0000 Subject: [gmx-users] question on dihedrals propers func 3 and impropers func 1 Message-ID: Dear users, Could I ask a question on dihedrals func types? Thanks! I used acpype to convert prmtop file and inpcrd file into gromacs files. However, in new generated top file, The dihedrals propers func is 3. and The dihedrals impropers func is 1. These two func types are different from propers func 9 and impropers func 4. (func type 9 and func type 4 can be found in Gromacs documents). Could I ask the meaning of func type 3 and func type 1 ? Thanks! Lei From alfredo at ices.utexas.edu Sun Feb 2 16:39:25 2020 From: alfredo at ices.utexas.edu (Cardenas, Alfredo E) Date: Sun, 02 Feb 2020 15:39:25 -0000 Subject: [gmx-users] Getting a high potential energy error when using some specific gpu options. Gromacs 2019.4 Message-ID: Hi, I am testing a new computer system with single nodes containing four GPU?s, for a membrane containing a peptide with numerous restraints. I have read in the gmx_users list that for this kind of systems maybe the more efficient use of a node is to run several simulations on it so I have tried several input options. Anyway, what I show here is an attempt to run a single trajectory on two specific GPUs of a node and using -pme gpu. The command is: mdrun -v -deffnm topolshort -nt 8 -pin on -pinoffset 8 -pinstride 1 -ntmpi 8 -ntomp 1 -npme 1 -pme gpu -gpu_id 23 I obtained the error: Program: mdrun, version 2019.4 Source file: src/gromacs/mdlib/sim_util.cpp (line 752) MPI rank: 6 (out of 8) Fatal error: Step 0: The total potential energy is 1.40845e+15, which is extremely high. The LJ and electrostatic contributions to the energy are 11111.2 and -118338, 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. Link to see the complete log file: https://utexas.box.com/s/eofa6ocil6mp947ahbvvtstt9qhnppsg When I removed ?-npme 1 -pme gpu?, the error doesn?t occur and the trajectory finish normally. What it could be the cause of the error? Thanks, Alfredo From alexmathewmd at gmail.com Sun Feb 2 17:46:29 2020 From: alexmathewmd at gmail.com (Alex Mathew) Date: Sun, 02 Feb 2020 16:46:29 -0000 Subject: [gmx-users] How to add osmotic stress Message-ID: How to introduce osmotic stress on a simulation system to study the transportation differences in varying conditions.( protein-membrane system) From spoel at xray.bmc.uu.se Sun Feb 2 18:52:20 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 02 Feb 2020 17:52:20 -0000 Subject: [gmx-users] How to add osmotic stress In-Reply-To: References: Message-ID: <32921230-1f36-4db9-a4a1-2f5b6d879be9@xray.bmc.uu.se> Den 2020-02-02 kl. 17:46, skrev Alex Mathew: > How to introduce osmotic stress on a simulation system to study the > transportation differences in varying conditions.( protein-membrane system) > Use a double membrane and different concentrations in the water phases. -- 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 From blau at kth.se Mon Feb 3 08:28:46 2020 From: blau at kth.se (Christian Blau) Date: Mon, 03 Feb 2020 07:28:46 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi) In-Reply-To: <001a01d5d80f$8a5df4a0$9f19dde0$@gmail.com> References: <001a01d5d80f$8a5df4a0$9f19dde0$@gmail.com> Message-ID: <533130e5-5ece-066d-fd7b-df70e9b0a50f@kth.se> HI Riccardo, in this case, it's the piping that does not work, so gromacs does not get the right "return". An alternative is printf "10\n12\n" Best, Christian On 2020-01-31 09:22, ric.concu at gmail.com wrote: > Dear all, > > This is an example of a line I have been using on Gromacs 5.0.4:" echo > "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is > the error message I'm receiving from Gromacs: "Error in user input: > Invalid selection '10 12 ' > B Near '12' > B B B syntax error " > Regards, > Riccardo > > -----Original Message----- > 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: jueves, 30 de enero de 2020 23:31 > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: gromacs.org_gmx-users Digest, Vol 189, Issue 80 > > 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. 3D monitors (tarzan p) > 2. Re: Analysis with .sh file (Li, Shi) > 3. Regarding rdf and number of molecules in the FSS of tetramer > (Ashma Khan) > 4. Customize gromac FF for lipid parameters (Yogesh Sharma) > 5. Re: Customize gromac FF for lipid parameters (Justin Lemkul) > 6. Re: gromacs-2020 build gcc/nvcc error (Ryan Woltz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jan 2020 14:23:59 +0000 (UTC) > From: tarzan p > To: "gmx-users at gromacs.org" > Subject: [gmx-users] 3D monitors > Message-ID: <2141569556.1500215.1580394239642 at mail.yahoo.com> > Content-Type: text/plain; charset=UTF-8 > > Hi all..Am looking for some good 3D monitors (either passive or active)Need > suggestions for some good 3D monitors for protein structure and interactions > visualization... > with best wishes > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Jan 2020 09:50:09 -0500 > From: "Li, Shi" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] Analysis with .sh file > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> >> Dear all, >> >> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 >> and I found out that now that while I'm trying to use a .sh, as I was >> doing in the version 5.0.4, now I'm receiving back an error since the >> syntax is wrong. I'm wondering if someone could please help me. >> >> > What is the script in your .sh file? There is not enough information to find > out what goes wrong. > > > >> Regards, >> >> Riccardo >> >> >> >> ------------------------------ >> >> > > ------------------------------ > > Message: 3 > Date: Thu, 30 Jan 2020 20:29:56 +0530 > From: Ashma Khan > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] Regarding rdf and number of molecules in the FSS > of tetramer > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear user's > I have calculated the rdf of urea molecules around the peptides for > different concentration of urea and obtained that peak height of first > solvation shell (FSS) decreases with increase in concentration of urea. > After that I have calculated the number of urea molecules in FSS and found > that urea molecules in the FSS increases with concentration of urea. There > is no correlation between the peak height of FSS and number of urea > molecules. Can anybody suggest me ? what is the reason The command I have > used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com > -seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select > "resname URE and within 0.5 of group protein" -selrpos whole_res_com > -seltype whole_res_com > > > -- > Ashma Khan > Research Scholar > Department of Chemistry > AMU, Aligarh > > > ------------------------------ > > Message: 4 > Date: Fri, 31 Jan 2020 01:32:43 +0530 > From: Yogesh Sharma > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] Customize gromac FF for lipid parameters > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hey everyone, > I have a membrane patch generated by charmm gui. I want to customize my > gromac forcefield in accordance with it. I want some suggestion in > extracting information from charmmff. I guess i need information to add in > ffbonded and ffnonbonded files. Can someone help me with it > > I don't want to run simulations in charmmff > > From alashkov83 at gmail.com Mon Feb 3 12:43:47 2020 From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=) Date: Mon, 03 Feb 2020 11:43:47 -0000 Subject: [gmx-users] FEP calculation with charged species Message-ID: Good afternoon. I calculated the FEP for the ligand-water system and the ligand-protein-lipid bilayer to calculate the free binding energy. I have a ligand with a total charge of +1. Rocklin et al (2013) described corrections for periodic boundary conditions in the case of Ewald summation. However, they either do not introduce counter ions there at all, or compensate only the charge of the protein and consider the case of protein in water. In my initial FEP calculation, the compensating charge balances the ligand charge too. How equivalent is the case described in the article? Can I apply article calculations directly to my case or is it better not to make electrostatic corrections at all? I calculated the values of the ligand solvation energy in the ligand-water system in the absence and in the presence of counterions and obtained similar results. It turns out that the corrections described in the article act in the same way in the case of the initial charge compensation by counterions and in the absence of such compensation? Alex From mailmd2011 at gmail.com Mon Feb 3 16:39:07 2020 From: mailmd2011 at gmail.com (Albert) Date: Mon, 03 Feb 2020 15:39:07 -0000 Subject: [gmx-users] how to generate tng format trajectory? Message-ID: Hello all, I just learned that the tng trajectory format file is even more smaller than the .xtc format file. I am just wondering how shall we specify the option in the .mdp file so that "gmx mdrun" could generate the .tng format trajectory accordingly? thanks a lot albert From Stephane.ABEL at cea.fr Mon Feb 3 16:49:57 2020 From: Stephane.ABEL at cea.fr (ABEL Stephane) Date: Mon, 03 Feb 2020 15:49:57 -0000 Subject: [gmx-users] Some atoms are not properly rotated with gmx_editconf Message-ID: <3E39B768BB199548AB18F7289E7534AF4E47B7FA@EXDAG0-B0.intra.cea.fr> Hello I would like my gramicidin A channel along the z axis. So I use the following commands in a bash script ## Select a group for determining the system size: System : 0 ## Select group for the determining the orientation ! GramicidinA : 15 ## Select a group that you want to align: TRP12_CA_DLEU_32_CA : 16 ## Select a group for output: System : 0 ## Align the Channel along the z axis echo 0 15 16 0 > vector.txt gmx_mpi editconf -f 1JNO_GramicidineA_pep_em_step0.pdb -o 1JNO_GramicidineA_pep_em_step0_reoriented_along_Zaxis.pdb -princ -rotate -0 90 0 -align 0 90 0 -n System.ndx -box 5.0 5.0 5.0 -center 2.5 2.5 2.5 -resnr 1 < vector.txt ## Center the channel mpirun -np 1 gmx_mpi trjconv -f 1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis.pdb -s 1JNO_GramicidineA_pep_em_step0.tpr -pbc mol -ur compact -center -o 1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb -n System.ndx The problem is that the channel is well aligned along the z axis but "not" the TRP12_CA_DLEU_32_CA atoms used for the vector. How to resolve this ? You could download the pdb file (below) and see what I mean with pymol https://www.dropbox.com/s/l5crrpxsy3fak6e/1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb?dl=0 Best regards St?phane From nicolas.goudard at univ-amu.fr Tue Feb 4 00:04:00 2020 From: nicolas.goudard at univ-amu.fr (Nicolas GOUDARD) Date: Mon, 03 Feb 2020 23:04:00 -0000 Subject: [gmx-users] GMX_MPI 2020 Message-ID: Hello I want to install Gromacs 2020 or 2020 beta 1 on centos 8.1 . There is not error when it compiles but when I execute gmx_mpi there is a segmentation fault How can I solve it ? Thanks you Best Regards #cat /etc/redhat-release CentOS Linux release 8.1.1911 (Core) #cat /etc/redhat-release CentOS Linux release 8.1.1911 (Core) [root at alta ~]# [root at alta ~]# cat /usr/share/Modules/modulefiles/gromacs2020_mpi #%Module###################################################################### ## ## gromacs modulefile ## proc ModulesHelp { } { puts stderr "gromacs 2020" return 0 } prepend-path LD_LIBRARY_PATH /share/programs/GROMACS-2020-MPI/lib prepend-path PATH /share/programs/GROMACS-2020-MPI/bin #wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta1.tar.gz #tar xvzf gromacs-2020-beta1.tar.gz #cd gromacs-2020-beta1/ #cmake .. -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/share/programs/GROMACS-2020-MPI -DCMAKE_INSTALL_LIBDIR=/share/programs/GROMACS-2020-MPI/lib -DGMX_USE_RDTSCP=ON #make -j4 #make install #source /share/programs/GROMACS-2020-MPI/bin/GMXRC #module unload gromacs2020_mpi #gmx_mpi [alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768) ==== backtrace ==== 0 /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0] 1 /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a] 2 /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b] 3 /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a] 4 /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a] 5 /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f] 6 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 7 /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae] 8 /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba] 9 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 10 /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093] 11 /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939] 12 /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a] 13 /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05] 14 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16] 15 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a] 16 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce] 17 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2] 18 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915] 19 /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494] 20 /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805] 21 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5] 22 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449] 23 gmx_mpi() [0x4052bb] 24 /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873] 25 gmx_mpi() [0x40538e] =================== Segmentation fault (core dumped) Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Mol?culaires de Marseille Aix-Marseille Universit? - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille T?l: +33(0)4 91 28 82 66 Site : http://www.univ-amu.fr - Email : nicolas.goudard at univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si n?cessaire. From nicolas.goudard at univ-amu.fr Tue Feb 4 00:05:27 2020 From: nicolas.goudard at univ-amu.fr (Nicolas GOUDARD) Date: Mon, 03 Feb 2020 23:05:27 -0000 Subject: [gmx-users] GMX_MPI 2020 Message-ID: <05B17CDA-39F3-47FA-B9CB-D55D111B3CC6@univ-amu.fr> Hello On Gromacs 2020 or 2020 beta 1 on centos 8.1 there is a segmentation fault How can I solve it ? #cat /etc/redhat-release CentOS Linux release 8.1.1911 (Core) #cat /etc/redhat-release CentOS Linux release 8.1.1911 (Core) [root at alta ~]# [root at alta ~]# cat /usr/share/Modules/modulefiles/gromacs2020_mpi #%Module###################################################################### ## ## gromacs modulefile ## proc ModulesHelp { } { puts stderr "gromacs 2020" return 0 } prepend-path LD_LIBRARY_PATH /share/programs/GROMACS-2020-MPI/lib prepend-path PATH /share/programs/GROMACS-2020-MPI/bin #wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta1.tar.gz #tar xvzf gromacs-2020-beta1.tar.gz #cd gromacs-2020-beta1/ #cmake .. -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/share/programs/GROMACS-2020-MPI -DCMAKE_INSTALL_LIBDIR=/share/programs/GROMACS-2020-MPI/lib -DGMX_USE_RDTSCP=ON #make -j4 #make install #source /share/programs/GROMACS-2020-MPI/bin/GMXRC #module unload gromacs2020_mpi #gmx_mpi [alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768) ==== backtrace ==== 0 /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0] 1 /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a] 2 /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b] 3 /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a] 4 /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a] 5 /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f] 6 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 7 /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae] 8 /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba] 9 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 10 /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093] 11 /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939] 12 /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a] 13 /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05] 14 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16] 15 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a] 16 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce] 17 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2] 18 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915] 19 /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494] 20 /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805] 21 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5] 22 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449] 23 gmx_mpi() [0x4052bb] 24 /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873] 25 gmx_mpi() [0x40538e] =================== Segmentation fault (core dumped) Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Mol?culaires de Marseille Aix-Marseille Universit? - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille T?l: +33(0)4 91 28 82 66 Site : http://www.univ-amu.fr - Email : nicolas.goudard at univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si n?cessaire. From miro.astore at gmail.com Tue Feb 4 01:34:19 2020 From: miro.astore at gmail.com (Miro Astore) Date: Tue, 04 Feb 2020 00:34:19 -0000 Subject: [gmx-users] misunderstanding comm-grps Message-ID: Hi everyone, I have tried using comm_grps to try and remove center of mass motion from my system. I used the following configuration comm_grps = non-Protein Protein nstcomm = 100 comm_mode = linear comm_grps = non-Protein Protein refcoord_scaling = com But I still get considerable drift in my protein. Am I misunderstanding what comm is actually doing and I should use the pulling code if I want my protein to stay in the center of the box? Best, Miro From dallas.warren at monash.edu Tue Feb 4 01:45:43 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Tue, 04 Feb 2020 00:45:43 -0000 Subject: [gmx-users] misunderstanding comm-grps In-Reply-To: References: Message-ID: What do you mean by "stay in the center of the box"? Since systems are run using the periodic boundary condition (PBC), what you essentially have is an infinite, repeating box in all directions. And what is the center of that box is entirely arbitrary, you can place it wherever you like. And you can apply that after the completiion of the simulation. See http://manual.gromacs.org/current/user-guide/terminology.html#gmx-pbc The removal of center of mass motion is applied in MDS to avoid the flying ice cube phenomena. That happens when all the molecules lock together into a crystal like structure, hardly moving relative to each other, freezing in place, but the entire group of molecules are moving together (hence the center of mass) at high speed. 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, 4 Feb 2020 at 11:34, Miro Astore wrote: > Hi everyone, > > I have tried using comm_grps to try and remove center of mass motion > from my system. > > I used the following configuration > > comm_grps = non-Protein Protein > nstcomm = 100 > comm_mode = linear > comm_grps = non-Protein Protein > refcoord_scaling = com > > But I still get considerable drift in my protein. Am I > misunderstanding what comm is actually doing and I should use the > pulling code if I want my protein to stay in the center of the box? > > Best, Miro > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Tue Feb 4 06:54:13 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Tue, 04 Feb 2020 05:54:13 -0000 Subject: [gmx-users] Generate the Topology with CGenFF :: Error message - CGenFF versions are not equivalent! :: *.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent! In-Reply-To: References: Message-ID: Dear all, At present the ProDrg server is not functioning properly in generating ligand topology files. How to generate topology files using ProDrg While try to Generate the topology using CGenFF server, it returns following Error message: CGenFF versions are not equivalent! :: 1MD.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent! How to manage this problem? -------------------------------------------------------------- NOTE 1: Code tested with python 2.7.12. Your version: 2.7.15+ (default, Oct 7 2019, 17:39:04) [GCC 7.4.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in 1MD.str : 4.0 --Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: CGenFF versions are not equivalent! NOTE 3: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (54) and top (0) are unequal Usually this means the specified residue name does not match between str and mol2 files ----------------------------------------------------------- From adarsh_p130085bt at nitc.ac.in Tue Feb 4 07:07:36 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Tue, 04 Feb 2020 06:07:36 -0000 Subject: [gmx-users] Generate the Topology with CGenFF :: Error message - CGenFF versions are not equivalent! :: *.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent! In-Reply-To: References: Message-ID: Dear all, At present the ProDrg server is not functioning properly in generating ligand topology files. How to generate topology files using ProDrg While try to Generate the topology with CGenFF server, it returns following Error message: CGenFF versions are not equivalent! :: 1MD.str 4.0 and charmm36-mar2019.ff/forcefield.doc : 4.1 are not equivalent! How to manage this problem? -------------------------------------------------------------- NOTE 1: Code tested with python 2.7.12. Your version: 2.7.15+ (default, Oct 7 2019, 17:39:04) [GCC 7.4.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in 1MD.str : 4.0 --Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: CGenFF versions are not equivalent! NOTE 3: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (54) and top (0) are unequal Usually this means the specified residue name does not match between str and mol2 files ----------------------------------------------------------- From ak543714 at gmail.com Tue Feb 4 07:33:56 2020 From: ak543714 at gmail.com (Amit Kumar) Date: Tue, 04 Feb 2020 06:33:56 -0000 Subject: [gmx-users] Regarding calculation of configurational entropy Message-ID: Dear gromacs user, I am trying to calculate configurational entropy using gmx anaeig of gromacs, I want to plot entropy vs time graph but I am getting following output: eigval[5142] = -9.14879e-07 eigval[5143] = -2.33309e-06 eigval[5144] = -3.50518e-06 eigval[5145] = -4.66171e-06 eigval[5146] = -5.99885e-06 eigval[5147] = -7.11318e-06 eigval[5148] = -8.01442e-06 eigval[5149] = -9.39166e-06 eigval[5150] = -1.04459e-05 eigval[5151] = -1.15148e-05 eigval[5152] = -1.28094e-05 eigval[5153] = -1.3987e-05 eigval[5154] = -1.50665e-05 eigval[5155] = -1.6175e-05 eigval[5156] = -1.73784e-05 eigval[5157] = -1.83775e-05 eigval[5158] = -1.96176e-05 eigval[5159] = -2.05775e-05 eigval[5160] = -2.16381e-05 eigval[5161] = -2.28186e-05 eigval[5162] = -2.41095e-05 eigval[5163] = -2.50757e-05 eigval[5164] = -2.62638e-05 eigval[5165] = -2.72389e-05 eigval[5166] = -2.81506e-05 eigval[5167] = -2.9425e-05 eigval[5168] = -3.03292e-05 eigval[5169] = -3.13687e-05 eigval[5170] = -3.26255e-05 eigval[5171] = -3.35174e-05 eigval[5172] = -3.45212e-05 eigval[5173] = -3.58501e-05 eigval[5174] = -3.6593e-05 eigval[5175] = -3.76517e-05 eigval[5176] = -3.89211e-05 eigval[5177] = -3.96407e-05 eigval[5178] = -4.06224e-05 eigval[5179] = -4.15366e-05 eigval[5180] = -4.28279e-05 eigval[5181] = -4.3513e-05 eigval[5182] = -4.45138e-05 eigval[5183] = -4.562e-05 eigval[5184] = -4.65709e-05 eigval[5185] = -4.76809e-05 eigval[5186] = -4.86234e-05 eigval[5187] = -4.92399e-05 eigval[5188] = -5.05317e-05 eigval[5189] = -5.15467e-05 eigval[5190] = -5.22315e-05 eigval[5191] = -5.34672e-05 eigval[5192] = -5.43978e-05 eigval[5193] = -5.51698e-05 eigval[5194] = -5.61273e-05 eigval[5195] = -5.69449e-05 eigval[5196] = -5.79809e-05 eigval[5197] = -5.89205e-05 eigval[5198] = -5.97684e-05 eigval[5199] = -6.03984e-05 eigval[5200] = -6.12329e-05 eigval[5201] = -6.2341e-05 eigval[5202] = -6.314e-05 eigval[5203] = -6.40677e-05 eigval[5204] = -6.48297e-05 eigval[5205] = -6.57083e-05 eigval[5206] = -6.69065e-05 eigval[5207] = -6.75107e-05 eigval[5208] = -6.84447e-05 eigval[5209] = -6.91988e-05 eigval[5210] = -6.99852e-05 eigval[5211] = -7.08491e-05 eigval[5212] = -7.12099e-05 eigval[5213] = -7.14211e-05 eigval[5214] = -7.24288e-05 eigval[5215] = -7.24905e-05 eigval[5216] = -7.34137e-05 eigval[5217] = -7.40195e-05 eigval[5218] = -7.48026e-05 eigval[5219] = -7.54402e-05 eigval[5220] = -7.63235e-05 eigval[5221] = -7.65044e-05 eigval[5222] = -7.70526e-05 eigval[5223] = -7.77833e-05 eigval[5224] = -7.84475e-05 eigval[5225] = -7.94353e-05 eigval[5226] = -8.03098e-05 eigval[5227] = -8.08805e-05 eigval[5228] = -8.1798e-05 eigval[5229] = -8.24363e-05 eigval[5230] = -8.30689e-05 eigval[5231] = -8.37781e-05 eigval[5232] = -8.47785e-05 eigval[5233] = -8.51702e-05 eigval[5234] = -8.5924e-05 eigval[5235] = -8.6987e-05 eigval[5236] = -8.74341e-05 eigval[5237] = -8.79993e-05 eigval[5238] = -8.85487e-05 eigval[5239] = -8.93534e-05 eigval[5240] = -9.02589e-05 eigval[5241] = -9.09801e-05 eigval[5242] = -9.13512e-05 eigval[5243] = -9.19218e-05 eigval[5244] = -9.25432e-05 eigval[5245] = -9.31305e-05 eigval[5246] = -9.3984e-05 eigval[5247] = -9.45856e-05 eigval[5248] = -9.5029e-05 eigval[5249] = -9.58923e-05 eigval[5250] = -9.66012e-05 eigval[5251] = -9.69965e-05 eigval[5252] = -9.73971e-05 eigval[5253] = -9.80373e-05 eigval[5254] = -9.87206e-05 eigval[5255] = -9.92092e-05 eigval[5256] = -9.99034e-05 eigval[5257] = -0.000100159 eigval[5258] = -0.000100874 eigval[5259] = -0.000101257 eigval[5260] = -0.000101832 eigval[5261] = -0.000102451 eigval[5262] = -0.000102838 eigval[5263] = -0.000103337 eigval[5264] = -0.000103816 eigval[5265] = -0.000104062 eigval[5266] = -0.000104524 eigval[5267] = -0.00010504 eigval[5268] = -0.000105673 eigval[5269] = -0.000105892 eigval[5270] = -0.000106473 eigval[5271] = -0.000107099 eigval[5272] = -0.000107394 eigval[5273] = -0.000107771 eigval[5274] = -0.000108434 eigval[5275] = -0.000108798 eigval[5276] = -0.000108992 eigval[5277] = -0.000109278 eigval[5278] = -0.000109677 eigval[5279] = -0.000110072 eigval[5280] = -0.000110326 eigval[5281] = -0.000110964 eigval[5282] = -0.000111025 eigval[5283] = -0.000111309 eigval[5284] = -0.000112023 eigval[5285] = -0.000112365 eigval[5286] = -0.00011257 eigval[5287] = -0.000112921 eigval[5288] = -0.000113374 eigval[5289] = -0.000113933 eigval[5290] = -0.000114647 eigval[5291] = -0.000115405 eigval[5292] = -0.000115669 eigval[5293] = -0.00011589 eigval[5294] = -0.000116295 eigval[5295] = -0.000116993 eigval[5296] = -0.000117111 eigval[5297] = -0.000117667 eigval[5298] = -0.000118582 eigval[5299] = -0.00011872 eigval[5300] = -0.000118885 eigval[5301] = -0.000119334 eigval[5302] = -0.000120538 eigval[5303] = -0.00012068 eigval[5304] = -0.000121256 eigval[5305] = -0.00012141 eigval[5306] = -0.000122242 eigval[5307] = -0.000122789 eigval[5308] = -0.000123013 eigval[5309] = -0.000123817 eigval[5310] = -0.000124575 eigval[5311] = -0.000124866 eigval[5312] = -0.000125117 eigval[5313] = -0.000126223 eigval[5314] = -0.00012707 eigval[5315] = -0.000127687 eigval[5316] = -0.000127919 eigval[5317] = -0.000128714 eigval[5318] = -0.000129043 eigval[5319] = -0.00012939 eigval[5320] = -0.000129535 eigval[5321] = -0.000130664 eigval[5322] = -0.000131691 eigval[5323] = -0.000132264 eigval[5324] = -0.000133152 eigval[5325] = -0.00013381 eigval[5326] = -0.000134219 eigval[5327] = -0.000135764 eigval[5328] = -0.000136149 eigval[5329] = -0.000138551 eigval[5330] = -0.000138698 eigval[5331] = -0.000139432 eigval[5332] = -0.000139957 eigval[5333] = -0.000140624 eigval[5334] = -0.000141187 eigval[5335] = -0.000141866 eigval[5336] = -0.000143352 eigval[5337] = -0.000143514 eigval[5338] = -0.000145445 eigval[5339] = -0.000146802 eigval[5340] = -0.00014872 eigval[5341] = -0.000149065 eigval[5342] = -0.000150165 eigval[5343] = -0.000150618 eigval[5344] = -0.000152546 eigval[5345] = -0.000154182 eigval[5346] = -0.000154271 eigval[5347] = -0.000156094 eigval[5348] = -0.00015781 eigval[5349] = -0.000158271 eigval[5350] = -0.00015992 eigval[5351] = -0.000162788 eigval[5352] = -0.000163307 eigval[5353] = -0.000166183 eigval[5354] = -0.000169429 eigval[5355] = -0.000172062 eigval[5356] = -0.000173377 eigval[5357] = -0.000173442 eigval[5358] = -0.000175975 eigval[5359] = -0.000179223 eigval[5360] = -0.000181775 eigval[5361] = -0.000183321 eigval[5362] = -0.000185641 eigval[5363] = -0.000193632 eigval[5364] = -0.000194667 eigval[5365] = -0.000232906 eigval[5366] = -0.000255899 The Entropy due to the Quasi Harmonic approximation is 27848.4 J/mol K The Entropy due to the Schlitter formula is nan J/mol K Exact command I used was: gmx anaeig -f nojumpcent1_41.xtc -v eig_heav_atom.trr -entropy -temp 298 -s prod1.tpr -n protein-H.ndx -comp eig_comp.xvg -rmsf eig_rmsf.xvg -proj eig_proj.xvg -2d 2deig_proj.xvg -b 0 -e 530000 before this I had used, gmx covar -f nojumpcent1_41.xtc -s prod1.tpr -o eig_heav_atom1.xvg -v eig_heav_atom1.trr -ascii eig_heav_atom1.dat to get covariance matrix (I had also tried calculating mass weighted covariance but gmx anaeig didn't run with it). I selected Protein-H for least square fit and covariance analysis. Can you help me to understand what is going on here and if I made mistakes then what it is? Thank You Amit Kumar From ak543714 at gmail.com Tue Feb 4 07:33:57 2020 From: ak543714 at gmail.com (Amit Kumar) Date: Tue, 04 Feb 2020 06:33:57 -0000 Subject: [gmx-users] Regarding calculation of configurational entropy Message-ID: Dear gromacs user, I am trying to calculate configurational entropy using gmx anaeig of gromacs, I want to plot entropy vs time graph but I am getting following output: eigval[5142] = -9.14879e-07 eigval[5143] = -2.33309e-06 eigval[5144] = -3.50518e-06 eigval[5145] = -4.66171e-06 eigval[5146] = -5.99885e-06 eigval[5147] = -7.11318e-06 eigval[5148] = -8.01442e-06 eigval[5149] = -9.39166e-06 eigval[5150] = -1.04459e-05 eigval[5151] = -1.15148e-05 eigval[5152] = -1.28094e-05 eigval[5153] = -1.3987e-05 eigval[5154] = -1.50665e-05 eigval[5155] = -1.6175e-05 eigval[5156] = -1.73784e-05 eigval[5157] = -1.83775e-05 eigval[5158] = -1.96176e-05 eigval[5159] = -2.05775e-05 eigval[5160] = -2.16381e-05 eigval[5161] = -2.28186e-05 eigval[5162] = -2.41095e-05 eigval[5163] = -2.50757e-05 eigval[5164] = -2.62638e-05 eigval[5165] = -2.72389e-05 eigval[5166] = -2.81506e-05 eigval[5167] = -2.9425e-05 eigval[5168] = -3.03292e-05 eigval[5169] = -3.13687e-05 eigval[5170] = -3.26255e-05 eigval[5171] = -3.35174e-05 eigval[5172] = -3.45212e-05 eigval[5173] = -3.58501e-05 eigval[5174] = -3.6593e-05 eigval[5175] = -3.76517e-05 eigval[5176] = -3.89211e-05 eigval[5177] = -3.96407e-05 eigval[5178] = -4.06224e-05 eigval[5179] = -4.15366e-05 eigval[5180] = -4.28279e-05 eigval[5181] = -4.3513e-05 eigval[5182] = -4.45138e-05 eigval[5183] = -4.562e-05 eigval[5184] = -4.65709e-05 eigval[5185] = -4.76809e-05 eigval[5186] = -4.86234e-05 eigval[5187] = -4.92399e-05 eigval[5188] = -5.05317e-05 eigval[5189] = -5.15467e-05 eigval[5190] = -5.22315e-05 eigval[5191] = -5.34672e-05 eigval[5192] = -5.43978e-05 eigval[5193] = -5.51698e-05 eigval[5194] = -5.61273e-05 eigval[5195] = -5.69449e-05 eigval[5196] = -5.79809e-05 eigval[5197] = -5.89205e-05 eigval[5198] = -5.97684e-05 eigval[5199] = -6.03984e-05 eigval[5200] = -6.12329e-05 eigval[5201] = -6.2341e-05 eigval[5202] = -6.314e-05 eigval[5203] = -6.40677e-05 eigval[5204] = -6.48297e-05 eigval[5205] = -6.57083e-05 eigval[5206] = -6.69065e-05 eigval[5207] = -6.75107e-05 eigval[5208] = -6.84447e-05 eigval[5209] = -6.91988e-05 eigval[5210] = -6.99852e-05 eigval[5211] = -7.08491e-05 eigval[5212] = -7.12099e-05 eigval[5213] = -7.14211e-05 eigval[5214] = -7.24288e-05 eigval[5215] = -7.24905e-05 eigval[5216] = -7.34137e-05 eigval[5217] = -7.40195e-05 eigval[5218] = -7.48026e-05 eigval[5219] = -7.54402e-05 eigval[5220] = -7.63235e-05 eigval[5221] = -7.65044e-05 eigval[5222] = -7.70526e-05 eigval[5223] = -7.77833e-05 eigval[5224] = -7.84475e-05 eigval[5225] = -7.94353e-05 eigval[5226] = -8.03098e-05 eigval[5227] = -8.08805e-05 eigval[5228] = -8.1798e-05 eigval[5229] = -8.24363e-05 eigval[5230] = -8.30689e-05 eigval[5231] = -8.37781e-05 eigval[5232] = -8.47785e-05 eigval[5233] = -8.51702e-05 eigval[5234] = -8.5924e-05 eigval[5235] = -8.6987e-05 eigval[5236] = -8.74341e-05 eigval[5237] = -8.79993e-05 eigval[5238] = -8.85487e-05 eigval[5239] = -8.93534e-05 eigval[5240] = -9.02589e-05 eigval[5241] = -9.09801e-05 eigval[5242] = -9.13512e-05 eigval[5243] = -9.19218e-05 eigval[5244] = -9.25432e-05 eigval[5245] = -9.31305e-05 eigval[5246] = -9.3984e-05 eigval[5247] = -9.45856e-05 eigval[5248] = -9.5029e-05 eigval[5249] = -9.58923e-05 eigval[5250] = -9.66012e-05 eigval[5251] = -9.69965e-05 eigval[5252] = -9.73971e-05 eigval[5253] = -9.80373e-05 eigval[5254] = -9.87206e-05 eigval[5255] = -9.92092e-05 eigval[5256] = -9.99034e-05 eigval[5257] = -0.000100159 eigval[5258] = -0.000100874 eigval[5259] = -0.000101257 eigval[5260] = -0.000101832 eigval[5261] = -0.000102451 eigval[5262] = -0.000102838 eigval[5263] = -0.000103337 eigval[5264] = -0.000103816 eigval[5265] = -0.000104062 eigval[5266] = -0.000104524 eigval[5267] = -0.00010504 eigval[5268] = -0.000105673 eigval[5269] = -0.000105892 eigval[5270] = -0.000106473 eigval[5271] = -0.000107099 eigval[5272] = -0.000107394 eigval[5273] = -0.000107771 eigval[5274] = -0.000108434 eigval[5275] = -0.000108798 eigval[5276] = -0.000108992 eigval[5277] = -0.000109278 eigval[5278] = -0.000109677 eigval[5279] = -0.000110072 eigval[5280] = -0.000110326 eigval[5281] = -0.000110964 eigval[5282] = -0.000111025 eigval[5283] = -0.000111309 eigval[5284] = -0.000112023 eigval[5285] = -0.000112365 eigval[5286] = -0.00011257 eigval[5287] = -0.000112921 eigval[5288] = -0.000113374 eigval[5289] = -0.000113933 eigval[5290] = -0.000114647 eigval[5291] = -0.000115405 eigval[5292] = -0.000115669 eigval[5293] = -0.00011589 eigval[5294] = -0.000116295 eigval[5295] = -0.000116993 eigval[5296] = -0.000117111 eigval[5297] = -0.000117667 eigval[5298] = -0.000118582 eigval[5299] = -0.00011872 eigval[5300] = -0.000118885 eigval[5301] = -0.000119334 eigval[5302] = -0.000120538 eigval[5303] = -0.00012068 eigval[5304] = -0.000121256 eigval[5305] = -0.00012141 eigval[5306] = -0.000122242 eigval[5307] = -0.000122789 eigval[5308] = -0.000123013 eigval[5309] = -0.000123817 eigval[5310] = -0.000124575 eigval[5311] = -0.000124866 eigval[5312] = -0.000125117 eigval[5313] = -0.000126223 eigval[5314] = -0.00012707 eigval[5315] = -0.000127687 eigval[5316] = -0.000127919 eigval[5317] = -0.000128714 eigval[5318] = -0.000129043 eigval[5319] = -0.00012939 eigval[5320] = -0.000129535 eigval[5321] = -0.000130664 eigval[5322] = -0.000131691 eigval[5323] = -0.000132264 eigval[5324] = -0.000133152 eigval[5325] = -0.00013381 eigval[5326] = -0.000134219 eigval[5327] = -0.000135764 eigval[5328] = -0.000136149 eigval[5329] = -0.000138551 eigval[5330] = -0.000138698 eigval[5331] = -0.000139432 eigval[5332] = -0.000139957 eigval[5333] = -0.000140624 eigval[5334] = -0.000141187 eigval[5335] = -0.000141866 eigval[5336] = -0.000143352 eigval[5337] = -0.000143514 eigval[5338] = -0.000145445 eigval[5339] = -0.000146802 eigval[5340] = -0.00014872 eigval[5341] = -0.000149065 eigval[5342] = -0.000150165 eigval[5343] = -0.000150618 eigval[5344] = -0.000152546 eigval[5345] = -0.000154182 eigval[5346] = -0.000154271 eigval[5347] = -0.000156094 eigval[5348] = -0.00015781 eigval[5349] = -0.000158271 eigval[5350] = -0.00015992 eigval[5351] = -0.000162788 eigval[5352] = -0.000163307 eigval[5353] = -0.000166183 eigval[5354] = -0.000169429 eigval[5355] = -0.000172062 eigval[5356] = -0.000173377 eigval[5357] = -0.000173442 eigval[5358] = -0.000175975 eigval[5359] = -0.000179223 eigval[5360] = -0.000181775 eigval[5361] = -0.000183321 eigval[5362] = -0.000185641 eigval[5363] = -0.000193632 eigval[5364] = -0.000194667 eigval[5365] = -0.000232906 eigval[5366] = -0.000255899 The Entropy due to the Quasi Harmonic approximation is 27848.4 J/mol K The Entropy due to the Schlitter formula is nan J/mol K Exact command I used was: gmx anaeig -f nojumpcent1_41.xtc -v eig_heav_atom.trr -entropy -temp 298 -s prod1.tpr -n protein-H.ndx -comp eig_comp.xvg -rmsf eig_rmsf.xvg -proj eig_proj.xvg -2d 2deig_proj.xvg -b 0 -e 530000 before this I had used, gmx covar -f nojumpcent1_41.xtc -s prod1.tpr -o eig_heav_atom1.xvg -v eig_heav_atom1.trr -ascii eig_heav_atom1.dat to get covariance matrix (I had also tried calculating mass weighted covariance but gmx anaeig didn't run with it). I selected Protein-H for least square fit and covariance analysis. Can you help me to understand what is going on here and if I made mistakes then what it is? Thank You Amit Kumar From adarsh_p130085bt at nitc.ac.in Tue Feb 4 07:41:34 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Tue, 04 Feb 2020 06:41:34 -0000 Subject: [gmx-users] Generate the Topology with CGenFF :: Error message Message-ID: Dear all, At present the ProDrg server is not functioning properly in generating ligand topology files. How to generate topology files using ProDrg While try to Generate the topology with CGenFF server, it returns following Error message How to manage this problem? -------------------------------------------------------------- NOTE 1: Code tested with python 2.7.12. Your version: 2.7.15+ (default, Oct 7 2019, 17:39:04) [GCC 7.4.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in 1MD19DB00931.str : 3.0.1 --Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: CGenFF versions are not equivalent! NOTE 3: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (54) and top (0) are unequal Usually this means the specified residue name does not match between str and mol2 files ----------------------------------------------------------- From spoel at xray.bmc.uu.se Tue Feb 4 09:16:18 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 04 Feb 2020 08:16:18 -0000 Subject: [gmx-users] Regarding calculation of configurational entropy In-Reply-To: References: Message-ID: Den 2020-02-04 kl. 07:33, skrev Amit Kumar: > Dear gromacs user, > I am trying to calculate configurational entropy using gmx anaeig of > gromacs, I want to plot entropy vs time graph but I am getting following > output: > eigval[5142] = -9.14879e-07 > eigval[5143] = -2.33309e-06 > eigval[5144] = -3.50518e-06 > eigval[5145] = -4.66171e-06 > eigval[5146] = -5.99885e-06 > eigval[5147] = -7.11318e-06 > eigval[5148] = -8.01442e-06 > eigval[5149] = -9.39166e-06 > eigval[5150] = -1.04459e-05 > eigval[5151] = -1.15148e-05 > eigval[5152] = -1.28094e-05 > eigval[5153] = -1.3987e-05 > eigval[5154] = -1.50665e-05 > eigval[5155] = -1.6175e-05 > eigval[5156] = -1.73784e-05 > eigval[5157] = -1.83775e-05 > eigval[5158] = -1.96176e-05 > eigval[5159] = -2.05775e-05 > eigval[5160] = -2.16381e-05 > eigval[5161] = -2.28186e-05 > eigval[5162] = -2.41095e-05 > eigval[5163] = -2.50757e-05 > eigval[5164] = -2.62638e-05 > eigval[5165] = -2.72389e-05 > eigval[5166] = -2.81506e-05 > eigval[5167] = -2.9425e-05 > eigval[5168] = -3.03292e-05 > eigval[5169] = -3.13687e-05 > eigval[5170] = -3.26255e-05 > eigval[5171] = -3.35174e-05 > eigval[5172] = -3.45212e-05 > eigval[5173] = -3.58501e-05 > eigval[5174] = -3.6593e-05 > eigval[5175] = -3.76517e-05 > eigval[5176] = -3.89211e-05 > eigval[5177] = -3.96407e-05 > eigval[5178] = -4.06224e-05 > eigval[5179] = -4.15366e-05 > eigval[5180] = -4.28279e-05 > eigval[5181] = -4.3513e-05 > eigval[5182] = -4.45138e-05 > eigval[5183] = -4.562e-05 > eigval[5184] = -4.65709e-05 > eigval[5185] = -4.76809e-05 > eigval[5186] = -4.86234e-05 > eigval[5187] = -4.92399e-05 > eigval[5188] = -5.05317e-05 > eigval[5189] = -5.15467e-05 > eigval[5190] = -5.22315e-05 > eigval[5191] = -5.34672e-05 > eigval[5192] = -5.43978e-05 > eigval[5193] = -5.51698e-05 > eigval[5194] = -5.61273e-05 > eigval[5195] = -5.69449e-05 > eigval[5196] = -5.79809e-05 > eigval[5197] = -5.89205e-05 > eigval[5198] = -5.97684e-05 > eigval[5199] = -6.03984e-05 > eigval[5200] = -6.12329e-05 > eigval[5201] = -6.2341e-05 > eigval[5202] = -6.314e-05 > eigval[5203] = -6.40677e-05 > eigval[5204] = -6.48297e-05 > eigval[5205] = -6.57083e-05 > eigval[5206] = -6.69065e-05 > eigval[5207] = -6.75107e-05 > eigval[5208] = -6.84447e-05 > eigval[5209] = -6.91988e-05 > eigval[5210] = -6.99852e-05 > eigval[5211] = -7.08491e-05 > eigval[5212] = -7.12099e-05 > eigval[5213] = -7.14211e-05 > eigval[5214] = -7.24288e-05 > eigval[5215] = -7.24905e-05 > eigval[5216] = -7.34137e-05 > eigval[5217] = -7.40195e-05 > eigval[5218] = -7.48026e-05 > eigval[5219] = -7.54402e-05 > eigval[5220] = -7.63235e-05 > eigval[5221] = -7.65044e-05 > eigval[5222] = -7.70526e-05 > eigval[5223] = -7.77833e-05 > eigval[5224] = -7.84475e-05 > eigval[5225] = -7.94353e-05 > eigval[5226] = -8.03098e-05 > eigval[5227] = -8.08805e-05 > eigval[5228] = -8.1798e-05 > eigval[5229] = -8.24363e-05 > eigval[5230] = -8.30689e-05 > eigval[5231] = -8.37781e-05 > eigval[5232] = -8.47785e-05 > eigval[5233] = -8.51702e-05 > eigval[5234] = -8.5924e-05 > eigval[5235] = -8.6987e-05 > eigval[5236] = -8.74341e-05 > eigval[5237] = -8.79993e-05 > eigval[5238] = -8.85487e-05 > eigval[5239] = -8.93534e-05 > eigval[5240] = -9.02589e-05 > eigval[5241] = -9.09801e-05 > eigval[5242] = -9.13512e-05 > eigval[5243] = -9.19218e-05 > eigval[5244] = -9.25432e-05 > eigval[5245] = -9.31305e-05 > eigval[5246] = -9.3984e-05 > eigval[5247] = -9.45856e-05 > eigval[5248] = -9.5029e-05 > eigval[5249] = -9.58923e-05 > eigval[5250] = -9.66012e-05 > eigval[5251] = -9.69965e-05 > eigval[5252] = -9.73971e-05 > eigval[5253] = -9.80373e-05 > eigval[5254] = -9.87206e-05 > eigval[5255] = -9.92092e-05 > eigval[5256] = -9.99034e-05 > eigval[5257] = -0.000100159 > eigval[5258] = -0.000100874 > eigval[5259] = -0.000101257 > eigval[5260] = -0.000101832 > eigval[5261] = -0.000102451 > eigval[5262] = -0.000102838 > eigval[5263] = -0.000103337 > eigval[5264] = -0.000103816 > eigval[5265] = -0.000104062 > eigval[5266] = -0.000104524 > eigval[5267] = -0.00010504 > eigval[5268] = -0.000105673 > eigval[5269] = -0.000105892 > eigval[5270] = -0.000106473 > eigval[5271] = -0.000107099 > eigval[5272] = -0.000107394 > eigval[5273] = -0.000107771 > eigval[5274] = -0.000108434 > eigval[5275] = -0.000108798 > eigval[5276] = -0.000108992 > eigval[5277] = -0.000109278 > eigval[5278] = -0.000109677 > eigval[5279] = -0.000110072 > eigval[5280] = -0.000110326 > eigval[5281] = -0.000110964 > eigval[5282] = -0.000111025 > eigval[5283] = -0.000111309 > eigval[5284] = -0.000112023 > eigval[5285] = -0.000112365 > eigval[5286] = -0.00011257 > eigval[5287] = -0.000112921 > eigval[5288] = -0.000113374 > eigval[5289] = -0.000113933 > eigval[5290] = -0.000114647 > eigval[5291] = -0.000115405 > eigval[5292] = -0.000115669 > eigval[5293] = -0.00011589 > eigval[5294] = -0.000116295 > eigval[5295] = -0.000116993 > eigval[5296] = -0.000117111 > eigval[5297] = -0.000117667 > eigval[5298] = -0.000118582 > eigval[5299] = -0.00011872 > eigval[5300] = -0.000118885 > eigval[5301] = -0.000119334 > eigval[5302] = -0.000120538 > eigval[5303] = -0.00012068 > eigval[5304] = -0.000121256 > eigval[5305] = -0.00012141 > eigval[5306] = -0.000122242 > eigval[5307] = -0.000122789 > eigval[5308] = -0.000123013 > eigval[5309] = -0.000123817 > eigval[5310] = -0.000124575 > eigval[5311] = -0.000124866 > eigval[5312] = -0.000125117 > eigval[5313] = -0.000126223 > eigval[5314] = -0.00012707 > eigval[5315] = -0.000127687 > eigval[5316] = -0.000127919 > eigval[5317] = -0.000128714 > eigval[5318] = -0.000129043 > eigval[5319] = -0.00012939 > eigval[5320] = -0.000129535 > eigval[5321] = -0.000130664 > eigval[5322] = -0.000131691 > eigval[5323] = -0.000132264 > eigval[5324] = -0.000133152 > eigval[5325] = -0.00013381 > eigval[5326] = -0.000134219 > eigval[5327] = -0.000135764 > eigval[5328] = -0.000136149 > eigval[5329] = -0.000138551 > eigval[5330] = -0.000138698 > eigval[5331] = -0.000139432 > eigval[5332] = -0.000139957 > eigval[5333] = -0.000140624 > eigval[5334] = -0.000141187 > eigval[5335] = -0.000141866 > eigval[5336] = -0.000143352 > eigval[5337] = -0.000143514 > eigval[5338] = -0.000145445 > eigval[5339] = -0.000146802 > eigval[5340] = -0.00014872 > eigval[5341] = -0.000149065 > eigval[5342] = -0.000150165 > eigval[5343] = -0.000150618 > eigval[5344] = -0.000152546 > eigval[5345] = -0.000154182 > eigval[5346] = -0.000154271 > eigval[5347] = -0.000156094 > eigval[5348] = -0.00015781 > eigval[5349] = -0.000158271 > eigval[5350] = -0.00015992 > eigval[5351] = -0.000162788 > eigval[5352] = -0.000163307 > eigval[5353] = -0.000166183 > eigval[5354] = -0.000169429 > eigval[5355] = -0.000172062 > eigval[5356] = -0.000173377 > eigval[5357] = -0.000173442 > eigval[5358] = -0.000175975 > eigval[5359] = -0.000179223 > eigval[5360] = -0.000181775 > eigval[5361] = -0.000183321 > eigval[5362] = -0.000185641 > eigval[5363] = -0.000193632 > eigval[5364] = -0.000194667 > eigval[5365] = -0.000232906 > eigval[5366] = -0.000255899 > The Entropy due to the Quasi Harmonic approximation is 27848.4 J/mol K > The Entropy due to the Schlitter formula is nan J/mol K > Exact command I used was: gmx anaeig -f nojumpcent1_41.xtc -v > eig_heav_atom.trr -entropy -temp 298 -s prod1.tpr -n protein-H.ndx -comp > eig_comp.xvg -rmsf eig_rmsf.xvg -proj eig_proj.xvg -2d 2deig_proj.xvg -b 0 > -e 530000 > before this I had used, gmx covar -f nojumpcent1_41.xtc -s prod1.tpr -o > eig_heav_atom1.xvg -v eig_heav_atom1.trr -ascii eig_heav_atom1.dat to get > covariance matrix (I had also tried calculating mass weighted covariance > but gmx anaeig didn't run with it). I selected Protein-H for least square > fit and covariance analysis. Can you help me to understand what is going on > here and if I made mistakes then what it is? > > Thank You > Amit Kumar > Did you use double precision? This is needed to get sufficient accuracy, -- 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 From drrahulsuresh at gmail.com Tue Feb 4 09:19:08 2020 From: drrahulsuresh at gmail.com (RAHUL SURESH) Date: Tue, 04 Feb 2020 08:19:08 -0000 Subject: [gmx-users] Selecting water molecules within a nanotube Message-ID: Hi Users. I am simulating a nanotube in water medium. The nanotube is aligned to the center of the box using gmx editconfig and solvate. But I want to remove the water molecules within the nanotube. How do I compute this ? Thank you -- *Regards,* *Rahul * From alessandra.villa.biosim at gmail.com Tue Feb 4 09:38:40 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 04 Feb 2020 08:38:40 -0000 Subject: [gmx-users] how to generate tng format trajectory? In-Reply-To: References: Message-ID: Hi, On Mon, Feb 3, 2020 at 4:39 PM Albert wrote: > Hello all, > > I just learned that the tng trajectory format file is even more smaller > than the .xtc format file. I am just wondering how shall we specify the > option in the .mdp file so that "gmx mdrun" could generate the .tng > format trajectory accordingly? > > You do not need any specific mdp parameter to generate tng file, it should be enough to specify the file format when running gmx mdrun gmx mdun -s topol.tpr -x traj.tng Best regards Alessandra > thanks a lot > > albert > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 4 10:35:19 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 04 Feb 2020 09:35:19 -0000 Subject: [gmx-users] Selecting water molecules within a nanotube In-Reply-To: References: Message-ID: Hi, On Tue, Feb 4, 2020 at 9:19 AM RAHUL SURESH wrote: > Hi Users. > > I am simulating a nanotube in water medium. The nanotube is aligned to the > center of the box using gmx editconfig and solvate. But I want to remove > the water molecules within the nanotube. How do I compute this ? > > I understand that you do not want the water molecules inside the nanotube. To get a starting configuration with no water in nanotube you could 1) generate a index file with a group containing all atoms expect water molecules inside the nanotube. To do that use gmx select (for the synthax look at http://manual.gromacs.org/documentation/current/onlinehelp/selections.html) 2) generate a gro file (gmx editconf) selecting the desired group Best regards Alessandra > Thank you > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 4 10:35:20 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 04 Feb 2020 09:35:20 -0000 Subject: [gmx-users] Selecting water molecules within a nanotube In-Reply-To: References: Message-ID: Hi, On Tue, Feb 4, 2020 at 9:19 AM RAHUL SURESH wrote: > Hi Users. > > I am simulating a nanotube in water medium. The nanotube is aligned to the > center of the box using gmx editconfig and solvate. But I want to remove > the water molecules within the nanotube. How do I compute this ? > > I understand that you do not want the water molecules inside the nanotube. To get a starting configuration with no water in nanotube you could 1) generate a index file with a group containing all atoms expect water molecules inside the nanotube. To do that use gmx select (for the synthax look at http://manual.gromacs.org/documentation/current/onlinehelp/selections.html) 2) generate a gro file (gmx editconf) selecting the desired group Best regards Alessandra > Thank you > > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 ric.concu at gmail.com Tue Feb 4 11:13:53 2020 From: ric.concu at gmail.com (ric.concu at gmail.com) Date: Tue, 04 Feb 2020 10:13:53 -0000 Subject: [gmx-users] Analysis using sh file Message-ID: <007b01d5db43$caf0fb20$60d2f160$@gmail.com> Dear all, I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 and I found out that now that while I'm trying to use a .sh, as I was doing in the version 5.0.4, now I'm receiving back an error since the syntax is wrong. I'm wondering if someone could please help me. This is an example of a line I have been using on Gromacs 5.0.4:" echo "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is the error message I'm receiving from Gromacs: "Error in user input: Invalid selection '10 12 ' Near '12' syntax error Regards, Riccardo From m.b.abdelaal at gmail.com Tue Feb 4 12:13:27 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 04 Feb 2020 11:13:27 -0000 Subject: [gmx-users] Graphene Sheet in GROMOS 54A7 Message-ID: Hello everybody :) I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the .top file knowing that I have the .itp file. Thanks Mohamed From alessandra.villa.biosim at gmail.com Tue Feb 4 14:14:07 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 04 Feb 2020 13:14:07 -0000 Subject: [gmx-users] Analysis using sh file In-Reply-To: <007b01d5db43$caf0fb20$60d2f160$@gmail.com> References: <007b01d5db43$caf0fb20$60d2f160$@gmail.com> Message-ID: Hi, On Tue, Feb 4, 2020 at 11:14 AM wrote: > Dear all, > > > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > > and I found out that now that while I'm trying to use a .sh, as I was > > doing in the version 5.0.4, now I'm receiving back an error since the > > syntax is wrong. I'm wondering if someone could please help me. > > > > > > This is an example of a line I have been using on Gromacs 5.0.4:" echo "10" > "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" > > and this is the error message I'm receiving from Gromacs: "Error in user > input: Invalid selection '10 12 ' Near '12' syntax error > > You could use the option -ref and -sel (see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html?highlight=gmx%20rdf ) In your case the command will be gmx rdf -f box_tot -s box-npt -n box -ref 10 -sel 12 -o Mol1 Best regards Alessandra > > Regards, > > Riccardo > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 4 14:19:53 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 04 Feb 2020 13:19:53 -0000 Subject: [gmx-users] Analysis using sh file In-Reply-To: <007b01d5db43$caf0fb20$60d2f160$@gmail.com> References: <007b01d5db43$caf0fb20$60d2f160$@gmail.com> Message-ID: Hi, On Tue, Feb 4, 2020 at 11:14 AM wrote: > Dear all, > > > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > > and I found out that now that while I'm trying to use a .sh, as I was > > doing in the version 5.0.4, now I'm receiving back an error since the > > syntax is wrong. I'm wondering if someone could please help me. > > > > > > This is an example of a line I have been using on Gromacs 5.0.4:" echo "10" > "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" > > and this is the error message I'm receiving from Gromacs: "Error in user > input: Invalid selection '10 12 ' Near '12' syntax error > > You could use the option -ref and -sel (see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html?highlight=gmx%20rdf ) In your case the command will be gmx rdf -f box_tot -s box-npt -n box -ref 10 -sel 12 -o Mol1 Best regards Alessandra > > Regards, > > Riccardo > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 marko at kth.se Tue Feb 4 15:53:51 2020 From: marko at kth.se (Marko Petrovic) Date: Tue, 04 Feb 2020 14:53:51 -0000 Subject: [gmx-users] runtime error: pdb2gmx issues in Python API Message-ID: Hello I'm trying to create a python implementation using the API of the entire lysozyme tutorial and have gotten stuck on the pdb2gmx step and can't decipher the error message nor figure out if my thinking is fundamentally wrong for this step. As can be seen in the code, I have tried to brute force my way to a solution as well. test=gmx.commandline_operation(executable = "pdb2gmx", arguments = ["-water", "spce" ,"-ff", "oplsaa" ] #,"-f",file_name #,"-o",out_name) , #) input_files = {"-f":file_name}, output_files = {"-o":out_name}) test.run() this gives the following error message as a result of a compound exception: raise exceptions.ApiError(message) from e gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing resources for {}. Full error message included in attachment. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: errorlog.txt URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From marko at kth.se Tue Feb 4 15:59:39 2020 From: marko at kth.se (Marko Petrovic) Date: Tue, 04 Feb 2020 14:59:39 -0000 Subject: [gmx-users] runtime error: pdb2gmx issues in Python API In-Reply-To: References: Message-ID: I forgot to include my questions: Questions: - What is the cause python exception? - Is there a more detailed documentation for gmx.commandline_operation() than gmxapi basic package With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 4 Feb 2020, at 15:53, Marko Petrovic > wrote: Hello I'm trying to create a python implementation using the API of the entire lysozyme tutorial and have gotten stuck on the pdb2gmx step and can't decipher the error message nor figure out if my thinking is fundamentally wrong for this step. As can be seen in the code, I have tried to brute force my way to a solution as well. test=gmx.commandline_operation(executable = "pdb2gmx", arguments = ["-water", "spce" ,"-ff", "oplsaa" ] #,"-f",file_name #,"-o",out_name) , #) input_files = {"-f":file_name}, output_files = {"-o":out_name}) test.run() this gives the following error message as a result of a compound exception: raise exceptions.ApiError(message) from e gmxapi.exceptions.ApiError: Uncaught {} while providing output-publishing resources for {}. Full error message included in attachment. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology From dallas.warren at monash.edu Tue Feb 4 19:12:06 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Tue, 04 Feb 2020 18:12:06 -0000 Subject: [gmx-users] Graphene Sheet in GROMOS 54A7 In-Reply-To: References: Message-ID: http://manual.gromacs.org/2020/reference-manual/topologies/topology-file-formats.html?highlight=itp#molecule-itp-file There is an example there of how you include an itp within a top On Tue, 4 Feb. 2020, 10:13 pm Mohamed Abdelaal, wrote: > Hello everybody :) > > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the > .top file knowing that I have the .itp file. > > 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 alanwilter at gmail.com Tue Feb 4 22:46:56 2020 From: alanwilter at gmail.com (Alan) Date: Tue, 04 Feb 2020 21:46:56 -0000 Subject: [gmx-users] question on dihedrals propers func 3 and impropers func 1 In-Reply-To: References: Message-ID: Which version of ACPYPE are you using? Please, get the latest here: https://github.com/alanwilter/acpype Check also about option: -z, --gmx4 write RB dihedrals old GMX 4.0 Thanks for using ACPYPE! Alan On Sat, 1 Feb 2020 at 18:21, Lei Qian wrote: > Dear users, > > Could I ask a question on dihedrals func types? Thanks! > > I used acpype to convert prmtop file and inpcrd file into gromacs files. > However, in new generated top file, > The dihedrals propers func is 3. and The dihedrals impropers func is 1. > > These two func types are different from propers func 9 and impropers func > 4. > (func type 9 and func type 4 can be found in Gromacs documents). > > Could I ask the meaning of func type 3 and func type 1 ? > > Thanks! > Lei > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Wanna help a great cause? Please: https://www.raymondnicolettrust.com/events/2020/parismarathon And many thanks! Alan Silva ????????????? From shanjayasinghe2011 at gmail.com Wed Feb 5 06:08:21 2020 From: shanjayasinghe2011 at gmail.com (Shan Jayasinghe) Date: Wed, 05 Feb 2020 05:08:21 -0000 Subject: [gmx-users] Micellar shape Message-ID: Dear Gromacs Users, I want to determine whether I got prolate or oblate micelle in my MD simulation. I calculated moment of inertia for a micelle after doing clustering. I want to know how do I determine whether it is prolate or oblate depending on moment of inertia calculations. Thank you. -- Best Regards Shan Jayasinghe From saranyahoney17 at gmail.com Wed Feb 5 07:19:12 2020 From: saranyahoney17 at gmail.com (saranya) Date: Wed, 05 Feb 2020 06:19:12 -0000 Subject: [gmx-users] Fwd: In-Reply-To: References: Message-ID: I have performed a simulation for a protein-metal cluster complex system for 500ns. While calculating MMPBSA analysis for the system, I had selected two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD profile of protein-metal cluster 500 ns simulation period and executed the commands for a single range of trajectory period. In the result of the binding energy of my system, values are void. Hence, I Kindly need your valuable suggestions in this regard. Herewith I have attached the obtained results of my system, #Complex Number: 1 =============== SUMMARY =============== van der Waal energy = -1144.250 +/- 28.405 kJ/mol Electrostattic energy = 0.000 +/- 0.000 kJ/mol Polar solvation energy = nan +/- nan kJ/mol SASA energy = -25.841 +/- 1.107 kJ/mol SAV energy = 0.000 +/- 0.000 kJ/mol WCA energy = 0.000 +/- 0.000 kJ/mol Binding energy = nan +/- nan kJ/mol =============== END =============== *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* From alessandra.villa.biosim at gmail.com Wed Feb 5 09:01:00 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 05 Feb 2020 08:01:00 -0000 Subject: [gmx-users] Fwd: In-Reply-To: References: Message-ID: HI, Are you using a third-party tools for MMPBSA analysis? You could ask directly to the authors Best regards Alessandra On Wed, Feb 5, 2020 at 7:19 AM saranya wrote: > I have performed a simulation for a protein-metal cluster complex system > for 500ns. While calculating MMPBSA analysis for the system, I had > selected > two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD > profile of protein-metal cluster 500 ns simulation period and executed the > commands for a single range of trajectory period. In the result of the > binding energy of my system, values are void. Hence, I Kindly need your > valuable suggestions in this regard. Herewith I have attached the obtained > results of my system, > > > #Complex Number: 1 > =============== > SUMMARY > =============== > > > van der Waal energy = -1144.250 +/- 28.405 kJ/mol > > Electrostattic energy = 0.000 +/- 0.000 kJ/mol > > Polar solvation energy = nan +/- nan kJ/mol > > SASA energy = -25.841 +/- 1.107 kJ/mol > > SAV energy = 0.000 +/- 0.000 kJ/mol > > WCA energy = 0.000 +/- 0.000 kJ/mol > > Binding energy = nan +/- nan kJ/mol > > =============== > END > =============== > > > > > *Saranya Vasudevan,* > > *Research Scholar,* > > *Molecular Quantum Mechanics Laboratory,* > > *Department of Physics,* > > *Bharathiar University,* > > *Coimbatore-46* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 5 09:01:01 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 05 Feb 2020 08:01:01 -0000 Subject: [gmx-users] Fwd: In-Reply-To: References: Message-ID: HI, Are you using a third-party tools for MMPBSA analysis? You could ask directly to the authors Best regards Alessandra On Wed, Feb 5, 2020 at 7:19 AM saranya wrote: > I have performed a simulation for a protein-metal cluster complex system > for 500ns. While calculating MMPBSA analysis for the system, I had > selected > two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD > profile of protein-metal cluster 500 ns simulation period and executed the > commands for a single range of trajectory period. In the result of the > binding energy of my system, values are void. Hence, I Kindly need your > valuable suggestions in this regard. Herewith I have attached the obtained > results of my system, > > > #Complex Number: 1 > =============== > SUMMARY > =============== > > > van der Waal energy = -1144.250 +/- 28.405 kJ/mol > > Electrostattic energy = 0.000 +/- 0.000 kJ/mol > > Polar solvation energy = nan +/- nan kJ/mol > > SASA energy = -25.841 +/- 1.107 kJ/mol > > SAV energy = 0.000 +/- 0.000 kJ/mol > > WCA energy = 0.000 +/- 0.000 kJ/mol > > Binding energy = nan +/- nan kJ/mol > > =============== > END > =============== > > > > > *Saranya Vasudevan,* > > *Research Scholar,* > > *Molecular Quantum Mechanics Laboratory,* > > *Department of Physics,* > > *Bharathiar University,* > > *Coimbatore-46* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 vedat.durmaz at gmx.net Wed Feb 5 10:59:01 2020 From: vedat.durmaz at gmx.net (Vedat Durmaz) Date: Wed, 05 Feb 2020 09:59:01 -0000 Subject: [gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue) In-Reply-To: References: Message-ID: <5858ef03-396a-6c29-7d6c-9706395e1468@gmx.net> Hi there, I'm pretty sure it's not a feature but a bug which I've faced in the GMX versions 2018.7, 2019.5 an 2020. When I try to calculate RMSD values for a protein system including a catalytic magnesium ion "Mg" using the command gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg -debug I get this error: Can not find mass in database for atom MG in residue 1370 MG ------------------------------------------------------- Program:???? gmx rms, version 2019.5 Source file: src/gromacs/fileio/confio.cpp (line 517) Fatal error: Masses were requested, but for some atom(s) masses could not be found in the database. Use a tpr file as input, if possible, or add these atoms to the mass database. Let's accept for the moment that using a .tpr file with -s (rather than a .pdb file) is no option for me. Consequently, gmx retrieves atom masses from atommass.dat which actually contains the Mg ion: ; NOTE: longest names match ; General atoms ; '???' or '*' matches any residue name ???? H????? 1.00790? ???? He???? 4.00260? ???? Li???? 6.94100? ???? Be???? 9.01220? ???? B???? 10.81100? ???? C???? 12.01070? ???? N???? 14.00670? ???? O???? 15.99940? ???? F???? 18.99840? ???? Ne??? 20.17970? ???? Na??? 22.98970? ???? Mg??? 24.30500??? <<< in this line ???? Al??? 26.98150? ???? Si??? 28.08550? ???? P???? 30.97380 Having a look at the log file of "gmx rms -debug ...", I see some strange output. Here's a snippet: searching residue:? ??? atom:??? H ?not successful searching residue:? ??? atom:?? He ?match:? ?????? H searching residue:? ??? atom:?? Li ?not successful searching residue:? ??? atom:?? Be ?not successful searching residue:? ??? atom:??? B ?not successful searching residue:? ??? atom:??? C ?not successful searching residue:? ??? atom:??? N ?not successful searching residue:? ??? atom:??? O ?not successful searching residue:? ??? atom:??? F ?not successful searching residue:? ??? atom:?? Ne ?match:? ?????? N searching residue:? ??? atom:?? Na ?match:? ?????? N searching residue:? ??? atom:?? Mg ?not successful searching residue:? ??? atom:?? Al ?not successful searching residue:? ??? atom:?? Si ?not successful searching residue:? ??? atom:??? P ?not successful searching residue:? ??? atom:??? S ?not successful searching residue:? ??? atom:?? Cl ?match:? ?????? C ?... searching residue:? ??? atom:?? Cu ?match:? ?????? C ... I don't know what exactly the rms command is doing in the scenes and also don't want to agonize over the cpp code. But to me it seems as if the element assignment is based only on the FIRST LETTER of each element name. If I use copper (Cu) instead of magnesium, the program runs fine. Now let's compare the Cu lines with the Mg lines in the debugging output above. searching residue:? ??? atom:?? Cu ?match:? ?????? C searching residue:? ??? atom:?? Mg ?not successful Obviously, Cu is found because the first letter of its element abbreviation, C (because Cu[index 0] is C) does exist as an element, but there is no element M, the first letter of Mg. A little test (respectively an improper workaround). If I add a line for the element "M" to atommass.dat like this ???? Na??? 22.98970? ???? Mg??? 24.30500 ???? M???? 24.30500????? <<< new line ???? Al??? 26.98150? then the rms command executed on the protein with Mg runs without any error. But this observation also implies that masses, the rms command retrieves from atommass.dat, are wrong because, e.g., to each of Cl, Cr, Cu and Co, the mass of C is assigned. I see 2 options for GMX developers. Either you check the rms<->atommass.dat interplay, or you disable the possibility to use PDB files with the -s option. However, I would strongly discourage from the latter decision since there are cases where you have an xtc trajectory possibly generated with another tool along with a pdb file, but you don't want to spend too much time in the generation of a proper tpr file. Thanks & best wishes, Vedat From jalemkul at vt.edu Wed Feb 5 13:10:37 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:10:37 -0000 Subject: [gmx-users] Energy plots for specific atoms/selections In-Reply-To: References: Message-ID: <97c08b83-ac6f-8ad0-95e9-e1158176fff7@vt.edu> On 1/31/20 6:23 PM, Daniel Burns wrote: > Hi, > > I want to get an xvg file that will show me the LJ, Coulomb, and dihedral > energies on a specific set of atoms. I've tried passing a .dat file with > the groups of atoms from gmx select to gmx enemat but I get an error > message saying that I must not have included those groups in my mdp file. > How do I incorporate them into my mdp file if I don't want specific mdp > options to work on them? > > I cannot figure out how to retrieve the data on my groups of interest. I've > tried -rerun and included an index of the atoms of interest as well > > If anybody has a detailed explanation, I would be grateful. Create an index file that defines the atoms of interest, create a matching trajectory with trjconv and new .tpr file with only those atoms using convert-tpr, then use mdrun -rerun with those new files. Be advised that simply chopping out atoms and computing energies like this is unlikely to have any physical 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 jalemkul at vt.edu Wed Feb 5 13:11:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:11:05 -0000 Subject: [gmx-users] Protein pore collapse during simulation. In-Reply-To: References: Message-ID: <6aca61fe-c11f-ff01-dd6b-6b71ab32bff7@vt.edu> On 2/1/20 5:05 AM, Yogesh Sharma wrote: > sir, > in efforts to find out the differences in the density of bilayers > generated by charmm and gromac(berger lipids) i used grid-mat. there are > significant differences in area per lipid. > > with these settings for both systems: > override_vectors 5.2,10.0,6.9 > grid 20 > conserve_ratio yes > protein yes > precision 1.3 > P_value 5.0 > #Lower Z limit: 3.036 Upper Z limit: 7.784 > > charmm with hydrogen (sq. A) > area per lipid upper leaflet: 10.5 > area per lipid bottom leaflet 5.45 > > charmm (bilayer saved without hydrogen) (sq. A) > area per lipid upper leaflet: 13 > area per lipid bottom leaflet 7 This looks like something is wrong with the way you've calculated the areas, but without access to your input files there's nothing more I can say. -Justin > gromac (sq. A) > area per lipid upper leaflet: 70 > area per lipid bottom leaflet 68 > Are charmm values below experimental observation for POPC i.e gelation of > bilayer? -- ================================================== 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 Feb 5 13:11:40 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:11:40 -0000 Subject: [gmx-users] Generate the Topology with CGenFF :: Error message In-Reply-To: References: Message-ID: <1b516dbd-68ed-0f26-0d76-e2f8e667e4c7@vt.edu> On 2/3/20 9:06 AM, Adarsh V. K. wrote: > Dear all, > At present the ProDrg server is not functioning properly in generating > ligand topology files. How to generate topology files using ProDrg > While try to Generate the topology with CGenFF server, it returns following > Error message > How to manage this problem? > -------------------------------------------------------------- > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.15+ (default, Oct > 7 2019, 17:39:04) [GCC 7.4.0] > > NOTE 2: Please be sure to use the same version of CGenFF in your > simulations that was used during parameter generation: > --Version of CGenFF detected in 1MD19DB00931.str : 3.0.1 > --Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 > > WARNING: CGenFF versions are not equivalent! > > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include > parameters that are already in CGenFF' option when uploading a molecule > into CGenFF. > Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (54) and > top (0) are unequal > Usually this means the specified residue name does not match between str > and mol2 files > ----------------------------------------------------------- The last line of the note tells you the problem. Correct the residue name in the stream file. -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 Feb 5 13:12:59 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:12:59 -0000 Subject: [gmx-users] misunderstanding comm-grps In-Reply-To: References: Message-ID: <5e32229e-c797-9f92-553d-2fa2af6f8c7b@vt.edu> On 2/3/20 7:33 PM, Miro Astore wrote: > Hi everyone, > > I have tried using comm_grps to try and remove center of mass motion > from my system. > > I used the following configuration > > comm_grps = non-Protein Protein > nstcomm = 100 > comm_mode = linear > comm_grps = non-Protein Protein Don't do this. Multiple COM motion removal groups are only appropriate in layered systems that have different diffusion behavior. > refcoord_scaling = com > > But I still get considerable drift in my protein. Am I > misunderstanding what comm is actually doing and I should use the > pulling code if I want my protein to stay in the center of the box? Dallas covered this nicely. The algorithm does not (and is not intended to) prevent diffusion. It subtracts erroneous contributions to the kinetic energy 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 jalemkul at vt.edu Wed Feb 5 13:13:59 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:13:59 -0000 Subject: [gmx-users] Micellar shape In-Reply-To: References: Message-ID: On 2/5/20 12:01 AM, Shan Jayasinghe wrote: > Dear Gromacs Users, > > I want to determine whether I got prolate or oblate micelle in my MD > simulation. I calculated moment of inertia for a micelle after doing > clustering. I want to know how do I determine whether it is prolate or > oblate depending on moment of inertia calculations. Compute the ellipticity. -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 Feb 5 13:14:25 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 12:14:25 -0000 Subject: [gmx-users] Gromacs bug related to rms and atommass.dat interplay (Can not find mass in database for atom MG in residue) In-Reply-To: <5858ef03-396a-6c29-7d6c-9706395e1468@gmx.net> References: <5858ef03-396a-6c29-7d6c-9706395e1468@gmx.net> Message-ID: <1fdb22e5-cb86-7bcb-6c2f-5c5355a2e2df@vt.edu> On 2/5/20 4:58 AM, Vedat Durmaz wrote: > Hi there, > > I'm pretty sure it's not a feature but a bug which I've faced in the GMX > versions 2018.7, 2019.5 an 2020. > > When I try to calculate RMSD values for a protein system including a > catalytic magnesium ion "Mg" using the command > > gmx rms -s mol.pdb -f mol.xtc -f2 mol.xtc -o mol-rmsd.xvg -debug > > I get this error: > > > Can not find mass in database for atom MG in residue 1370 MG > > ------------------------------------------------------- > Program:???? gmx rms, version 2019.5 > Source file: src/gromacs/fileio/confio.cpp (line 517) > > Fatal error: > Masses were requested, but for some atom(s) masses could not be found in the > database. Use a tpr file as input, if possible, or add these atoms to > the mass > database. > > Let's accept for the moment that using a .tpr file with -s (rather than > a .pdb file) is no option for me. Consequently, gmx retrieves atom > masses from atommass.dat which actually contains the Mg ion: > > > ; NOTE: longest names match > ; General atoms > ; '???' or '*' matches any residue name > ???? H????? 1.00790 > ???? He???? 4.00260 > ???? Li???? 6.94100 > ???? Be???? 9.01220 > ???? B???? 10.81100 > ???? C???? 12.01070 > ???? N???? 14.00670 > ???? O???? 15.99940 > ???? F???? 18.99840 > ???? Ne??? 20.17970 > ???? Na??? 22.98970 > ???? Mg??? 24.30500??? <<< in this line > ???? Al??? 26.98150 > ???? Si??? 28.08550 > ???? P???? 30.97380 > > > Having a look at the log file of "gmx rms -debug ...", I see some > strange output. Here's a snippet: > > > searching residue:? ??? atom:??? H > ?not successful > searching residue:? ??? atom:?? He > ?match:? ?????? H > searching residue:? ??? atom:?? Li > ?not successful > searching residue:? ??? atom:?? Be > ?not successful > searching residue:? ??? atom:??? B > ?not successful > searching residue:? ??? atom:??? C > ?not successful > searching residue:? ??? atom:??? N > ?not successful > searching residue:? ??? atom:??? O > ?not successful > searching residue:? ??? atom:??? F > ?not successful > searching residue:? ??? atom:?? Ne > ?match:? ?????? N > searching residue:? ??? atom:?? Na > ?match:? ?????? N > searching residue:? ??? atom:?? Mg > ?not successful > searching residue:? ??? atom:?? Al > ?not successful > searching residue:? ??? atom:?? Si > ?not successful > searching residue:? ??? atom:??? P > ?not successful > searching residue:? ??? atom:??? S > ?not successful > searching residue:? ??? atom:?? Cl > ?match:? ?????? C > ?... > searching residue:? ??? atom:?? Cu > ?match:? ?????? C > ... > > > I don't know what exactly the rms command is doing in the scenes and > also don't want to agonize over the cpp code. But to me it seems as if > the element assignment is based only on the FIRST LETTER of each element > name. If I use copper (Cu) instead of magnesium, the program runs fine. > Now let's compare the Cu lines with the Mg lines in the debugging output > above. > > searching residue:? ??? atom:?? Cu > ?match:? ?????? C > > searching residue:? ??? atom:?? Mg > ?not successful > > Obviously, Cu is found because the first letter of its element > abbreviation, C (because Cu[index 0] is C) does exist as an element, but > there is no element M, the first letter of Mg. A little test > (respectively an improper workaround). If I add a line for the element > "M" to atommass.dat like this > > ???? Na??? 22.98970 > ???? Mg??? 24.30500 > ???? M???? 24.30500????? <<< new line > ???? Al??? 26.98150 > > then the rms command executed on the protein with Mg runs without any > error. But this observation also implies that masses, the rms command > retrieves from atommass.dat, are wrong because, e.g., to each of Cl, Cr, > Cu and Co, the mass of C is assigned. > > > I see 2 options for GMX developers. Either you check the > rms<->atommass.dat interplay, or you disable the possibility to use PDB > files with the -s option. However, I would strongly discourage from the > latter decision since there are cases where you have an xtc trajectory > possibly generated with another tool along with a pdb file, but you > don't want to spend too much time in the generation of a proper tpr file. Please file a bug report on redmine.gromacs.org. -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 dburns at iastate.edu Wed Feb 5 16:06:33 2020 From: dburns at iastate.edu (Daniel Burns) Date: Wed, 05 Feb 2020 15:06:33 -0000 Subject: [gmx-users] Energy plots for specific atoms/selections In-Reply-To: <97c08b83-ac6f-8ad0-95e9-e1158176fff7@vt.edu> References: <97c08b83-ac6f-8ad0-95e9-e1158176fff7@vt.edu> Message-ID: Thanks, Justin. I wanted to confirm that the plumed scaled topology function is working properly on the selected atoms but maybe this isn't the right way. I've already confirmed that the system's total energy is different between a scaled and unscaled system but the tutorial makes it sounds as if you can expect a precise value based on your scaling factor if you plot the energies for just the scaled atoms. Thanks again! Dan On Wed, Feb 5, 2020 at 6:10 AM Justin Lemkul wrote: > > > On 1/31/20 6:23 PM, Daniel Burns wrote: > > Hi, > > > > I want to get an xvg file that will show me the LJ, Coulomb, and dihedral > > energies on a specific set of atoms. I've tried passing a .dat file with > > the groups of atoms from gmx select to gmx enemat but I get an error > > message saying that I must not have included those groups in my mdp file. > > How do I incorporate them into my mdp file if I don't want specific mdp > > options to work on them? > > > > I cannot figure out how to retrieve the data on my groups of interest. > I've > > tried -rerun and included an index of the atoms of interest as well > > > > If anybody has a detailed explanation, I would be grateful. > > Create an index file that defines the atoms of interest, create a > matching trajectory with trjconv and new .tpr file with only those atoms > using convert-tpr, then use mdrun -rerun with those new files. Be > advised that simply chopping out atoms and computing energies like this > is unlikely to have any physical 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 > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 mbhendle at iitk.ac.in Wed Feb 5 18:55:02 2020 From: mbhendle at iitk.ac.in (mbhendle) Date: Wed, 05 Feb 2020 17:55:02 -0000 Subject: [gmx-users] How to add two different "defaults" parameters in topology file Message-ID: <02a57e0d79a7d003fed998c9894efd9a@iitk.ac.in> Hello all, I am trying to simulate polymers in tip4p-ice and for that I need to set two different "defaults" parameters for polymer chain and TIP4P-ICE in topology file. The "moleculetype" for Polymer chain and water is also different: [ defaults] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ (for polymer) 1 3 yes 0.5 0.5 [ defaults] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ (for TIP4P-ICE) 1 2 no 1 1 [moleculetype] ;Name nrexcl Other 3 ;(Polymer) SOL 1 ;(TIP4P-ICE) For this purpose, I have created two different ".itp" files for polymer chain and TIP4P-ICE. But while running "gmx grompp" gromacs is showing "Invalid order for directive moleculetype". I also tried putting two defaults parameters into ".top" file itself. But it also showed error. Please suggest how to do it. Thanks & Regards, Mangesh Bhendale From yogesh.rma13 at gmail.com Wed Feb 5 19:46:23 2020 From: yogesh.rma13 at gmail.com (Yogesh Sharma) Date: Wed, 05 Feb 2020 18:46:23 -0000 Subject: [gmx-users] overriding -ignh flag Message-ID: hi everyone, I want to override -ignh tag as this tag is stripping hydrogens off amino acid side chains, which might incorporate artifacts. my N and C terminals are NH3+ and coo- gmx pdb2gmx -f y.pdb -o y_pro.gro -water spc -his -ter i am getting Fatal error: Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms. ATOM 1 N MET X 1 36.214 42.372 20.531 0.00 0.00 ATOM 2 HT1 MET X 1 35.813 41.445 20.781 0.00 0.00 ATOM 3 HT2 MET X 1 35.746 42.657 19.648 0.00 0.00 ATOM 4 HT3 MET X 1 35.967 43.009 21.315 0.00 0.00 ATOM 5 CA MET X 1 37.678 42.198 20.410 0.00 0.00 ATOM 6 HA MET X 1 38.179 43.150 20.502 0.00 0.00 ATOM 7 CB MET X 1 38.105 41.245 21.499 0.00 0.00 ATOM 8 HB1 MET X 1 38.862 40.523 21.124 0.00 0.00 ATOM 9 HB2 MET X 1 37.271 40.587 21.823 0.00 0.00 ATOM 10 CG MET X 1 38.740 41.847 22.761 0.00 0.00 ATOM 11 HG1 MET X 1 39.031 40.967 23.374 0.00 0.00 ATOM 12 HG2 MET X 1 38.131 42.586 23.324 0.00 0.00 ATOM 13 SD MET X 1 40.389 42.642 22.497 0.00 0.00 ATOM 14 CE MET X 1 40.740 42.470 24.299 0.00 0.00 ATOM 15 HE1 MET X 1 40.704 41.389 24.553 0.00 0.00 ATOM 16 HE2 MET X 1 40.132 43.023 25.047 0.00 0.00 ATOM 17 HE3 MET X 1 41.809 42.739 24.433 0.00 0.00 ATOM 18 C MET X 1 38.114 41.717 19.047 0.00 0.00 ATOM 19 O MET X 1 37.405 40.927 18.465 0.00 0.00 HA is not even NH3+ hydrogen. what should be the appropriate nomenclature here? Many of hydrogen atoms are not listed in .rtp files. how should i refine my pdb without compromising with hydrogens? From knellerdw at ornl.gov Wed Feb 5 19:49:23 2020 From: knellerdw at ornl.gov (Kneller, Daniel) Date: Wed, 05 Feb 2020 18:49:23 -0000 Subject: [gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)? Message-ID: Hello Gromacs Gurus, I'm studying the vibration dynamics of protein. I'm trying to calculate the density of states (dos) for protein in an MD simulation. Dos is supposed to be calculated by a Fourier transform of the velocity autocorrelation function. Both gmx dos and gmx velacc with the -os option appear in the documentation to do this but they give different plots with different axis. Can someone clarify the difference between these two calculations? Thank you for your time, Daniel Kneller Postdoctoral Research Associate Neutron Scattering Division Neutron Sciences Directorate Oak Ridge National Laboratory From spoel at xray.bmc.uu.se Wed Feb 5 20:55:12 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 05 Feb 2020 19:55:12 -0000 Subject: [gmx-users] What is the difference between density of states (gmx dos) and vibrational power spectrum (gmx velacc -os)? In-Reply-To: References: Message-ID: Den 2020-02-05 kl. 19:49, skrev Kneller, Daniel: > Hello Gromacs Gurus, > > I'm studying the vibration dynamics of protein. > I'm trying to calculate the density of states (dos) for protein in an MD simulation. > Dos is supposed to be calculated by a Fourier transform of the velocity autocorrelation function. > > Both gmx dos and gmx velacc with the -os option appear in the documentation to do this but they give different plots with different axis. Both tools need long simulations where velocities are saved often, say every few fs. Then they need converged simulations, which is not going to happen with a protein. These tools are more geared for simulations of liquids. > > Can someone clarify the difference between these two calculations? > > Thank you for your time, > > Daniel Kneller > Postdoctoral Research Associate > Neutron Scattering Division > Neutron Sciences Directorate > Oak Ridge National Laboratory > > -- 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 From jalemkul at vt.edu Wed Feb 5 21:03:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 20:03:39 -0000 Subject: [gmx-users] overriding -ignh flag In-Reply-To: References: Message-ID: <2458b6ca-3b1d-6c6f-34c2-0e17e497cf8a@vt.edu> On 2/5/20 1:46 PM, Yogesh Sharma wrote: > hi everyone, > I want to override -ignh tag as this tag is stripping hydrogens off amino > acid side chains, which might incorporate artifacts. my N and C terminals > are NH3+ and coo- > > gmx pdb2gmx -f y.pdb -o y_pro.gro -water spc -his -ter > i am getting Fatal error: > Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while > sorting atoms. > > ATOM 1 N MET X 1 36.214 42.372 20.531 0.00 0.00 > > ATOM 2 HT1 MET X 1 35.813 41.445 20.781 0.00 0.00 > > ATOM 3 HT2 MET X 1 35.746 42.657 19.648 0.00 0.00 > > ATOM 4 HT3 MET X 1 35.967 43.009 21.315 0.00 0.00 > > ATOM 5 CA MET X 1 37.678 42.198 20.410 0.00 0.00 > > ATOM 6 HA MET X 1 38.179 43.150 20.502 0.00 0.00 > > ATOM 7 CB MET X 1 38.105 41.245 21.499 0.00 0.00 > > ATOM 8 HB1 MET X 1 38.862 40.523 21.124 0.00 0.00 > > ATOM 9 HB2 MET X 1 37.271 40.587 21.823 0.00 0.00 > > ATOM 10 CG MET X 1 38.740 41.847 22.761 0.00 0.00 > > ATOM 11 HG1 MET X 1 39.031 40.967 23.374 0.00 0.00 > > ATOM 12 HG2 MET X 1 38.131 42.586 23.324 0.00 0.00 > > ATOM 13 SD MET X 1 40.389 42.642 22.497 0.00 0.00 > > ATOM 14 CE MET X 1 40.740 42.470 24.299 0.00 0.00 > > ATOM 15 HE1 MET X 1 40.704 41.389 24.553 0.00 0.00 > > ATOM 16 HE2 MET X 1 40.132 43.023 25.047 0.00 0.00 > > ATOM 17 HE3 MET X 1 41.809 42.739 24.433 0.00 0.00 > > ATOM 18 C MET X 1 38.114 41.717 19.047 0.00 0.00 > > ATOM 19 O MET X 1 37.405 40.927 18.465 0.00 0.00 > HA is not even NH3+ hydrogen. what should be the appropriate nomenclature > here? Many of hydrogen atoms are not listed in .rtp files. how should i > refine my pdb without compromising with hydrogens? You don't say which force field you're using but if the H atoms aren't in the .rtp file that means you're using a united-atom force field (e.g. GROMOS) and that is precisely what the force field requires. UA force fields do not have aliphatic H atoms, including HA. -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 Feb 5 21:05:41 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 05 Feb 2020 20:05:41 -0000 Subject: [gmx-users] How to add two different "defaults" parameters in topology file In-Reply-To: <02a57e0d79a7d003fed998c9894efd9a@iitk.ac.in> References: <02a57e0d79a7d003fed998c9894efd9a@iitk.ac.in> Message-ID: On 2/5/20 12:54 PM, mbhendle wrote: > Hello all, > > I am trying to simulate polymers in tip4p-ice and for that I need to set > two different "defaults" parameters for polymer chain and TIP4P-ICE in > topology file. The "moleculetype" for Polymer chain and water is also > different: > > [ defaults] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ (for polymer) > 1 3 yes 0.5 0.5 > > [ defaults] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ (for TIP4P-ICE) > 1 2 no 1 1 > > [moleculetype] > > ;Name nrexcl > > Other 3 ;(Polymer) > > SOL 1 ;(TIP4P-ICE) > > For this purpose, I have created two different ".itp" files for polymer > chain and TIP4P-ICE. But while running "gmx grompp" gromacs is showing > "Invalid order for directive moleculetype". I also tried putting two > defaults parameters into ".top" file itself. But it also showed error. > > Please suggest how to do it. You can't have two [defaults] directives. The gen-pairs, fudgeLJ, and fudgeQQ values only affect 1-4 interactions, which are not applicable to water, so I don't understand why they're relevant. You certainly can't mix different combination rules in a system, but you could specify different nonbonded parameters via [nonbond_params] rather than trying to specify different combination rules. -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 akash.pandya.15 at ucl.ac.uk Wed Feb 5 21:22:22 2020 From: akash.pandya.15 at ucl.ac.uk (Pandya, Akash) Date: Wed, 05 Feb 2020 20:22:22 -0000 Subject: [gmx-users] RDF calculation from surface of protein Message-ID: Hi all, I am trying to calculate the RDF between the protein surface and the centre of mass of my ligand and water molecules. Please find below the command I used: gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 -cn number.xvg -surf mol -seltype mol_com I get the following error: Inconsistency in user input: -surf only works with -ref that consists of atoms For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I am wondering what this error means? My ref group does contain atoms? Any guidance will be much appreciated :) Akash From miro.astore at gmail.com Wed Feb 5 23:11:37 2020 From: miro.astore at gmail.com (Miro Astore) Date: Wed, 05 Feb 2020 22:11:37 -0000 Subject: [gmx-users] misunderstanding comm-grps In-Reply-To: <5e32229e-c797-9f92-553d-2fa2af6f8c7b@vt.edu> References: <5e32229e-c797-9f92-553d-2fa2af6f8c7b@vt.edu> Message-ID: Oh thank you very much I think I got confused looking at older documentation. What sort of artefacts get created by using comm-grps = Protein non-Protein? On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: > > > > On 2/3/20 7:33 PM, Miro Astore wrote: > > Hi everyone, > > > > I have tried using comm_grps to try and remove center of mass motion > > from my system. > > > > I used the following configuration > > > > comm_grps = non-Protein Protein > > nstcomm = 100 > > comm_mode = linear > > comm_grps = non-Protein Protein > > Don't do this. Multiple COM motion removal groups are only appropriate > in layered systems that have different diffusion behavior. > > > > refcoord_scaling = com > > > > But I still get considerable drift in my protein. Am I > > misunderstanding what comm is actually doing and I should use the > > pulling code if I want my protein to stay in the center of the box? > > Dallas covered this nicely. The algorithm does not (and is not intended > to) prevent diffusion. It subtracts erroneous contributions to the > kinetic energy 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. From olga.gluschenko at gmail.com Thu Feb 6 03:16:59 2020 From: olga.gluschenko at gmail.com (Olga Selyutina) Date: Thu, 06 Feb 2020 02:16:59 -0000 Subject: [gmx-users] modeling of zwitter-ions Message-ID: Hello, I'm simulating a molecule which is aminoacid connected with drug throuch a "bridge" of a few C-C bonds. Molecule should be in zwitter-ionic form, where negative and positive charges are distributed in pi-systems of drug and amino-acid, accordingly. Which is the best way to build the topology of such zwitter-ion? And one more question. The solvent is acetonitrile and it's important to take into account the solvation effects in this system. I'm working in gromos54a7 forcefield. Which acenotitrile model is better for solvatation effects? -- Best regards, Olga Selyutina From ak543714 at gmail.com Thu Feb 6 04:02:40 2020 From: ak543714 at gmail.com (Amit Kumar) Date: Thu, 06 Feb 2020 03:02:40 -0000 Subject: [gmx-users] Question about gromacs mailing list and configurational entropy Message-ID: Dear gromacs users, After subscribing to the gromacs mailing list I am getting only daily digest, I am not getting a question-answer thread, so posting my question once I cannot reply in the thread. I have also asked previously this question and got a reply from David van der Spoel too and after that, I am getting a value of schlitter's entropy but getting only one value of schlitter's value while I want it for every frame to plot time vs entropy graph. So can you tell me what is happening and how to troubleshoot this? Thank You Amit Kumar From yogesh.rma13 at gmail.com Thu Feb 6 05:01:34 2020 From: yogesh.rma13 at gmail.com (Yogesh Sharma) Date: Thu, 06 Feb 2020 04:01:34 -0000 Subject: [gmx-users] overriding -ignh flag Message-ID: Sir i am using gromos54a7 ff -- * with regards* *Yogesh Sharma* From jishrat17 at gmail.com Thu Feb 6 05:09:26 2020 From: jishrat17 at gmail.com (ISHRAT JAHAN) Date: Thu, 06 Feb 2020 04:09:26 -0000 Subject: [gmx-users] RDF calculation from surface of protein In-Reply-To: References: Message-ID: -surf flag is used with -ref flag. Provide the reference file in the -ref flag. On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash wrote: > Hi all, > > I am trying to calculate the RDF between the protein surface and the > centre of mass of my ligand and water molecules. Please find below the > command I used: > > gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin > 0.02 -cn number.xvg -surf mol -seltype mol_com > > > I get the following error: > > > > Inconsistency in user input: > -surf only works with -ref that consists of atoms > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > I am wondering what this error means? My ref group does contain atoms? Any > guidance will be much appreciated :) > > > 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. > -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh From nicolas.goudard at univ-amu.fr Thu Feb 6 07:24:14 2020 From: nicolas.goudard at univ-amu.fr (Nicolas GOUDARD) Date: Thu, 06 Feb 2020 06:24:14 -0000 Subject: [gmx-users] : SOLVED GMX_MPI 2020 gmx_mpi segmentation fault References: <05B17CDA-39F3-47FA-B9CB-D55D111B3CC6@univ-amu.fr> Message-ID: <4CD9BEE6-4146-4E03-86EC-30AD00DECE07@univ-amu.fr> Hello I solve my problem myself, with a colleague The problem was : On CentOS Linux release 8.1.1911 (Core) the gmx_mpi returned a segmentation fault, . The source of the problem was the openmpi version 4.0.1 provided by CenOS: (dnf install openmpi) So we have downloaded openmpi 4.0.2 from the OmpenMpi website , then we have compiled Gromacs 2020 with openmpi 4.0.2 and the problem has been solved !! Thanks [alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768) ==== backtrace ==== 0 /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0] 1 /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a] 2 /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b] 3 /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a] 4 /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a] 5 /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f] 6 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 7 /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae] 8 /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba] 9 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] 10 /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093] 11 /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939] 12 /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a] 13 /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05] 14 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16] 15 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a] 16 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce] 17 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2] 18 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915] 19 /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494] 20 /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805] 21 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5] 22 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449] 23 gmx_mpi() [0x4052bb] 24 /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873] 25 gmx_mpi() [0x40538e] =================== Segmentation fault (core dumped) Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Mol?culaires de Marseille Aix-Marseille Universit? - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille T?l: +33(0)4 91 28 82 66 Site : http://www.univ-amu.fr - Email : nicolas.goudard at univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si n?cessaire. > D?but du message r?exp?di? : > > De: Nicolas GOUDARD > Objet: [gmx-users] GMX_MPI 2020 > Date: 3 f?vrier 2020 ? 23:58:14 UTC+1 > ?: > R?pondre ?: > > Hello > On Gromacs 2020 or 2020 beta 1 on centos 8.1 there is a segmentation fault > How can I solve it ? > > #cat /etc/redhat-release > CentOS Linux release 8.1.1911 (Core) > > #cat /etc/redhat-release > CentOS Linux release 8.1.1911 (Core) > [root at alta ~]# > [root at alta ~]# cat /usr/share/Modules/modulefiles/gromacs2020_mpi > #%Module###################################################################### > ## > ## gromacs modulefile > ## > proc ModulesHelp { } { > puts stderr "gromacs 2020" > return 0 > } > prepend-path LD_LIBRARY_PATH /share/programs/GROMACS-2020-MPI/lib > prepend-path PATH /share/programs/GROMACS-2020-MPI/bin > > > #wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta1.tar.gz > #tar xvzf gromacs-2020-beta1.tar.gz > #cd gromacs-2020-beta1/ > #cmake .. -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/share/programs/GROMACS-2020-MPI -DCMAKE_INSTALL_LIBDIR=/share/programs/GROMACS-2020-MPI/lib -DGMX_USE_RDTSCP=ON > #make -j4 > #make install > #source /share/programs/GROMACS-2020-MPI/bin/GMXRC > #module unload gromacs2020_mpi > #gmx_mpi > > [alta:23110:0:23110] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f06e1072768) > ==== backtrace ==== > 0 /usr/lib64/libucs.so.0(+0x18bb0) [0x7f06e0a05bb0] > 1 /usr/lib64/libucs.so.0(+0x18d8a) [0x7f06e0a05d8a] > 2 /usr/lib64/libuct.so.0(+0x1655b) [0x7f06e1f3755b] > 3 /lib64/ld-linux-x86-64.so.2(+0xfd2a) [0x7f06f382cd2a] > 4 /lib64/ld-linux-x86-64.so.2(+0xfe2a) [0x7f06f382ce2a] > 5 /lib64/ld-linux-x86-64.so.2(+0x13e3f) [0x7f06f3830e3f] > 6 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] > 7 /lib64/ld-linux-x86-64.so.2(+0x136ae) [0x7f06f38306ae] > 8 /usr/lib64/libdl.so.2(+0x11ba) [0x7f06f0e011ba] > 9 /usr/lib64/libc.so.6(_dl_catch_exception+0x77) [0x7f06f137bff7] > 10 /usr/lib64/libc.so.6(_dl_catch_error+0x33) [0x7f06f137c093] > 11 /usr/lib64/libdl.so.2(+0x1939) [0x7f06f0e01939] > 12 /usr/lib64/libdl.so.2(dlopen+0x4a) [0x7f06f0e0125a] > 13 /usr/lib64/openmpi/lib/libopen-pal.so.40(+0x6df05) [0x7f06ee649f05] > 14 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_repository_open+0x206) [0x7f06ee627b16] > 15 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_component_find+0x35a) [0x7f06ee626a5a] > 16 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_components_register+0x2e) [0x7f06ee6323ce] > 17 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_register+0x252) [0x7f06ee6328b2] > 18 /usr/lib64/openmpi/lib/libopen-pal.so.40(mca_base_framework_open+0x15) [0x7f06ee632915] > 19 /usr/lib64/openmpi/lib/libmpi.so.40(ompi_mpi_init+0x674) [0x7f06f23de494] > 20 /usr/lib64/openmpi/lib/libmpi.so.40(PMPI_Init_thread+0x55) [0x7f06f240e805] > 21 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx4initEPiPPPc+0x85) [0x7f06f287dad5] > 22 /share/programs/GROMACS-2020-MPI/lib/libgromacs_mpi.so.5(_ZN3gmx18initForCommandLineEPiPPPc+0x19) [0x7f06f2cc9449] > 23 gmx_mpi() [0x4052bb] > 24 /usr/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f06f1266873] > 25 gmx_mpi() [0x40538e] > =================== > Segmentation fault (core dumped) > > Nicolas Goudard - Informaticien UMR CNRS 7313 - ISM2 - Institut des Sciences Mol?culaires de Marseille > Aix-Marseille Universit? - case 561 - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille > T?l: +33(0)4 91 28 82 66 > Site : http://www.univ-amu.fr - Email : nicolas.goudard at univ-amu.fr > Afin de respecter l'environnement, merci de n'imprimer cet email que si n?cessaire. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 smohammadtorabi at yahoo.com Thu Feb 6 08:33:35 2020 From: smohammadtorabi at yahoo.com (mohammad torabi) Date: Thu, 06 Feb 2020 07:33:35 -0000 Subject: [gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation References: <286682041.186574.1580974410231.ref@mail.yahoo.com> Message-ID: <286682041.186574.1580974410231@mail.yahoo.com> Dear users of Gromacs, I am starting with Gromacs for a short time. I want to prepare a simulation system including 2 components (Protein + ionic liquid) but their available force fields have different sources (OPLS-AA existing in Gromacs data bank and a specific FF based on?Lopes & Padua IL force field outside the Gromacs data bank). How can I properly use (mix) these 2 different force fields for my system components in the topology file of Gromacs code. Best Regards,S. M. Torabi From alessandra.villa.biosim at gmail.com Thu Feb 6 09:25:20 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 06 Feb 2020 08:25:20 -0000 Subject: [gmx-users] Question about gromacs mailing list Message-ID: Hi, On Thu, Feb 6, 2020 at 4:02 AM Amit Kumar wrote: > Dear gromacs users, > After subscribing to the gromacs mailing list I am getting only daily > digest, I am not getting a question-answer thread, so posting my question > once I cannot reply in the thread. > > You have probably selected "digest mode" when you enrolled in the mailing-list. You could change this setting by login to the subscription page. To do that use the link you find in the welcome email that you got once you enrolled. In your case should be something like https://maillist.sys.kth.se/mailman/options/gromacs.org_gmx-users/ak543714%40gmail.com Best regards Alessandra From 177cy500.bratin at nitk.edu.in Thu Feb 6 10:35:40 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Thu, 06 Feb 2020 09:35:40 -0000 Subject: [gmx-users] Energy plots for specific atoms/selections In-Reply-To: References: Message-ID: Hi In this regard you have to follow the protein-ligand tutorial given by Dr lemkul. In mdp file you can mention the atoms of your interest and rerun the existing .xtc file... On Sat 1 Feb, 2020, 4:54 AM Daniel Burns, wrote: > Hi, > > I want to get an xvg file that will show me the LJ, Coulomb, and dihedral > energies on a specific set of atoms. I've tried passing a .dat file with > the groups of atoms from gmx select to gmx enemat but I get an error > message saying that I must not have included those groups in my mdp file. > How do I incorporate them into my mdp file if I don't want specific mdp > options to work on them? > > I cannot figure out how to retrieve the data on my groups of interest. I've > tried -rerun and included an index of the atoms of interest as well > > If anybody has a detailed explanation, I would be grateful. > > Thank you, > > Dan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 177cy500.bratin at nitk.edu.in Thu Feb 6 10:39:14 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Thu, 06 Feb 2020 09:39:14 -0000 Subject: [gmx-users] How to use LBFGS minimization Message-ID: Dear all I want to use LBFGS algorithm for minimizing my system..what parameters is required for that...any suggestions or any tutorial is there for that. From micpel at kth.se Thu Feb 6 10:59:05 2020 From: micpel at kth.se (Michele Pellegrino) Date: Thu, 06 Feb 2020 09:59:05 -0000 Subject: [gmx-users] adding an external body force Message-ID: <1580983136424.43259@kth.se> Hi, I was wondering how to apply an external forcing term to one group; looking at the 2020 documentation I found: " accelerate group On each atom in an "accelerate group" an acceleration a_g is imposed. This is equivalent to an external force. " However I would argue it is not equivalent at all: the contibution of an external body force would add an acceleration term, not impose it, right? To make a more concrete example, what if I want to simulate gravity by setting 'accelerate' to some value? Would I obtain free-falling or would gravity be added on top of the force field from atomic intercations? Thanks for your attention. Michele From r.a.luirink at vu.nl Thu Feb 6 12:06:21 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Thu, 06 Feb 2020 11:06:21 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Message-ID: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> Hello, I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such). I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions. When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue? Best, Rosa From dallas.warren at monash.edu Thu Feb 6 13:22:34 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Thu, 06 Feb 2020 12:22:34 -0000 Subject: [gmx-users] How possible applying two different force field parameters for two-component in Gromacs simulation In-Reply-To: <286682041.186574.1580974410231@mail.yahoo.com> References: <286682041.186574.1580974410231.ref@mail.yahoo.com> <286682041.186574.1580974410231@mail.yahoo.com> Message-ID: The first question you have to ask is are those two compatible, have the same equations/relationships, and derived/parameterised in exactly the same manner? If the answer is no, then go no further, you cannot mix two incompatible forcefields in that manner. On Thu, 6 Feb. 2020, 6:33 pm mohammad torabi, wrote: > Dear users of Gromacs, > I am starting with Gromacs for a short time. I want to prepare a > simulation system including 2 components (Protein + ionic liquid) but their > available force fields have different sources (OPLS-AA existing in Gromacs > data bank and a specific FF based on Lopes & Padua IL force field outside > the Gromacs data bank). How can I properly use (mix) these 2 different > force fields for my system components in the topology file of Gromacs code. > Best Regards,S. M. Torabi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 r.a.luirink at vu.nl Thu Feb 6 13:54:01 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Thu, 06 Feb 2020 12:54:01 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> Message-ID: What I have tried is, instead of adding them to the [ pairs ] block, is change the epsilon value manually via the [ nonbon_params ] block. However, I can?t manually change the electrostatic interactions to account for the fudgeQQ (0.8333) for these specific pairs (or at least, I haven?t found a way to do so). From: "Luirink, R.A." Date: Thursday, 6 February 2020 at 11:49 To: "gmx-users at gromacs.org" Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Hello, I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such). I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions. When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue? Best, Rosa From r.a.luirink at vu.nl Thu Feb 6 14:44:15 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Thu, 06 Feb 2020 13:44:15 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> Message-ID: <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> Gromacs version 2018.6 btw. ?On 06/02/2020, 13:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: What I have tried is, instead of adding them to the [ pairs ] block, is change the epsilon value manually via the [ nonbon_params ] block. However, I can?t manually change the electrostatic interactions to account for the fudgeQQ (0.8333) for these specific pairs (or at least, I haven?t found a way to do so). From: "Luirink, R.A." Date: Thursday, 6 February 2020 at 11:49 To: "gmx-users at gromacs.org" Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Hello, I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such). I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions. When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue? Best, Rosa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 Feb 6 14:44:49 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 06 Feb 2020 13:44:49 -0000 Subject: [gmx-users] misunderstanding comm-grps In-Reply-To: References: <5e32229e-c797-9f92-553d-2fa2af6f8c7b@vt.edu> Message-ID: On 2/5/20 5:11 PM, Miro Astore wrote: > Oh thank you very much I think I got confused looking at older documentation. > > What sort of artefacts get created by using > > comm-grps = Protein non-Protein? You're separately subtracting net COM velocities from two species that should be treated uniformly. I have seen simulations randomly crash in these cases. -Justin > On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: >> >> >> On 2/3/20 7:33 PM, Miro Astore wrote: >>> Hi everyone, >>> >>> I have tried using comm_grps to try and remove center of mass motion >>> from my system. >>> >>> I used the following configuration >>> >>> comm_grps = non-Protein Protein >>> nstcomm = 100 >>> comm_mode = linear >>> comm_grps = non-Protein Protein >> Don't do this. Multiple COM motion removal groups are only appropriate >> in layered systems that have different diffusion behavior. >> >> >>> refcoord_scaling = com >>> >>> But I still get considerable drift in my protein. Am I >>> misunderstanding what comm is actually doing and I should use the >>> pulling code if I want my protein to stay in the center of the box? >> Dallas covered this nicely. The algorithm does not (and is not intended >> to) prevent diffusion. It subtracts erroneous contributions to the >> kinetic energy 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 jalemkul at vt.edu Thu Feb 6 14:45:43 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 06 Feb 2020 13:45:43 -0000 Subject: [gmx-users] modeling of zwitter-ions In-Reply-To: References: Message-ID: <27d2d082-570f-cbaf-fe4c-c5ba9443f3c6@vt.edu> On 2/5/20 9:16 PM, Olga Selyutina wrote: > Hello, > I'm simulating a molecule which is aminoacid connected with drug throuch a > "bridge" of a few C-C bonds. Molecule should be in zwitter-ionic form, > where negative and positive charges are distributed in pi-systems of drug > and amino-acid, accordingly. Which is the best way to build the topology of > such zwitter-ion? You'll have to parametrize it yourself. Aromatic groups in amino acids don't carry net charge. > And one more question. The solvent is acetonitrile and it's important to > take into account the solvation effects in this system. I'm working in > gromos54a7 forcefield. Which acenotitrile model is better for solvatation > effects? > You need a solvent model that has been parametrized in a manner consistent with the protein force field. -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 Feb 6 14:46:14 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 06 Feb 2020 13:46:14 -0000 Subject: [gmx-users] overriding -ignh flag In-Reply-To: References: Message-ID: <9fadcafb-592a-2a86-100f-1bd15e8aafaa@vt.edu> On 2/5/20 11:01 PM, Yogesh Sharma wrote: > Sir i am using gromos54a7 ff > Refer to my previous answer. Most of the H atoms will be deleted, as required by the force field. -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 Feb 6 14:46:53 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 06 Feb 2020 13:46:53 -0000 Subject: [gmx-users] Energy plots for specific atoms/selections In-Reply-To: References: Message-ID: <9f3bd288-2dfb-2293-cea2-07623f804385@vt.edu> On 2/6/20 4:35 AM, Bratin Kumar Das wrote: > Hi > In this regard you have to follow the protein-ligand tutorial given by > Dr lemkul. In mdp file you can mention the atoms of your interest and rerun > the existing .xtc file... The OP is not referring to the same case as an interaction energy; the approach is different (see my previous post on how to do this). -Justin > On Sat 1 Feb, 2020, 4:54 AM Daniel Burns, wrote: > >> Hi, >> >> I want to get an xvg file that will show me the LJ, Coulomb, and dihedral >> energies on a specific set of atoms. I've tried passing a .dat file with >> the groups of atoms from gmx select to gmx enemat but I get an error >> message saying that I must not have included those groups in my mdp file. >> How do I incorporate them into my mdp file if I don't want specific mdp >> options to work on them? >> >> I cannot figure out how to retrieve the data on my groups of interest. I've >> tried -rerun and included an index of the atoms of interest as well >> >> If anybody has a detailed explanation, I would be grateful. >> >> Thank you, >> >> Dan >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 Feb 6 14:47:47 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 06 Feb 2020 13:47:47 -0000 Subject: [gmx-users] adding an external body force In-Reply-To: <1580983136424.43259@kth.se> References: <1580983136424.43259@kth.se> Message-ID: On 2/6/20 4:58 AM, Michele Pellegrino wrote: > Hi, > > > I was wondering how to apply an external forcing term to one group; looking at the 2020 documentation I found: > > > " > > accelerate group > On each atom in an "accelerate group" an acceleration a_g is imposed. This is equivalent to an external force. > > " > > > However I would argue it is not equivalent at all: the contibution of an external body force would add an acceleration term, not impose it, right? > > To make a more concrete example, what if I want to simulate gravity by setting 'accelerate' to some value? Would I obtain free-falling or would gravity be added on top of the force field from atomic intercations? The use of acceleration groups simply adds an acceleration to the one that arises from the forces in the simulation and acts in the update step. -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 micpel at kth.se Thu Feb 6 15:30:20 2020 From: micpel at kth.se (Michele Pellegrino) Date: Thu, 06 Feb 2020 14:30:20 -0000 Subject: [gmx-users] adding an external body force In-Reply-To: References: <1580983136424.43259@kth.se>, Message-ID: <1580999413542.2738@kth.se> Justin, thank you very much for the clarification. I believe the documentation should report 'add', instead of 'impose' (otherwise it may be confusing). Regards, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Justin Lemkul Sent: 06 February 2020 14:47 To: gmx-users at gromacs.org Subject: Re: [gmx-users] adding an external body force On 2/6/20 4:58 AM, Michele Pellegrino wrote: > Hi, > > > I was wondering how to apply an external forcing term to one group; looking at the 2020 documentation I found: > > > " > > accelerate group > On each atom in an "accelerate group" an acceleration a_g is imposed. This is equivalent to an external force. > > " > > > However I would argue it is not equivalent at all: the contibution of an external body force would add an acceleration term, not impose it, right? > > To make a more concrete example, what if I want to simulate gravity by setting 'accelerate' to some value? Would I obtain free-falling or would gravity be added on top of the force field from atomic intercations? The use of acceleration groups simply adds an acceleration to the one that arises from the forces in the simulation and acts in the update step. -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 sekekeretsu at gmail.com Thu Feb 6 15:37:54 2020 From: sekekeretsu at gmail.com (Seketoulie Keretsu) Date: Thu, 06 Feb 2020 14:37:54 -0000 Subject: [gmx-users] Problem with mpirun Message-ID: Dear Sir/Madam, We just installed gromacs 2019 today (MPI compiled) and we're currently testing the commands with MPI. The installations went fine however,we are having issues with the commands. $ echo $PATH /opt/vmd/1.9.3/bin:/opt/g_mmpbsa/bin:/opt/gromacs/2019.5/bin However, when we execute the commands we get the following response. mpirun -np 8 gmx_mpi mdrun -s md_0_10.tpr -o md_0_10.trr -cpi md_0_10.cpt -c md_0_10.gro -e md_0_10.edr -g md_0_10.log =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 15 PID 23681 RUNNING AT biopo1 = KILLED BY SIGNAL: 4 (Illegal instruction) =================================================================================== We get the same error for 'mpirun -np 16 gmx_mpi mdrun -h' or ' mpirun -np 8 gmx_mpi mdrun -v -deffnm md_0_10' What are we missing here, please advise. Sincerely, Seket From spoel at xray.bmc.uu.se Thu Feb 6 16:42:16 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 06 Feb 2020 15:42:16 -0000 Subject: [gmx-users] Gromacs question In-Reply-To: References: Message-ID: Den 2020-02-06 kl. 15:15, skrev Kneller, Daniel: > Hi Dr. van der Spoel, > > I had hoped to reply using the user-lists but I realize now that I had > the user-lists in digest mode and did not want to start another thread. CC-ing there anyway just such that it gets archived. > > Thank you for responding to my question about using gmx dos and the > vibrational power spectrum option for gmx velacc for protein. > I am interested in quantifying only the vibrational frequency of protein > secondary structure (10-60 cm^-1 ). > In this case, would gmx dos be viable given no limitations on computing > resources? > > I understand that in order to calculate density of states, one needs a > simulation with integration steps every 1-2 fs and saved trajectories > about every 2-4 fs. What would be considered a long enough simulation to > be meaningful? What would be required to show sufficient convergence? Is > it simply a matter of replicates or something more? > From my experience with liquids, 100 ps is enough for a liquid with low viscosity, but not for a liquid with high viscosity. Then there are typically hundreds of molecules to average over. What that means for a protein is hard to tell, but for sure you need 100 times the time scale (of 10 ps) to come up to the same level of sampling, then the protein is very viscous compared to a liquid, structure and dynamics have a long correlation time. If you have a truly stable protein you may be better of doing a normal mode analysis. > > Thank you, > > Daniel > > > *Daniel Kneller* > Postdoctoral Research Associate > Neutron Scattering Division > Neutron Sciences Directorate > Oak Ridge National Laboratory > > -- 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 From r.a.luirink at vu.nl Thu Feb 6 16:53:58 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Thu, 06 Feb 2020 15:53:58 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> Message-ID: <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> Here some output to illustrate what I mean. This is what you would expect and what I also get for standard atom-atom interactions, not 1-4 and not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 (kJ/mol) LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 (kJ/mol) Coul-14:CXD-CDLAL 0 0 0 0 (kJ/mol) LJ-14:CXD-CDLAL 0 0 0 0 (kJ/mol) This is what you would expect for 1-4 interactions (which I get for standard 1-4 interactions, but not the ones I specified) not LJ-SR and not Coul-SR but LJ-14 and Coul-14: Coul-SR:CXN-CDLAL 0 0 0 0 (kJ/mol) LJ-SR:CXN-CDLAL 0 0 0 0 (kJ/mol) Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 -1.69012e-05 (kJ/mol) LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 -7.03428e-05 (kJ/mol) And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR as LJ-14 and Coul-14: Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 (kJ/mol) LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 (kJ/mol) Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 (kJ/mol) LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 (kJ/mol) It seems like a bug to me, or I have overlooked something.. ?On 06/02/2020, 14:44, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: Gromacs version 2018.6 btw. On 06/02/2020, 13:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: What I have tried is, instead of adding them to the [ pairs ] block, is change the epsilon value manually via the [ nonbon_params ] block. However, I can?t manually change the electrostatic interactions to account for the fudgeQQ (0.8333) for these specific pairs (or at least, I haven?t found a way to do so). From: "Luirink, R.A." Date: Thursday, 6 February 2020 at 11:49 To: "gmx-users at gromacs.org" Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Hello, I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such). I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions. When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue? Best, Rosa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 mbhendle at iitk.ac.in Thu Feb 6 20:18:59 2020 From: mbhendle at iitk.ac.in (mbhendle) Date: Thu, 06 Feb 2020 19:18:59 -0000 Subject: [gmx-users] nrexcl for TIP4P-ICE water model Message-ID: <1697a91813d0d33d9f5c1292b150c472@iitk.ac.in> Hello all, I want to use tip4p-ice water for my simulations and the tip4p-ice topology "_tip4p-ice.itp_" (i am using )is same as: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model [1] Is nrexcl=1 correct ??? As the other topologies (eg. spc, spce, tip4p) in oplsaa have nrexcl=2. Will it affect my results. As nrexcl is used to set 1-4 non-bonded interactions on/off and water does't have any. Thanks & Regards, Mangesh Bhendale Links: ------ [1] http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model From 177cy500.bratin at nitk.edu.in Fri Feb 7 02:23:29 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Fri, 07 Feb 2020 01:23:29 -0000 Subject: [gmx-users] Graphene Sheet in GROMOS 54A7 In-Reply-To: References: Message-ID: Hi, What .itp file you have .. On Tue 4 Feb, 2020, 4:44 PM Mohamed Abdelaal, wrote: > Hello everybody :) > > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the > .top file knowing that I have the .itp file. > > 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 jalemkul at vt.edu Fri Feb 7 02:38:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 07 Feb 2020 01:38:21 -0000 Subject: [gmx-users] nrexcl for TIP4P-ICE water model In-Reply-To: <1697a91813d0d33d9f5c1292b150c472@iitk.ac.in> References: <1697a91813d0d33d9f5c1292b150c472@iitk.ac.in> Message-ID: <4a101e52-c633-bcd6-b253-6a3c87bc9903@vt.edu> On 2/6/20 2:18 PM, mbhendle wrote: > Hello all, > > I want to use tip4p-ice water for my simulations and the tip4p-ice > topology "_tip4p-ice.itp_" (i am using )is same as: > > http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model > [1] > > Is nrexcl=1 correct ??? > As the other topologies (eg. spc, spce, tip4p) in oplsaa have nrexcl=2. > Will it affect my results. The value of nrexcl is made irrelevant in that topology by the subsequent definition of [exclusions] for all possible intramolecular interactions. > As nrexcl is used to set 1-4 non-bonded interactions on/off and water > does't have any. The value of nrexcl sets the distance in terms of bonds for the excluded interactions; it is not only applicable for excluding 1-4 interactions. In conventional biomolecular force fields, nrexcl=3 does exclude interactions within 3 bonds. But you can set the value (in principle) to anything you want. As water cannot have 3 consecutive bonds, the proper value to exclude all intramolecular interactions is 2. -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 alessandra.villa.biosim at gmail.com Fri Feb 7 09:38:28 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Fri, 07 Feb 2020 08:38:28 -0000 Subject: [gmx-users] How to use LBFGS minimization In-Reply-To: References: Message-ID: Hi, On Thu, Feb 6, 2020 at 10:39 AM Bratin Kumar Das < 177cy500.bratin at nitk.edu.in> wrote: > Dear all > I want to use LBFGS algorithm for minimizing my system..what > parameters is required for that...any suggestions or any tutorial is there > for that. > the mdp parameter for LBFGS is > integrator= l-bfgs to be combined with other mdp for energy minimization and other system specific setting ( http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html) some information on LBFGS http://manual.gromacs.org/documentation/current/reference-manual/algorithms/energy-minimization.html?highlight=energy%20minimization Best regards Alessandra -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 i.ilie at bioc.uzh.ch Fri Feb 7 14:38:24 2020 From: i.ilie at bioc.uzh.ch (i.ilie at bioc.uzh.ch) Date: Fri, 07 Feb 2020 13:38:24 -0000 Subject: [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain Message-ID: Dear gmx users, I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs does not recognize the methylated C as part of the DNA but takes it as "Other" and it breaks my DNA into different chains. Any thoughts on how I could avoid D5MC being recognized as "Other" and correctly take it as "DNA"? Thank you. Best, Ioana From m.b.abdelaal at gmail.com Fri Feb 7 14:39:30 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Fri, 07 Feb 2020 13:39:30 -0000 Subject: [gmx-users] Graphene Sheet in GROMOS 54A7 In-Reply-To: References: Message-ID: many thanks for your reply :) I have the graphene sheet topology file .itp not .top. I am trying to evaporate some molecules on the graphene sheet. Unfortunately, I didn't find information in the manual about how to do such an evaporation on the graphene sheet. what I have now is the graphene sheet topology .itp and the topology file .itp for the molecule that I want to evaporate on the graphene sheet. I can't find a lot of information about evaporation of molecules using GROMACS. I would be really grateful If somebody can guide me, where to search or to get the below information: 1. how to put the graphene sheet inside the box if i only have its topology file .itp. 2. how to perform the evaporation process itself, knowing that I have the .pdb and the .itp file for the molecule that I want to evaporate. Thanks, Mohamed On Fri, Feb 7, 2020 at 1:23 AM Bratin Kumar Das <177cy500.bratin at nitk.edu.in> wrote: > Hi, > What .itp file you have .. > > On Tue 4 Feb, 2020, 4:44 PM Mohamed Abdelaal, > wrote: > > > Hello everybody :) > > > > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get > the > > .top file knowing that I have the .itp file. > > > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 shakirashukoor1993 at gmail.com Fri Feb 7 19:02:19 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Fri, 07 Feb 2020 18:02:19 -0000 Subject: [gmx-users] MARTINI forcefield Message-ID: Hi all Is anyone familiar about electron density profiles using gmx density for lipid bilayer modeled with MARTINI forcefield in gromacs. I am confused with the electrons.dat file to be provided with the calculations. What should be the number of electrons to be provided in the calculations for the MARTINI beads. Can anyone help me with the calculations? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From ykchen at jlu.edu.cn Sat Feb 8 13:18:22 2020 From: ykchen at jlu.edu.cn (Yakun) Date: Sat, 08 Feb 2020 12:18:22 -0000 Subject: [gmx-users] error found when doing tpi calculations Message-ID: <212de548.1c122.17024b5dc69.Coremail.ykchen@jlu.edu.cn> Dear all, I am using test particle insertion (tpi) method to calculate the henry constant for CO2 dissovling in spce water. I have read the manual and also a webpage (https://www.svedruziclab.com/tutorials/gromacs/6-tpi/). However, the last step 'gmx mdrun -deffnm tpi -rerun npt' gave me the following error message 'Fatal error: Can not do TPI for multi-atom molecule with a twin-range cut-off For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors' I guessed that I have make rvdw and rcoulomb different. But setting different data for rvdw and rcoulomb did not work. Anyone know what I did wrong. Any advice? Thanks in advance Yakun Chen From qasimpars at gmail.com Sat Feb 8 19:29:41 2020 From: qasimpars at gmail.com (Qasim Pars) Date: Sat, 08 Feb 2020 18:29:41 -0000 Subject: [gmx-users] restraint-lambdas and bonded-lambdas for binding free energy calculations Message-ID: Dear users, I am trying to do the binding free energy calculations. For complex simulations (Ligand decoupling from complex) I use "intermolecular_interactions" for Boresch restraints at the end of the topology file of complex structure: [ intermolecular_interactions ] [ bonds ] ... [ angle_restraints ] ... [ dihedral_restraints ] ... I use "coul-lambdas " and "vdw-lambdas" in all the mdp files but I am not sure whether I also should use "restraint-lambdas" and "bonded-lambdas". My questions are: - Should I also use both "restraint-lambdas" and "bonded-lambdas" or one of them in the mdp files? - The dihedral_restraints and bonds under intermolecular_interactions aren't controlled by "restraint-lambdas" and "bonded-lambdas" in the mdp files, respectively, right? Thanks in advance, -- Qasim Pars From kevin.boyd at uconn.edu Sat Feb 8 19:34:54 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Sat, 08 Feb 2020 18:34:54 -0000 Subject: [gmx-users] Problem with mpirun In-Reply-To: References: Message-ID: Hi, Can you send us the output of gmx_mpi --version? I typically see illegal instructions when I compile gromacs on one architecture but accidentally try to run it on another. Kevin On Thu, Feb 6, 2020 at 6:38 AM Seketoulie Keretsu wrote: > Dear Sir/Madam, > > We just installed gromacs 2019 today (MPI compiled) and we're currently > testing the commands with MPI. The installations went fine however,we are > having issues with the commands. > > $ echo $PATH > /opt/vmd/1.9.3/bin:/opt/g_mmpbsa/bin:/opt/gromacs/2019.5/bin > > However, when we execute the commands we get the following response. > > mpirun -np 8 gmx_mpi mdrun -s md_0_10.tpr -o md_0_10.trr -cpi md_0_10.cpt > -c md_0_10.gro -e md_0_10.edr -g md_0_10.log > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = RANK 15 PID 23681 RUNNING AT biopo1 > = KILLED BY SIGNAL: 4 (Illegal instruction) > > =================================================================================== > > We get the same error for 'mpirun -np 16 gmx_mpi mdrun -h' or ' mpirun -np > 8 gmx_mpi mdrun -v -deffnm md_0_10' > > What are we missing here, please advise. > > Sincerely, > Seket > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 mohammad.madani at uconn.edu Sun Feb 9 10:38:59 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Sun, 09 Feb 2020 09:38:59 -0000 Subject: [gmx-users] problem with mpi run in REMD simulation Message-ID: Dear all users I want to run a REMD simulation on the stampede2 cluster. I have 376 replicas. when I run the simulation on 28 nodes and 1880 mpi task ( 5core per replica) I get the error. [proxy:0:0 at c403-004.stampede2.tacc.utexas.edu] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file traj.trr (No such file or directory) I do not know what is the problem. Could you please help me? this is my bash script file: #!/bin/bash #SBATCH -J myjob #SBATCH -o myjob.%j.out #SBATCH -e myjob.%j.err #SBATCH --mail-user=mohammad.madani at uconn.edu #SBATCH --mail-type=ALL #SBATCH -A TG-MCB180008 #SBATCH -p normal #SBATCH -N 28 #SBATCH -n 1880 #SBATCH -t 48:00:00 module load gromacs/2019.4 module load intel/18.0.2 module load impi/18.0.2 module mvapich2/2.3.1 ibrun /opt/apps/intel18/impi/18.0.2/gromacs/2019.4/bin/mdrun_mpi -s -o traj.trr -c nvt.gro -e ener.edr -g md.log -replex 500 -multidir equil0 equil1 ..... equil375 Many thanks [image: Mailtrack] Sender notified by Mailtrack 02/09/20, 04:38:01 AM From mark.j.abraham at gmail.com Sun Feb 9 20:30:16 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sun, 09 Feb 2020 19:30:16 -0000 Subject: [gmx-users] problem with mpi run in REMD simulation In-Reply-To: References: Message-ID: Hi, First, make sure you can run a normal single-replica simulation with MPI on this machine, so that you know you have the mechanics right. Follow the cluster's documentation for setting up the scripts and calling MPI. I suspect your problem starts here, perhaps with having a suitable working directory to which to write your output files. Next, be aware that locality is very important for the cores that participate in a single simulation. It's not enough to choose five cores per replica and deduce that 28 nodes can give enough total cores. Each replica should be assigned cores within the same node (or lose lots of performance), so you will have to do some arithmetic to choose how many replicas per node are suitable to fit all of the cores of those replicas within a node. The best choice for the number of replicas will depend on the number of cores per node. Mark On Sun., 9 Feb. 2020, 10:39 Mohammad Madani, wrote: > Dear all users > I want to run a REMD simulation on the stampede2 cluster. > I have 376 replicas. when I run the simulation on 28 nodes and 1880 mpi > task ( 5core per replica) I get the error. > > [proxy:0:0 at c403-004.stampede2.tacc.utexas.edu] HYDU_create_process > (../../utils/launch/launch.c:825): execvp error on file traj.trr (No such > file or directory) > > I do not know what is the problem. > > Could you please help me? > > this is my bash script file: > #!/bin/bash > #SBATCH -J myjob > #SBATCH -o myjob.%j.out > #SBATCH -e myjob.%j.err > > #SBATCH --mail-user=mohammad.madani at uconn.edu > #SBATCH --mail-type=ALL > #SBATCH -A TG-MCB180008 > > #SBATCH -p normal > #SBATCH -N 28 > #SBATCH -n 1880 > #SBATCH -t 48:00:00 > > module load gromacs/2019.4 > > module load intel/18.0.2 > > module load impi/18.0.2 > module mvapich2/2.3.1 > ibrun /opt/apps/intel18/impi/18.0.2/gromacs/2019.4/bin/mdrun_mpi -s -o > traj.trr -c nvt.gro -e ener.edr -g md.log -replex 500 -multidir equil0 > equil1 ..... equil375 > > Many thanks > > > [image: Mailtrack] > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > Sender > notified by > Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > 02/09/20, > 04:38:01 AM > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 shanjayasinghe2011 at gmail.com Sun Feb 9 22:08:53 2020 From: shanjayasinghe2011 at gmail.com (Shan Jayasinghe) Date: Sun, 09 Feb 2020 21:08:53 -0000 Subject: [gmx-users] Micellar shape In-Reply-To: References: Message-ID: Thank you very much. On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: > > > On 2/5/20 12:01 AM, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > > > I want to determine whether I got prolate or oblate micelle in my MD > > simulation. I calculated moment of inertia for a micelle after doing > > clustering. I want to know how do I determine whether it is prolate or > > oblate depending on moment of inertia calculations. > > Compute the ellipticity. > > -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. > -- Best Regards Shan Jayasinghe From mohammad.madani at uconn.edu Mon Feb 10 04:34:06 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Mon, 10 Feb 2020 03:34:06 -0000 Subject: [gmx-users] problem with mpi run in REMD simulation In-Reply-To: References: Message-ID: Dear Mark Thank you for your reply. Could you please say me Whether using 47 nodes and each node has 48 cores for 376 replicas is good or not? In fact 6 core per replicas and all cores that use for each replica is in the one node. Also, I use stampede 2 cluster for my simulation of remd. When I use KNL nodes my simulation was failed but when I use skx nodes remd works well. On Sun, Feb 9, 2020 at 2:30 PM Mark Abraham wrote: > Hi, > > First, make sure you can run a normal single-replica simulation with MPI on > this machine, so that you know you have the mechanics right. Follow the > cluster's documentation for setting up the scripts and calling MPI. I > suspect your problem starts here, perhaps with having a suitable working > directory to which to write your output files. > > Next, be aware that locality is very important for the cores that > participate in a single simulation. It's not enough to choose five cores > per replica and deduce that 28 nodes can give enough total cores. Each > replica should be assigned cores within the same node (or lose lots of > performance), so you will have to do some arithmetic to choose how many > replicas per node are suitable to fit all of the cores of those replicas > within a node. The best choice for the number of replicas will depend on > the number of cores per node. > > Mark > > On Sun., 9 Feb. 2020, 10:39 Mohammad Madani, > wrote: > > > Dear all users > > I want to run a REMD simulation on the stampede2 cluster. > > I have 376 replicas. when I run the simulation on 28 nodes and 1880 mpi > > task ( 5core per replica) I get the error. > > > > [proxy:0:0 at c403-004.stampede2.tacc.utexas.edu] HYDU_create_process > > (../../utils/launch/launch.c:825): execvp error on file traj.trr (No such > > file or directory) > > > > I do not know what is the problem. > > > > Could you please help me? > > > > this is my bash script file: > > #!/bin/bash > > #SBATCH -J myjob > > #SBATCH -o myjob.%j.out > > #SBATCH -e myjob.%j.err > > > > #SBATCH --mail-user=mohammad.madani at uconn.edu > > #SBATCH --mail-type=ALL > > #SBATCH -A TG-MCB180008 > > > > #SBATCH -p normal > > #SBATCH -N 28 > > #SBATCH -n 1880 > > #SBATCH -t 48:00:00 > > > > module load gromacs/2019.4 > > > > module load intel/18.0.2 > > > > module load impi/18.0.2 > > module mvapich2/2.3.1 > > ibrun /opt/apps/intel18/impi/18.0.2/gromacs/2019.4/bin/mdrun_mpi -s -o > > traj.trr -c nvt.gro -e ener.edr -g md.log -replex 500 -multidir equil0 > > equil1 ..... equil375 > > > > Many thanks > > > > > > [image: Mailtrack] > > < > > > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > > > Sender > > notified by > > Mailtrack > > < > > > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > > > 02/09/20, > > 04:38:01 AM > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 ykchen at jlu.edu.cn Mon Feb 10 09:06:38 2020 From: ykchen at jlu.edu.cn (Yakun) Date: Mon, 10 Feb 2020 08:06:38 -0000 Subject: [gmx-users] error found when doing tpi calculations In-Reply-To: <212de548.1c122.17024b5dc69.Coremail.ykchen@jlu.edu.cn> References: <212de548.1c122.17024b5dc69.Coremail.ykchen@jlu.edu.cn> Message-ID: <6585de21.1c73b.1702e11447b.Coremail.ykchen@jlu.edu.cn> Dear all, I got the problem fixed already. I found the corresponding source code in tpi.cpp saying ''' ..... if (a_tp1 - a_tp0 > 1 && (inputrec->rlist < inputrec->rcoulomb || inputrec->rlist < inputrec->rvdw)) { gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off"); } .... ''' Then I set rlist=rvdw=rcoulomb, problem solved. However, anybody know for my kind of system, is there any optimal parameters to get a better tpi results? Thanks in advance > Dear all, > I am using test particle insertion (tpi) method to calculate the henry constant for CO2 dissovling in spce water. I have read the manual and also a webpage (https://www.svedruziclab.com/tutorials/gromacs/6-tpi/). However, the last step 'gmx mdrun -deffnm tpi -rerun npt' gave me the following error message > 'Fatal error: > Can not do TPI for multi-atom molecule with a twin-range cut-off > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors' > I guessed that I have make rvdw and rcoulomb different. But setting different data for rvdw and rcoulomb did not work. > Anyone know what I did wrong. Any advice? Thanks in advance > > Yakun Chen > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Mon Feb 10 09:32:47 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Mon, 10 Feb 2020 08:32:47 -0000 Subject: [gmx-users] Viscosity calculations of gmx tcaf and gmx energy Message-ID: Dear GMX users, I would like to discuss about the viscosity calculation of gromacs. From the references, I found two different ways to find viscosity of solution such as gmx tcaf and gmx energy methods. I performed 1 ns simulation and saved the data every 10 fs. Then, I extracted the viscosity using about two ways. The data were briefly included in following parts. If you have any experience, please advise me on how the calculations are reliable and which method is more convenient in the literatures. gmx tcaf gives following results ********************** @ xaxis label "k (nm\S-1\N)" @ yaxis label "\xh\f{} (10\S-3\N kg m\S-1\N s\S-1\N)" @TYPE xy 1.278 0.378769 ... 2.213 0.286505 ... 2.556 0.276616 *************************** gmx energy gives several results (a) Bulk viscosity ***************************** @ title "Bulk Viscosity" @ xaxis label "Time (ps)" @ yaxis label "\xh\f{} (cp)" @TYPE xy @ s0 legend "Shear" @ s1 legend "Bulk" 0.01 0.273252 0.515646 0.02 0.169156 0.692718 ... 499.98 1.42159 -0.0215052 499.99 1.42339 -0.00296548 **************************** (b) Shear viscosity integral **************************** @ title "Shear viscosity integral" @ xaxis label "Time (ps)" @ yaxis label "(kg m\S-1\N s\S-1\N ps)" @TYPE xy 0 0 0 0 0 0.01 2.62525e-06 2.62677e-06 2.63998e-06 2.63067e-06 ... 249.99 0.198069 0.356375 0.0775561 0.210666 250 0.198084 0.356393 0.0775584 0.210678 *********************************** (c) Shear viscosity using Einstein relation ********** @ xaxis label "Time (ps)" @ yaxis label "(kg m\S-1\N s\S-1\N)" @TYPE xy 0.005 0 0 0 0 0.015 0.000262525 0.000262677 0.000263998 0.000263067 ... 249.995 0.00153552 0.00183501 0.000227655 0.0011994 250.005 0.0015403 0.00183696 0.000226584 0.00120128 ********** Best regards, Mijiddorj From shakirashukoor1993 at gmail.com Mon Feb 10 11:28:33 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Mon, 10 Feb 2020 10:28:33 -0000 Subject: [gmx-users] Electron density profile calculation Message-ID: Hi all Is anyone familiar with Gromacs analysis of MARTINI modeled lipid bilayer systems. -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From mark.j.abraham at gmail.com Mon Feb 10 11:32:41 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 10 Feb 2020 10:32:41 -0000 Subject: [gmx-users] problem with mpi run in REMD simulation In-Reply-To: References: Message-ID: Hi, On Mon, 10 Feb 2020 at 04:34, Mohammad Madani wrote: > Dear Mark > Thank you for your reply. > Could you please say me Whether using 47 nodes and each node has 48 cores > for 376 replicas is good or not? > In fact 6 core per replicas and all cores that use for each replica is in > the one node. > Yes, 4 or 6 cores per replica is a much better choice, because they are divisors of 48. Whether 47 replicas is a wise choice is a further question. Assuming the usual case where you're only interested in the sampling at the bottom T, I strongly suggest starting with a short preliminary simulation with many fewer replicas (e.g. 10) over a narrower T range and observe how long you have to simulate to even get one replica to be at the top T and then reach the bottom T. That time will be much much longer for 376 replicas. My guess is that you won't want to spend that much computer time :-) Also, I use stampede 2 cluster for my simulation of remd. When I use KNL > nodes my simulation was failed but when I use skx nodes remd works well. > KNL/SKX is irrelevant to GROMACS and REMD. If there's issues, then they are almost certainly in how the version of GROMACS was built, how the job is being run, or how the job is using the GROMACS version. Mark > On Sun, Feb 9, 2020 at 2:30 PM Mark Abraham > wrote: > > > Hi, > > > > First, make sure you can run a normal single-replica simulation with MPI > on > > this machine, so that you know you have the mechanics right. Follow the > > cluster's documentation for setting up the scripts and calling MPI. I > > suspect your problem starts here, perhaps with having a suitable working > > directory to which to write your output files. > > > > Next, be aware that locality is very important for the cores that > > participate in a single simulation. It's not enough to choose five cores > > per replica and deduce that 28 nodes can give enough total cores. Each > > replica should be assigned cores within the same node (or lose lots of > > performance), so you will have to do some arithmetic to choose how many > > replicas per node are suitable to fit all of the cores of those replicas > > within a node. The best choice for the number of replicas will depend on > > the number of cores per node. > > > > Mark > > > > On Sun., 9 Feb. 2020, 10:39 Mohammad Madani, > > wrote: > > > > > Dear all users > > > I want to run a REMD simulation on the stampede2 cluster. > > > I have 376 replicas. when I run the simulation on 28 nodes and 1880 mpi > > > task ( 5core per replica) I get the error. > > > > > > [proxy:0:0 at c403-004.stampede2.tacc.utexas.edu] HYDU_create_process > > > (../../utils/launch/launch.c:825): execvp error on file traj.trr (No > such > > > file or directory) > > > > > > I do not know what is the problem. > > > > > > Could you please help me? > > > > > > this is my bash script file: > > > #!/bin/bash > > > #SBATCH -J myjob > > > #SBATCH -o myjob.%j.out > > > #SBATCH -e myjob.%j.err > > > > > > #SBATCH --mail-user=mohammad.madani at uconn.edu > > > #SBATCH --mail-type=ALL > > > #SBATCH -A TG-MCB180008 > > > > > > #SBATCH -p normal > > > #SBATCH -N 28 > > > #SBATCH -n 1880 > > > #SBATCH -t 48:00:00 > > > > > > module load gromacs/2019.4 > > > > > > module load intel/18.0.2 > > > > > > module load impi/18.0.2 > > > module mvapich2/2.3.1 > > > ibrun /opt/apps/intel18/impi/18.0.2/gromacs/2019.4/bin/mdrun_mpi -s -o > > > traj.trr -c nvt.gro -e ener.edr -g md.log -replex 500 -multidir equil0 > > > equil1 ..... equil375 > > > > > > Many thanks > > > > > > > > > [image: Mailtrack] > > > < > > > > > > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > > > > > Sender > > > notified by > > > Mailtrack > > > < > > > > > > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > > > > > 02/09/20, > > > 04:38:01 AM > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 Mon Feb 10 16:44:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 10 Feb 2020 15:44:35 -0000 Subject: [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain In-Reply-To: References: Message-ID: On 2/7/20 8:38 AM, i.ilie at bioc.uzh.ch wrote: > Dear gmx users, > > I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs does not recognize the methylated C as part of the DNA but takes it as "Other" and it breaks my DNA into different chains. Any thoughts on how I could avoid D5MC being recognized as "Other" and correctly take it as "DNA"? Add it as a DNA residue in residuetypes.dat. -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 vikasdubey1008 at gmail.com Tue Feb 11 08:06:52 2020 From: vikasdubey1008 at gmail.com (Live King) Date: Tue, 11 Feb 2020 07:06:52 -0000 Subject: [gmx-users] Electric field settings in GROMACS Message-ID: Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not observing such behavior despite running the all-atom simulation for 400ns in any case. I am using gromacs 2018.2, my mdp file is standard charmm-gui production with electric field option. for example 500mV electric field in Z-direction : electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = 500 mV * Are there any settings to run the electric field simulation that I miss? Any help will be greatly appreciated. Thank you, From islamshahee at gmail.com Tue Feb 11 09:11:36 2020 From: islamshahee at gmail.com (SHAHEE ISLAM) Date: Tue, 11 Feb 2020 08:11:36 -0000 Subject: [gmx-users] density map calculation of lipid around 10 angstrom of protein Message-ID: hello i am trying to calculate 2D number-density maps of lipid around 10 angstrom of protein. My system consist both coarse grained protein and lipid (using martini force field).the command is gmx densmap -f *.xtc -s *.tpr -n *.ndx -aver z -bin 0.02 -xmin -1 -xmax -1 -o *.xpm but the error i am getting is hi(0.000000)<=lo(0.000000) can anyone please guide me about this error. thanking you shahee From nt2614888 at gmail.com Tue Feb 11 13:53:00 2020 From: nt2614888 at gmail.com (Neha Tiwari) Date: Tue, 11 Feb 2020 12:53:00 -0000 Subject: [gmx-users] Query Message-ID: Dear Gromacs Experts, I want to parametrize Ferric citrate and have already performed DFT calculations using different basis sets, but I am unable to upload the refined molecule on, ATB so that I can get its topology files to proceed further. Please help. Thanks in advance. Neha. From devargyachakraborty.kgp at gmail.com Tue Feb 11 14:12:46 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Tue, 11 Feb 2020 13:12:46 -0000 Subject: [gmx-users] simulation on graphite sheet Message-ID: Hello, I was thinking of simulating a liquid on graphite surface and have made a system but couldnt simulate it. while doing the nvt simulation, after some time i am getting lincs error. can anybody help me, if you want i can send you the files. Thanks, Devargya chakraborty PhD scholar computational nano-science lab IIT-patna From marko at kth.se Tue Feb 11 14:21:11 2020 From: marko at kth.se (Marko Petrovic) Date: Tue, 11 Feb 2020 13:21:11 -0000 Subject: [gmx-users] Python API Documentation question Message-ID: Hello As I'm quite new to both gromacs in and of itself and the python API I'm struggling a bit figuring out how to go about getting simulations running using the API. I've managed to write a Python script creating and running shell command line commands to run through the Lysozyme tutorial, but that totally circumvents the API. The API has a function "commandline_operation" which I believe should also be usable for this, unfortunately I can't say I'm totally clear on the nomenclature used in the documentation so I'm unsure of what or where I go wrong. For example the executable parameter and arguments parameter in "gmx grompp"... is gmx the executable withh grompp a parameter or grompp the executable and the rest of the line parameters? And input_files and output_files, are they meant to be declared in those parameters only, in arguments only or both, and do flag keys need the dash prefix? I will be very thankful for any help anyone can give regarding this. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology From dburns at iastate.edu Tue Feb 11 19:56:15 2020 From: dburns at iastate.edu (Daniel Burns) Date: Tue, 11 Feb 2020 18:56:15 -0000 Subject: [gmx-users] REMD stall out Message-ID: Hi, I continue to have trouble getting an REMD job to run. It never makes it to the point that it generates trajectory files but it never gives any error either. I have switched from a large TREMD with 72 replicas to the Plumed Hamiltonian method with only 6 replicas. Everything is now on one node and each replica has 6 cores. I've turned off the dynamic load balancing on this attempt per the recommendation from the Plumed site. Any ideas on how to troubleshoot? Thank you, Dan From chellisaimanohar at gmail.com Tue Feb 11 22:46:44 2020 From: chellisaimanohar at gmail.com (sai manohar) Date: Tue, 11 Feb 2020 21:46:44 -0000 Subject: [gmx-users] Query In-Reply-To: References: Message-ID: You cannot generate the desired parameters (.itp) for metals in the ATB server. In fact even CGenFF or RED server are also not useful for metals. However, if you have access to any DFT modeling in house to perform QM calculations using Gaussian etc., you can generate/build your own force field for these particular kind of molecules. Hope that's helpful. On Tue, Feb 11, 2020, 18:23 Neha Tiwari wrote: > Dear Gromacs Experts, > I want to parametrize Ferric citrate and have already performed DFT > calculations using different basis sets, but I am unable to upload the > refined molecule on, ATB so that I can get its topology files to proceed > further. > Please help. > > Thanks in advance. > Neha. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 tiasha18 at iitg.ac.in Wed Feb 12 08:53:46 2020 From: tiasha18 at iitg.ac.in (TIASHA ADHIKARY) Date: Wed, 12 Feb 2020 07:53:46 -0000 Subject: [gmx-users] Free energy perturbation of ligand Message-ID: Hello, I am trying to calculate FEP using gromacs. I have used pmx for initial structure and .itp file. I am getting the following warning WARNING 1 [file MOL.itp, line 185]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B Even if I ignore this warning, structure is not minimizing. "Steepest Descents converged to machine precision in 185 steps, but did not reach the requested Fmax < 100. Potential Energy = 1.8540598e+08 Maximum force = 5.4468039e+04 on atom 6 Norm of force = 2.0960916e+03" I am not understanding how to solve this error. I will be highly obliged if anybody help me. Thanks in advance. Regards, Tiasha Adhikary M.Tech, IIT Guwahati From tiasha18 at iitg.ac.in Wed Feb 12 08:53:47 2020 From: tiasha18 at iitg.ac.in (TIASHA ADHIKARY) Date: Wed, 12 Feb 2020 07:53:47 -0000 Subject: [gmx-users] Free energy perturbation of ligand Message-ID: Hello, I am trying to calculate FEP using gromacs. I have used pmx for initial structure and .itp file. I am getting the following warning WARNING 1 [file MOL.itp, line 185]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B Even if I ignore this warning, structure is not minimizing. "Steepest Descents converged to machine precision in 185 steps, but did not reach the requested Fmax < 100. Potential Energy = 1.8540598e+08 Maximum force = 5.4468039e+04 on atom 6 Norm of force = 2.0960916e+03" I am not understanding how to solve this error. I will be highly obliged if anybody help me. Thanks in advance. Regards, Tiasha Adhikary M.Tech, IIT Guwahati From alessandra.villa.biosim at gmail.com Wed Feb 12 08:56:08 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 12 Feb 2020 07:56:08 -0000 Subject: [gmx-users] simulation on graphite sheet In-Reply-To: References: Message-ID: Hi, On Tue, Feb 11, 2020 at 2:13 PM Devargya Chakraborty < devargyachakraborty.kgp at gmail.com> wrote: > Hello, > I was thinking of simulating a liquid on graphite surface and have made a > system but couldnt simulate it. while doing the nvt simulation, after some > time i am getting lincs error. can anybody help me, if you want i can send > you the files. > > Just some general suggestions: 1) Perform energy minimization before setting the MD simulation. 2) check that you are using a time step compatible with the applied force field, and that the constraint conditions are in line with force field. (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=lincs#bonds ) 3) check the system is properly equilibrated (e.i temperature) Best regards Alessandra > Thanks, > > Devargya chakraborty > PhD scholar > computational nano-science lab > IIT-patna > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 12 09:14:20 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 12 Feb 2020 08:14:20 -0000 Subject: [gmx-users] Free energy perturbation of ligand In-Reply-To: References: Message-ID: Hi, On Wed, Feb 12, 2020 at 8:54 AM TIASHA ADHIKARY wrote: > Hello, > I am trying to calculate FEP using gromacs. I have used pmx for initial > structure and .itp file. > I am getting the following warning > > WARNING 1 [file MOL.itp, line 185]: > Some parameters for bonded interaction involving perturbed atoms are > specified explicitly in state A, but not B - copying A to B > > Even if I ignore this warning, structure is not minimizing. > > "Steepest Descents converged to machine precision in 185 steps, > but did not reach the requested Fmax < 100. > Potential Energy = 1.8540598e+08 > Maximum force = 5.4468039e+04 on atom 6 > Norm of force = 2.0960916e+03" > > My guess is that your problem is in energy minimization step and not in free energy calculation (NOTE I am not familiar with pmx). The warning does not affect your energy minimization. If you perform the energy minimization without state B, you should get the same. To solve the problem, you could modify energy minimization setting (maybe you could use other methods or changing the criteria - see below) or/and check that there is not something "wrong" in your starting structure. http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#run-control http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=steep#energy-minimization Best regards Alessandra > I am not understanding how to solve this error. I will be highly obliged > if anybody help me. > > Thanks in advance. > > Regards, > Tiasha Adhikary > M.Tech, IIT Guwahati > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 peter.mawanga.lagos at gmail.com Wed Feb 12 11:41:27 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Wed, 12 Feb 2020 10:41:27 -0000 Subject: [gmx-users] Experimental to Simulation Time Period Conversion Message-ID: Dear group members My sincere apologies for the non-Gromacs related question, but I require this information urgently and hence posted my query here. Could someone please provide me with any guidelines to appropriately model experimental processes with molecular dynamics simulations? Since the simulation periods are usually much shorter than the experimental time scales, I was searching for a generally acceptable time reduction factor or some literature towards that direction. Any information or suggestion would be greatly appreciated. -- Cheers Peter From cristina.gonzalezfdez at unican.es Wed Feb 12 12:26:54 2020 From: cristina.gonzalezfdez at unican.es (Gonzalez Fernandez, Cristina) Date: Wed, 12 Feb 2020 11:26:54 -0000 Subject: [gmx-users] Protein stabilization Message-ID: <90ad2be1a42b4842a0607e74ddd05d1e@unican.es> Dear Gromacs users, I'm trying to perform a protein-lipid complex simulation. While the interaction between these molecules seems reasonable, the protein Root Mean Square Deviation is too high, and I don't know how to stabilice it. Could you recommend me any simulation trick to stabilize the protein and improve the simulation? Thank you in advance!! Cristina From johnwhittake at zedat.fu-berlin.de Wed Feb 12 12:51:37 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 12 Feb 2020 11:51:37 -0000 Subject: [gmx-users] Experimental to Simulation Time Period Conversion In-Reply-To: References: Message-ID: <53168.160.45.109.123.1581508192.webmail@webmail.zedat.fu-berlin.de> > Dear group members > > My sincere apologies for the non-Gromacs related question, but I require > this information urgently and hence posted my query here. > > Could someone please provide me with any guidelines to appropriately model > experimental processes with molecular dynamics simulations? What experimental processes are you talking about? Most timescales of interest for physical processes range from picoseconds to seconds to thousands of years. As you note, most timescales are out of reach of MD (simulating anything interesting over the microsecond timescale is extremely difficult). > > Since the simulation periods are usually much shorter than the > experimental > time scales, I was searching for a generally acceptable time reduction > factor or some literature towards that direction. What do you mean by "time reduction factor"? What exactly are you doing? There are enhanced sampling methods which sort of "accelerate" the pace of the process/system you are studying... Perhaps looking in that direction might give you some ideas. Best, John > > Any information or suggestion would be greatly appreciated. > > -- > Cheers > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 johnwhittake at zedat.fu-berlin.de Wed Feb 12 12:51:37 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 12 Feb 2020 11:51:37 -0000 Subject: [gmx-users] Experimental to Simulation Time Period Conversion In-Reply-To: References: Message-ID: <53168.160.45.109.123.1581508192.webmail@webmail.zedat.fu-berlin.de> > Dear group members > > My sincere apologies for the non-Gromacs related question, but I require > this information urgently and hence posted my query here. > > Could someone please provide me with any guidelines to appropriately model > experimental processes with molecular dynamics simulations? What experimental processes are you talking about? Most timescales of interest for physical processes range from picoseconds to seconds to thousands of years. As you note, most timescales are out of reach of MD (simulating anything interesting over the microsecond timescale is extremely difficult). > > Since the simulation periods are usually much shorter than the > experimental > time scales, I was searching for a generally acceptable time reduction > factor or some literature towards that direction. What do you mean by "time reduction factor"? What exactly are you doing? There are enhanced sampling methods which sort of "accelerate" the pace of the process/system you are studying... Perhaps looking in that direction might give you some ideas. Best, John > > Any information or suggestion would be greatly appreciated. > > -- > Cheers > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 peter.mawanga.lagos at gmail.com Wed Feb 12 14:23:17 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Wed, 12 Feb 2020 13:23:17 -0000 Subject: [gmx-users] Experimental to Simulation Time Period Conversion In-Reply-To: <53168.160.45.109.123.1581508192.webmail@webmail.zedat.fu-berlin.de> References: <53168.160.45.109.123.1581508192.webmail@webmail.zedat.fu-berlin.de> Message-ID: Thanks a lot sir for your reply. Since experiments take place over hours but the simulations can at best approach millisecond levels. I was wondering if there is an acceptable time conversion factor from experiments to simulations. For example, the simulation data generated over a 350 ns period can be taken as an acceptable representation of a 24 hours long experiment. On Wed, Feb 12, 2020 at 12:52 PM John Whittaker < johnwhittake at zedat.fu-berlin.de> wrote: > > Dear group members > > > > My sincere apologies for the non-Gromacs related question, but I require > > this information urgently and hence posted my query here. > > > > Could someone please provide me with any guidelines to appropriately > model > > experimental processes with molecular dynamics simulations? > > What experimental processes are you talking about? Most timescales of > interest for physical processes range from picoseconds to seconds to > thousands of years. As you note, most timescales are out of reach of MD > (simulating anything interesting over the microsecond timescale is > extremely difficult). > > > > > Since the simulation periods are usually much shorter than the > > experimental > > time scales, I was searching for a generally acceptable time reduction > > factor or some literature towards that direction. > > What do you mean by "time reduction factor"? What exactly are you doing? > There are enhanced sampling methods which sort of "accelerate" the pace of > the process/system you are studying... Perhaps looking in that direction > might give you some ideas. > > Best, > > John > > > > > Any information or suggestion would be greatly appreciated. > > > > -- > > Cheers > > Peter > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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. > -- Cheers Peter From jalemkul at vt.edu Wed Feb 12 14:45:40 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 12 Feb 2020 13:45:40 -0000 Subject: [gmx-users] Query In-Reply-To: References: Message-ID: <11607902-8a39-09f8-62a1-c6de7f224048@vt.edu> On 2/11/20 4:46 PM, sai manohar wrote: > You cannot generate the desired parameters (.itp) for metals in the ATB > server. In fact even CGenFF or RED server are also not useful for metals. > However, if you have access to any DFT modeling in house to perform QM > calculations using Gaussian etc., you can generate/build your own force > field for these particular kind of molecules. > > Hope that's helpful. To add on to this, one would not parametrize ferric citrate, but would instead parametrize citrate (which CGenFF and other servers can handle) and Fe3+ separately (based on free energy of hydration or whatever other experimental data exist) and then verify that the interactions between the ion and relevant ligand and protein moieties is adequately described (against QM, usually). -Justin > On Tue, Feb 11, 2020, 18:23 Neha Tiwari wrote: > >> Dear Gromacs Experts, >> I want to parametrize Ferric citrate and have already performed DFT >> calculations using different basis sets, but I am unable to upload the >> refined molecule on, ATB so that I can get its topology files to proceed >> further. >> Please help. >> >> Thanks in advance. >> Neha. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 Feb 12 14:46:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 12 Feb 2020 13:46:57 -0000 Subject: [gmx-users] Experimental to Simulation Time Period Conversion In-Reply-To: References: <53168.160.45.109.123.1581508192.webmail@webmail.zedat.fu-berlin.de> Message-ID: On 2/12/20 8:23 AM, Peter Mawanga wrote: > Thanks a lot sir for your reply. > > Since experiments take place over hours but the simulations can at best > approach millisecond levels. I was wondering if there is an acceptable time > conversion factor from experiments to simulations. For example, the > simulation data generated over a 350 ns period can be taken as an > acceptable representation of a 24 hours long experiment. No, I think there is no justification for such a statement. The time scales are entirely different. Simulations can only address questions within the accessible time regime. Enhanced sampling methods may help you better sample states that would only be otherwise observed via impractically long simulations, but you often lose the kinetic argument in favor of thermodynamics (i.e. you can describe the ensemble but not the time taken to interconvert between different states). -Justin > On Wed, Feb 12, 2020 at 12:52 PM John Whittaker < > johnwhittake at zedat.fu-berlin.de> wrote: > >>> Dear group members >>> >>> My sincere apologies for the non-Gromacs related question, but I require >>> this information urgently and hence posted my query here. >>> >>> Could someone please provide me with any guidelines to appropriately >> model >>> experimental processes with molecular dynamics simulations? >> What experimental processes are you talking about? Most timescales of >> interest for physical processes range from picoseconds to seconds to >> thousands of years. As you note, most timescales are out of reach of MD >> (simulating anything interesting over the microsecond timescale is >> extremely difficult). >> >>> Since the simulation periods are usually much shorter than the >>> experimental >>> time scales, I was searching for a generally acceptable time reduction >>> factor or some literature towards that direction. >> What do you mean by "time reduction factor"? What exactly are you doing? >> There are enhanced sampling methods which sort of "accelerate" the pace of >> the process/system you are studying... Perhaps looking in that direction >> might give you some ideas. >> >> Best, >> >> John >> >>> Any information or suggestion would be greatly appreciated. >>> >>> -- >>> Cheers >>> Peter >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe 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. >> > -- ================================================== 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 Feb 12 14:48:03 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 12 Feb 2020 13:48:03 -0000 Subject: [gmx-users] Protein stabilization In-Reply-To: <90ad2be1a42b4842a0607e74ddd05d1e@unican.es> References: <90ad2be1a42b4842a0607e74ddd05d1e@unican.es> Message-ID: On 2/12/20 6:20 AM, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > > > I'm trying to perform a protein-lipid complex simulation. While the interaction between these molecules seems reasonable, the protein Root Mean Square Deviation is too high, and I don't know how to stabilice it. Could you recommend me any simulation trick to stabilize the protein and improve the simulation? > If only such a magic wand existed that made our unexpected outcomes turn into something we want :) If a simulation does not reproduce known behavior, something is wrong with the model, its preparation, the force field parameters, simulation is too short, etc. -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 micpel at kth.se Wed Feb 12 16:30:07 2020 From: micpel at kth.se (Michele Pellegrino) Date: Wed, 12 Feb 2020 15:30:07 -0000 Subject: [gmx-users] generating Doxygen documentation Message-ID: <1581521404890.55927@kth.se> Hi, I am trying to generate the Doxygen documentation for GROMACS from the files in /docs/doxygen. I following 2020 manual, I run 'make doxygen-all' in the build directory, succesfully; I don't know what to do next: I tried to run cmake in the doxygen directory to generate the Doxyfiles, but I get the following errors: """ CMake Error at CMakeLists.txt:36 (include): include could not find load file: gmxCustomCommandUtilities CMake Error at CMakeLists.txt:37 (include): include could not find load file: gmxOptionUtilities CMake Error at CMakeLists.txt:53 (gmx_dependent_option): Unknown CMake command "gmx_dependent_option". """ What should I do? Thanks for your attention, Michele p.s. I am referring to the github master branch current version From mark.j.abraham at gmail.com Wed Feb 12 17:41:26 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 12 Feb 2020 16:41:26 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: <1581521404890.55927@kth.se> References: <1581521404890.55927@kth.se> Message-ID: Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > Hi, > > > I am trying to generate the Doxygen documentation for GROMACS from the > files in /docs/doxygen. > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > succesfully; I don't know what to do next: I tried to run cmake in the > doxygen directory to generate the Doxyfiles, but I get the following errors: > > """ > > CMake Error at CMakeLists.txt:36 (include): > include could not find load file: > > gmxCustomCommandUtilities > > > CMake Error at CMakeLists.txt:37 (include): > include could not find load file: > > gmxOptionUtilities > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > Unknown CMake command "gmx_dependent_option". > > """ > > What should I do? > > > Thanks for your attention, > > Michele > > > p.s. I am referring to the github master branch current version > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 jihong.aafia.ma at gmail.com Wed Feb 12 19:13:56 2020 From: jihong.aafia.ma at gmail.com (Jihong Ma) Date: Wed, 12 Feb 2020 18:13:56 -0000 Subject: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) Message-ID: Dear colleagues, The Society of Engineering Science (SES) 57th Annual Technical Meeting will be held at Hyatt Regency Minneapolis, September 28-30, 2020 ( https://ccaps.umn.edu/SES). As part of this meeting, we are organizing a mini-symposium addressing the *advances in polymer modeling and simulations* under Track 7 - Soft, Active Materials and Applications in Soft Robotics. The production of newer classes of polymers, such as polymerized ionic liquids and nanoporous polymers, opened up exciting possibilities for various applications including electrochemical energy generation and storage, water purification, sensing and releasing biological molecules, development of light-weight structures. Modeling these complex architectures presents significant challenges related, for instance, to the system size, accuracy of the classical and coarse-grained potentials, presence of multi-scale effects, and critical discrepancies with experiment. This mini-symposium aims to bring together scientists and engineers working at the forefront of the modeling and simulation to exchange and share their experiences and recent research results. We cordially invite all the interested scholars to submit your abstract to this mini-symposium. The deadline for submission is *March 17, 2020*. We look forward to your presentations at our symposium. Best regards, Jihong Ma, University of Vermont Traian Dumitrica, University of Minnesota - Twin Cities From paul.bauer.q at gmail.com Wed Feb 12 19:21:42 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Wed, 12 Feb 2020 18:21:42 -0000 Subject: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) In-Reply-To: References: Message-ID: <66c307db-4dc4-6dde-965d-3a1ea8fcfcc5@gmail.com> Hello, please do ***NOT*** use the mailing list for those kinds of announcements in the future. It is supposed to be for people discussing and asking for help with GROMACS, not for advertising conferences. Thanks Paul On 12/02/2020 19:13, Jihong Ma wrote: > Dear colleagues, > > The Society of Engineering Science (SES) 57th Annual Technical Meeting will > be held at Hyatt Regency Minneapolis, September 28-30, 2020 ( > https://ccaps.umn.edu/SES). > > As part of this meeting, we are organizing a mini-symposium addressing > the *advances > in polymer modeling and simulations* under Track 7 - Soft, Active Materials > and Applications in Soft Robotics. > > The production of newer classes of polymers, such as polymerized ionic > liquids and nanoporous polymers, opened up exciting possibilities for > various applications including electrochemical energy generation and > storage, water purification, sensing and releasing biological molecules, > development of light-weight structures. Modeling these complex > architectures presents significant challenges related, for instance, to the > system size, accuracy of the classical and coarse-grained potentials, > presence of multi-scale effects, and critical discrepancies with experiment. > > This mini-symposium aims to bring together scientists and engineers working > at the forefront of the modeling and simulation to exchange and share their > experiences and recent research results. > > We cordially invite all the interested scholars to submit your abstract to > this mini-symposium. The deadline for submission is *March 17, 2020*. > > We look forward to your presentations at our symposium. > > > > Best regards, > > Jihong Ma, University of Vermont > > Traian Dumitrica, University of Minnesota - Twin Cities -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From ericirrgang at gmail.com Wed Feb 12 19:23:25 2020 From: ericirrgang at gmail.com (Eric Irrgang) Date: Wed, 12 Feb 2020 18:23:25 -0000 Subject: [gmx-users] runtime error: pdb2gmx issues in Python API Message-ID: Hi Marko, I apologize for the slow response. "pdb2gmx" is not an executable, but an argument. Try gmx.commandline_operation( 'gmx', ['pdb2gmx', '-water', 'spce', '-ff', 'oplsaa'] ...) I hope to be able to improve the documentation soon, but the exception should have been more helpful. I have created issue #3376 at https://redmine.gromacs.org/issues/3376 Best, Eric On Tue, Feb 4, 2020 at 5:55 PM < gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > > test=gmx.commandline_operation(executable = "pdb2gmx", > arguments = ["-water", "spce" > ,"-ff", "oplsaa" > ] > ... From sperezconesa at gmail.com Wed Feb 12 19:36:46 2020 From: sperezconesa at gmail.com (Sergio Perez) Date: Wed, 12 Feb 2020 18:36:46 -0000 Subject: [gmx-users] lmfit not working Message-ID: Dear gmx comunity, I am trying to use gmx analyze for the block analysis and I get this error: Fatal error: This build of GROMACS was not configured with support for lmfit, so the requested fitting cannot be performed. See the install guide for instructions on how to build GROMACS with lmfit supported. I have installed gromacs with the option -DGMX_USE_LMFIT=INTERNAL, so I am guessing I don't need to install anything in addition. I have tryed both 2019.4 and 2020 but the same happens. I saw on redmine there had been issues with this. Should I post this on redmine? Thanks a lot! Sergio From benson_muite at emailplus.org Wed Feb 12 19:51:34 2020 From: benson_muite at emailplus.org (Benson Muite) Date: Wed, 12 Feb 2020 18:51:34 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: References: <1581521404890.55927@kth.se> Message-ID: <2a6fd2c8-33fe-4f8b-add0-18514b943b81@www.fastmail.com> Hi, What platform are you building on? Last time I tried this, there were a few extra dependencies I needed to install. Benson On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote: > Hi, > > When they succeed, the doxygen targets produce files like > > $builddir/docs/html/doxygen/html-*/index.xhtml > > which you can open in your browser. The doxygen for the released versions > is on the web however, so it's much easier to just use or refer to that. > > Mark > > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > > > Hi, > > > > > > I am trying to generate the Doxygen documentation for GROMACS from the > > files in /docs/doxygen. > > > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > > succesfully; I don't know what to do next: I tried to run cmake in the > > doxygen directory to generate the Doxyfiles, but I get the following errors: > > > > """ > > > > CMake Error at CMakeLists.txt:36 (include): > > include could not find load file: > > > > gmxCustomCommandUtilities > > > > > > CMake Error at CMakeLists.txt:37 (include): > > include could not find load file: > > > > gmxOptionUtilities > > > > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > > Unknown CMake command "gmx_dependent_option". > > > > """ > > > > What should I do? > > > > > > Thanks for your attention, > > > > Michele > > > > > > p.s. I am referring to the github master branch current version > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 sperezconesa at gmail.com Wed Feb 12 20:10:42 2020 From: sperezconesa at gmail.com (Sergio Perez) Date: Wed, 12 Feb 2020 19:10:42 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: <2a6fd2c8-33fe-4f8b-add0-18514b943b81@www.fastmail.com> References: <1581521404890.55927@kth.se> <2a6fd2c8-33fe-4f8b-add0-18514b943b81@www.fastmail.com> Message-ID: I'm using Ubuntu 18.04.3 LTS On Wed, Feb 12, 2020 at 7:52 PM Benson Muite wrote: > > Hi, > What platform are you building on? Last time I tried this, there were a > few extra dependencies I needed to install. > Benson > > On Thu, Feb 13, 2020, at 12:34 AM, Mark Abraham wrote: > > Hi, > > > > When they succeed, the doxygen targets produce files like > > > > $builddir/docs/html/doxygen/html-*/index.xhtml > > > > which you can open in your browser. The doxygen for the released versions > > is on the web however, so it's much easier to just use or refer to that. > > > > Mark > > > > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > > > > > Hi, > > > > > > > > > I am trying to generate the Doxygen documentation for GROMACS from the > > > files in /docs/doxygen. > > > > > > I following 2020 manual, I run 'make doxygen-all' in the build > directory, > > > succesfully; I don't know what to do next: I tried to run cmake in the > > > doxygen directory to generate the Doxyfiles, but I get the following > errors: > > > > > > """ > > > > > > CMake Error at CMakeLists.txt:36 (include): > > > include could not find load file: > > > > > > gmxCustomCommandUtilities > > > > > > > > > CMake Error at CMakeLists.txt:37 (include): > > > include could not find load file: > > > > > > gmxOptionUtilities > > > > > > > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > > > Unknown CMake command "gmx_dependent_option". > > > > > > """ > > > > > > What should I do? > > > > > > > > > Thanks for your attention, > > > > > > Michele > > > > > > > > > p.s. I am referring to the github master branch current version > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 jihong.aafia.ma at gmail.com Wed Feb 12 20:15:35 2020 From: jihong.aafia.ma at gmail.com (Jihong Ma) Date: Wed, 12 Feb 2020 19:15:35 -0000 Subject: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020) In-Reply-To: <66c307db-4dc4-6dde-965d-3a1ea8fcfcc5@gmail.com> References: <66c307db-4dc4-6dde-965d-3a1ea8fcfcc5@gmail.com> Message-ID: Sounds good. Thanks. On Wed, Feb 12, 2020 at 1:22 PM Paul bauer wrote: > Hello, > > please do ***NOT*** use the mailing list for those kinds of > announcements in the future. > It is supposed to be for people discussing and asking for help with > GROMACS, not for advertising conferences. > > Thanks > > Paul > > On 12/02/2020 19:13, Jihong Ma wrote: > > Dear colleagues, > > > > The Society of Engineering Science (SES) 57th Annual Technical Meeting > will > > be held at Hyatt Regency Minneapolis, September 28-30, 2020 ( > > https://ccaps.umn.edu/SES). > > > > As part of this meeting, we are organizing a mini-symposium addressing > > the *advances > > in polymer modeling and simulations* under Track 7 - Soft, Active > Materials > > and Applications in Soft Robotics. > > > > The production of newer classes of polymers, such as polymerized ionic > > liquids and nanoporous polymers, opened up exciting possibilities for > > various applications including electrochemical energy generation and > > storage, water purification, sensing and releasing biological molecules, > > development of light-weight structures. Modeling these complex > > architectures presents significant challenges related, for instance, to > the > > system size, accuracy of the classical and coarse-grained potentials, > > presence of multi-scale effects, and critical discrepancies with > experiment. > > > > This mini-symposium aims to bring together scientists and engineers > working > > at the forefront of the modeling and simulation to exchange and share > their > > experiences and recent research results. > > > > We cordially invite all the interested scholars to submit your abstract > to > > this mini-symposium. The deadline for submission is *March 17, 2020*. > > > > We look forward to your presentations at our symposium. > > > > > > > > Best regards, > > > > Jihong Ma, University of Vermont > > > > Traian Dumitrica, University of Minnesota - Twin Cities > > > -- > 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 micpel at kth.se Wed Feb 12 20:39:03 2020 From: micpel at kth.se (Michele Pellegrino) Date: Wed, 12 Feb 2020 19:39:03 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: References: <1581521404890.55927@kth.se>, Message-ID: <1581536340977.3706@kth.se> Mark, no such directory is produced after make (evein if the output is 'Built target doxygen-all'). The only Doxyfile I can utilize to generate html/latex documentation is 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. It seems I need to run cmake somewhere, somehow, but it's not really clear to me in which directory (and with which options(s)). Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham Sent: 12 February 2020 17:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] generating Doxygen documentation Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > Hi, > > > I am trying to generate the Doxygen documentation for GROMACS from the > files in /docs/doxygen. > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > succesfully; I don't know what to do next: I tried to run cmake in the > doxygen directory to generate the Doxyfiles, but I get the following errors: > > """ > > CMake Error at CMakeLists.txt:36 (include): > include could not find load file: > > gmxCustomCommandUtilities > > > CMake Error at CMakeLists.txt:37 (include): > include could not find load file: > > gmxOptionUtilities > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > Unknown CMake command "gmx_dependent_option". > > """ > > What should I do? > > > Thanks for your attention, > > Michele > > > p.s. I am referring to the github master branch current version > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 micpel at kth.se Wed Feb 12 20:46:28 2020 From: micpel at kth.se (Michele Pellegrino) Date: Wed, 12 Feb 2020 19:46:28 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: <1581536340977.3706@kth.se> References: <1581521404890.55927@kth.se>, , <1581536340977.3706@kth.se> Message-ID: <1581536781424.75686@kth.se> Moreover: the link to Jenkins does not work (section 7.8.1, "Building the documentation"): http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Michele Pellegrino Sent: 12 February 2020 20:39 To: gmx-users at gromacs.org Subject: Re: [gmx-users] generating Doxygen documentation Mark, no such directory is produced after make (evein if the output is 'Built target doxygen-all'). The only Doxyfile I can utilize to generate html/latex documentation is 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. It seems I need to run cmake somewhere, somehow, but it's not really clear to me in which directory (and with which options(s)). Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham Sent: 12 February 2020 17:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] generating Doxygen documentation Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > Hi, > > > I am trying to generate the Doxygen documentation for GROMACS from the > files in /docs/doxygen. > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > succesfully; I don't know what to do next: I tried to run cmake in the > doxygen directory to generate the Doxyfiles, but I get the following errors: > > """ > > CMake Error at CMakeLists.txt:36 (include): > include could not find load file: > > gmxCustomCommandUtilities > > > CMake Error at CMakeLists.txt:37 (include): > include could not find load file: > > gmxOptionUtilities > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > Unknown CMake command "gmx_dependent_option". > > """ > > What should I do? > > > Thanks for your attention, > > Michele > > > p.s. I am referring to the github master branch current version > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 paul.bauer.q at gmail.com Wed Feb 12 21:03:07 2020 From: paul.bauer.q at gmail.com (Paul Bauer) Date: Wed, 12 Feb 2020 20:03:07 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: <1581536781424.75686@kth.se> References: <1581521404890.55927@kth.se> <1581536340977.3706@kth.se> <1581536781424.75686@kth.se> Message-ID: The correct address is http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml Need to fix a link somewhere then I think. /Paul On Wed, 12 Feb 2020, 20:46 Michele Pellegrino, wrote: > Moreover: the link to Jenkins does not work (section 7.8.1, "Building the > documentation"): > > > http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml > > Cheers, > Michele > ________________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele > Pellegrino > Sent: 12 February 2020 20:39 > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] generating Doxygen documentation > > Mark, > > no such directory is produced after make (evein if the output is 'Built > target doxygen-all'). > The only Doxyfile I can utilize to generate html/latex documentation is > 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. > > It seems I need to run cmake somewhere, somehow, but it's not really clear > to me in which directory (and with which options(s)). > > Cheers, > Michele > ________________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: 12 February 2020 17:34 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] generating Doxygen documentation > > Hi, > > When they succeed, the doxygen targets produce files like > > $builddir/docs/html/doxygen/html-*/index.xhtml > > which you can open in your browser. The doxygen for the released versions > is on the web however, so it's much easier to just use or refer to that. > > Mark > > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > > > Hi, > > > > > > I am trying to generate the Doxygen documentation for GROMACS from the > > files in /docs/doxygen. > > > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > > succesfully; I don't know what to do next: I tried to run cmake in the > > doxygen directory to generate the Doxyfiles, but I get the following > errors: > > > > """ > > > > CMake Error at CMakeLists.txt:36 (include): > > include could not find load file: > > > > gmxCustomCommandUtilities > > > > > > CMake Error at CMakeLists.txt:37 (include): > > include could not find load file: > > > > gmxOptionUtilities > > > > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > > Unknown CMake command "gmx_dependent_option". > > > > """ > > > > What should I do? > > > > > > Thanks for your attention, > > > > Michele > > > > > > p.s. I am referring to the github master branch current version > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 micpel at kth.se Wed Feb 12 21:05:27 2020 From: micpel at kth.se (Michele Pellegrino) Date: Wed, 12 Feb 2020 20:05:27 -0000 Subject: [gmx-users] generating Doxygen documentation In-Reply-To: References: <1581521404890.55927@kth.se> <1581536340977.3706@kth.se> <1581536781424.75686@kth.se>, Message-ID: <1581537924596.6533@kth.se> Paul, thank you very much! Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Paul Bauer Sent: 12 February 2020 21:02 To: gmx-users at gromacs.org Subject: Re: [gmx-users] generating Doxygen documentation The correct address is http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml Need to fix a link somewhere then I think. /Paul On Wed, 12 Feb 2020, 20:46 Michele Pellegrino, wrote: > Moreover: the link to Jenkins does not work (section 7.8.1, "Building the > documentation"): > > > http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml > > Cheers, > Michele > ________________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Michele > Pellegrino > Sent: 12 February 2020 20:39 > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] generating Doxygen documentation > > Mark, > > no such directory is produced after make (evein if the output is 'Built > target doxygen-all'). > The only Doxyfile I can utilize to generate html/latex documentation is > 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'. > > It seems I need to run cmake somewhere, somehow, but it's not really clear > to me in which directory (and with which options(s)). > > Cheers, > Michele > ________________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark > Abraham > Sent: 12 February 2020 17:34 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] generating Doxygen documentation > > Hi, > > When they succeed, the doxygen targets produce files like > > $builddir/docs/html/doxygen/html-*/index.xhtml > > which you can open in your browser. The doxygen for the released versions > is on the web however, so it's much easier to just use or refer to that. > > Mark > > On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino wrote: > > > Hi, > > > > > > I am trying to generate the Doxygen documentation for GROMACS from the > > files in /docs/doxygen. > > > > I following 2020 manual, I run 'make doxygen-all' in the build directory, > > succesfully; I don't know what to do next: I tried to run cmake in the > > doxygen directory to generate the Doxyfiles, but I get the following > errors: > > > > """ > > > > CMake Error at CMakeLists.txt:36 (include): > > include could not find load file: > > > > gmxCustomCommandUtilities > > > > > > CMake Error at CMakeLists.txt:37 (include): > > include could not find load file: > > > > gmxOptionUtilities > > > > > > CMake Error at CMakeLists.txt:53 (gmx_dependent_option): > > Unknown CMake command "gmx_dependent_option". > > > > """ > > > > What should I do? > > > > > > Thanks for your attention, > > > > Michele > > > > > > p.s. I am referring to the github master branch current version > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 sallyli9512 at gmail.com Wed Feb 12 22:22:04 2020 From: sallyli9512 at gmail.com (Sally Li) Date: Wed, 12 Feb 2020 21:22:04 -0000 Subject: [gmx-users] Test particle insertion in a specific region Message-ID: Dear Gromacs Users, I'm now simulating a water droplet with some vacuum space in a NVT ensemble. I'd like to calculate the excess free energy for different shells of the droplet via test particle insertion method, which I assume I should first calculate the COM of the droplet, and then divide the droplet into different bins and do TPI insertion for different bins. I'm new ro Gromacs. Could anyone tell me how to do test particle insertion in specific spherical shells or specific region? I didn't see region options in TPI integrator. I guess I may miss something. Thank you in advance. Best wishes, Sally From ali.khodayari at student.kuleuven.be Wed Feb 12 22:59:34 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Wed, 12 Feb 2020 21:59:34 -0000 Subject: [gmx-users] Tabulated potentials Message-ID: Dear Gromacs users, I?ve got a question regarding the tabulated potentials for bonded interactions. Gromacs recognises and reads the non-bonded potential tables through the energy groups specified. But how can I refer each bond type to its table? I have derived coarse-grained potentials for a cellobiose-water system. There are 11 beads (4 bead types) in each cellobiose molecule, and each water molecule is coarse-grained as one bead. Overall, there are 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 dihedral potential tables for two types of dihedrals. The tables are named as table_b1.xvg, table_b2.xvg, and so on. Now my question is, how does gromacs recognise which table is regarding which bonded term? The simulation crashes at the very beginning giving me the following error: A tabulated bond interaction table number 1 is out of the table range: r 0.511823, between table indices 511 and 512, table length 501 I believe this is caused due to high forces on atoms indeed, but it might be also because tables are not specified to the correct bond type. Kind regards, Ali From vikasdubey1008 at gmail.com Wed Feb 12 23:08:02 2020 From: vikasdubey1008 at gmail.com (Live King) Date: Wed, 12 Feb 2020 22:08:02 -0000 Subject: [gmx-users] Can't observe ion separation under the influence of electric field Message-ID: Dear all, I am running a simple test case with a lipid bilayer (DMPC), water, and ions (150mM KCL) under the influence of a constant electric field ( 300mV, 500mV, and 700mV). *I expected positive and negative ions to separate in the presence of an external electric field*. However, I am not observing such behavior despite running the all-atom simulation for 400ns in any case. I am using gromacs 2018.2, my mdp file is standard charmm-gui production with electric field option. for example 500mV electric field in Z-direction : electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = 500 mV * Are there any settings to run the electric field simulation that I miss? Any help will be greatly appreciated. Thank you, From pathum.weerawarna at northwestern.edu Thu Feb 13 06:37:54 2020 From: pathum.weerawarna at northwestern.edu (Pathum Manjula Weerawarna) Date: Thu, 13 Feb 2020 05:37:54 -0000 Subject: [gmx-users] Estimation of configurational entropy Message-ID: Hi everyone, I'm trying to estimate the configurational entropy of a small molecule using gmx anaeig. However, it does not allow me to use a mass-weighted covariance matrix for the calculation (only allow me to use mass-unweighted CV matrix). Theoretically, the use of a mass unweighted CV matrix for entropy calculation is inaccurate (frequencies going to be smaller). Does anybody know the accuracy of the entropy calculated using gmx anaeig? Also, is there any way to use a mass-weighted CV matrix for this calculation? Thank you so much for the help best Pathum ________________________________ Pathum M. Weerawarna, Ph.D. Postdoctoral Fellow Silverman Research Group Department of Chemistry Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone: (316) 990-8542 Email : pathum.weerawarna at northwestern.edu pathumweerawarna at gmail.com [cid:1e2d5c51-a722-45d1-a750-8b9bf00f3e05] From spoel at xray.bmc.uu.se Thu Feb 13 07:22:52 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 13 Feb 2020 06:22:52 -0000 Subject: [gmx-users] Estimation of configurational entropy In-Reply-To: References: Message-ID: Den 2020-02-13 kl. 05:10, skrev Pathum Manjula Weerawarna: > Hi everyone, > > I'm trying to estimate the configurational entropy of a small molecule using gmx anaeig. However, it does not allow me to use a mass-weighted covariance matrix for the calculation (only allow me to use mass-unweighted CV matrix). Theoretically, the use of a mass unweighted CV matrix for entropy calculation is inaccurate (frequencies going to be smaller). Does anybody know the accuracy of the entropy calculated using gmx anaeig? Also, is there any way to use a mass-weighted CV matrix for this calculation? The entropy is only the conformational entropy and can therefore be used for determining relative entropies, for instance for ligand binding (J Chem Theory Comput 9 pp. 4542-4551 (2013)). If you want to compute absolute entropies then for now normal mode analysis is the most efficient, even though it has limitations as well. See J Phys Chem A. 122 pp. 8982-8988 (2018). Sorry to promote my own papers but this is what I know :) > > Thank you so much for the help > > best > Pathum > > > ________________________________ > Pathum M. Weerawarna, Ph.D. > Postdoctoral Fellow > Silverman Research Group > Department of Chemistry > Northwestern University > 2145 Sheridan Road > Evanston, IL 60208-3113 > > Phone: (316) 990-8542 > Email : pathum.weerawarna at northwestern.edu > pathumweerawarna at gmail.com > [cid:1e2d5c51-a722-45d1-a750-8b9bf00f3e05] > > > -- 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 From spoel at xray.bmc.uu.se Thu Feb 13 07:42:57 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Thu, 13 Feb 2020 06:42:57 -0000 Subject: [gmx-users] Can't observe ion separation under the influence of electric field In-Reply-To: References: Message-ID: <3ed43491-cfa5-4faa-dc3e-8df6a9c68b7f@xray.bmc.uu.se> Den 2020-02-12 kl. 23:07, skrev Live King: > Dear all, > > I am running a simple test case with a lipid bilayer (DMPC), water, and > ions (150mM KCL) under the influence of a constant electric field ( 300mV, > 500mV, and 700mV). *I expected positive and negative ions to separate in > the presence of an external electric field*. However, I am not observing > such behavior despite running the all-atom simulation for 400ns in any > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui > production with electric field option. > > for example 500mV electric field in Z-direction : > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = > 500 mV * > > > Are there any settings to run the electric field simulation that I miss? > Any help will be greatly appreciated. > Did you make density plots to check? Do you get an output field.xvg that prints the field strength? It may be optional though. The force on the atoms will be quite small still compared to interatomic forces therefore the effect may be limited. F = q E (convert to right units). In GROMACS MD units a typical interatomic force is ~ 1000 kJ/mol/nm^2. > > Thank you, > -- 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 From r.a.luirink at vu.nl Thu Feb 13 09:48:48 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Thu, 13 Feb 2020 08:48:48 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> Message-ID: <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> Anyone has advice/feedback? ?On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: Here some output to illustrate what I mean. This is what you would expect and what I also get for standard atom-atom interactions, not 1-4 and not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 (kJ/mol) LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 (kJ/mol) Coul-14:CXD-CDLAL 0 0 0 0 (kJ/mol) LJ-14:CXD-CDLAL 0 0 0 0 (kJ/mol) This is what you would expect for 1-4 interactions (which I get for standard 1-4 interactions, but not the ones I specified) not LJ-SR and not Coul-SR but LJ-14 and Coul-14: Coul-SR:CXN-CDLAL 0 0 0 0 (kJ/mol) LJ-SR:CXN-CDLAL 0 0 0 0 (kJ/mol) Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 -1.69012e-05 (kJ/mol) LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 -7.03428e-05 (kJ/mol) And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR as LJ-14 and Coul-14: Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 (kJ/mol) LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 (kJ/mol) Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 (kJ/mol) LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 (kJ/mol) It seems like a bug to me, or I have overlooked something.. On 06/02/2020, 14:44, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: Gromacs version 2018.6 btw. On 06/02/2020, 13:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." wrote: What I have tried is, instead of adding them to the [ pairs ] block, is change the epsilon value manually via the [ nonbon_params ] block. However, I can?t manually change the electrostatic interactions to account for the fudgeQQ (0.8333) for these specific pairs (or at least, I haven?t found a way to do so). From: "Luirink, R.A." Date: Thursday, 6 February 2020 at 11:49 To: "gmx-users at gromacs.org" Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output Hello, I try to specify a pair of atoms to be treated as a 1-4 interaction (I replaced a covalent bond to a soft core restraint for free energy calculation purposes, and now gromacs does not recognize it anymore as 1-4 interaction, but it should still be treated as such). I added the pair to the [ pairs ] block in the topology. I did the same for 1-3 interactions, where I set the parameters to 0 for LJ interactions. When I check the energy between these pairs of atoms, I indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and exactly twice the average value of LJ_14, where I have a fudge of 0.5). How can I fix this issue? Best, Rosa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 matthias.urban at iwm.fraunhofer.de Thu Feb 13 11:52:11 2020 From: matthias.urban at iwm.fraunhofer.de (Urban, Matthias) Date: Thu, 13 Feb 2020 10:52:11 -0000 Subject: [gmx-users] genion without stdin Message-ID: <7a73144291464ca48809ebc4f00a3aef@iwm.fraunhofer.de> Hello mailinglist, is there a way to prevent "gmx genion" from expecting input via stdin? I am using gromacs v2020 with gmxapi. Thanks in advance. Cheers, Matthias From blau at kth.se Thu Feb 13 11:59:32 2020 From: blau at kth.se (Christian Blau) Date: Thu, 13 Feb 2020 10:59:32 -0000 Subject: [gmx-users] genion without stdin In-Reply-To: <7a73144291464ca48809ebc4f00a3aef@iwm.fraunhofer.de> References: <7a73144291464ca48809ebc4f00a3aef@iwm.fraunhofer.de> Message-ID: Hello Matthias, yes, if you use an indexfile with exactly one index group inside, this index group will be automatically picked. (like [ solvent ] 1001 1002 1003 1004 1005 1006 1007 1008 1009? ... and nothing else Best, Christian On 2020-02-13 11:49, Urban, Matthias wrote: > Hello mailinglist, > > > is there a way to prevent "gmx genion" from expecting input via stdin? > > > I am using gromacs v2020 with gmxapi. > > > Thanks in advance. > > > Cheers, > > > Matthias From atila.petrosian at gmail.com Thu Feb 13 15:57:19 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Thu, 13 Feb 2020 14:57:19 -0000 Subject: [gmx-users] grompp error : Atomtype HC not found Message-ID: Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Tieleman's web site for lipid molecules. --------------------------------------- My topology file is as follows: --------------------------------------- #include "ffgmx.itp" #include "lipid.itp" #include "dppc.itp" #include "lig.itp" #ifdef POSRES_LIG #include "lig_posre.itp" #endif #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif [ system ] ; name dppc/lig/lig/sol [ molecules ] ; Compound #mols DPP 128 LIG 2 SOL 7173 --------------------------------------- My lig.itp file is as follows: --------------------------------------- . . . . ; [ moleculetype ] ; Name nrexcl LIG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 HC 1 LIG H27 1 0.131 1.0080 2 CAro 1 LIG C24 2 -0.130 12.0110 3 CAro 1 LIG C23 3 -0.130 12.0110 4 HC 1 LIG H26 4 0.131 1.0080 5 CAro 1 LIG C22 5 -0.119 12.0110 6 HC 1 LIG H25 6 0.135 1.0080 7 CAro 1 LIG C21 7 -0.039 12.0110 8 CAro 1 LIG C26 8 -0.119 12.0110 9 HC 1 LIG H29 9 0.135 1.0080 10 CAro 1 LIG C25 10 -0.130 12.0110 11 HC 1 LIG H28 11 0.131 1.0080 12 C 1 LIG C18 12 -0.051 12.0110 13 CH2 1 LIG C19 13 0.055 14.0270 14 CH3 1 LIG C20 14 0.020 15.0350 15 CAro 1 LIG C11 15 -0.025 12.0110 16 CAro 1 LIG C12 16 -0.040 12.0110 17 CAro 1 LIG C13 17 -0.117 12.0110 18 HC 1 LIG H15 18 0.137 1.0080 19 CAro 1 LIG C14 19 -0.133 12.0110 20 HC 1 LIG H16 20 0.131 1.0080 21 CAro 1 LIG C15 21 -0.129 12.0110 22 HC 1 LIG H17 22 0.131 1.0080 23 CAro 1 LIG C16 23 -0.133 12.0110 24 HC 1 LIG H18 24 0.131 1.0080 25 CAro 1 LIG C17 25 -0.117 12.0110 26 HC 1 LIG H19 26 0.137 1.0080 27 CAro 1 LIG C8 27 -0.076 12.0110 28 CAro 1 LIG C7 28 -0.079 12.0110 29 HC 1 LIG H12 29 0.139 1.0080 30 CAro 1 LIG C6 30 -0.184 12.0110 31 HC 1 LIG H11 31 0.143 1.0080 32 CAro 1 LIG C5 32 0.087 12.0110 33 CAro 1 LIG C10 33 -0.184 12.0110 34 HC 1 LIG H14 34 0.143 1.0080 35 CAro 1 LIG C9 35 -0.079 12.0110 36 HC 1 LIG H13 36 0.139 1.0080 37 OE 1 LIG O1 37 -0.219 15.9994 38 CH2 1 LIG C4 38 0.149 14.0270 39 CH2 1 LIG C3 39 0.101 14.0270 40 NTer 1 LIG N1 40 -0.267 14.0067 41 CH3 1 LIG C1 41 0.097 15.0350 42 CH3 1 LIG C2 42 0.097 15.0350 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1090 1.2300e+07 2 3 2 0.1390 8.6600e+06 . . . . . --------------------------------------- After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top -o system.gro, I encountered with the following error: --------------------------------------- ERROR 1 [file lig.itp, line 65]: Atomtype HC not found --------------------------------------- How to resole it? Best, Atila From alessandra.villa.biosim at gmail.com Thu Feb 13 16:28:08 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 13 Feb 2020 15:28:08 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: References: Message-ID: Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > Dear Gromacs users, > > I?ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through the > energy groups specified. But how can I refer each bond type to its table? > > I have derived coarse-grained potentials for a cellobiose-water system. > There are 11 beads (4 bead types) in each cellobiose molecule, and each > water molecule is coarse-grained as one bead. Overall, there are 3 bonded > terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 > dihedral potential tables for two types of dihedrals. The tables are named > as table_b1.xvg, table_b2.xvg, and so on. > Now my question is, how does gromacs recognise which table is regarding > which bonded term? The simulation crashes at the very beginning giving me > the following error: > > In topol.top one specifies which table is used for which interaction (bond, angle, dihedral). See the table below for the synthases http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file Best regards Alessandra > A tabulated bond interaction table number 1 is out of the table range: r > 0.511823, between table indices 511 and 512, table length 501 > > I believe this is caused due to high forces on atoms indeed, but it might > be also because tables are not specified to the correct bond type. > > > 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 alessandra.villa.biosim at gmail.com Thu Feb 13 16:28:09 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 13 Feb 2020 15:28:09 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: References: Message-ID: Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > Dear Gromacs users, > > I?ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through the > energy groups specified. But how can I refer each bond type to its table? > > I have derived coarse-grained potentials for a cellobiose-water system. > There are 11 beads (4 bead types) in each cellobiose molecule, and each > water molecule is coarse-grained as one bead. Overall, there are 3 bonded > terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 > dihedral potential tables for two types of dihedrals. The tables are named > as table_b1.xvg, table_b2.xvg, and so on. > Now my question is, how does gromacs recognise which table is regarding > which bonded term? The simulation crashes at the very beginning giving me > the following error: > > In topol.top one specifies which table is used for which interaction (bond, angle, dihedral). See the table below for the synthases http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file Best regards Alessandra > A tabulated bond interaction table number 1 is out of the table range: r > 0.511823, between table indices 511 and 512, table length 501 > > I believe this is caused due to high forces on atoms indeed, but it might > be also because tables are not specified to the correct bond type. > > > 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 h_sahakyan at mb.sci.am Thu Feb 13 18:20:43 2020 From: h_sahakyan at mb.sci.am (Harutyun Sahakyan) Date: Thu, 13 Feb 2020 17:20:43 -0000 Subject: [gmx-users] Can't observe ion separation under the influence of electric field In-Reply-To: References: Message-ID: <8e8f67eddbe432be57f7fcc0785fabb4@mb.sci.am> You can use compel and build a double bilayer system to separate ions. However, if you separate positive and negative ions, you will have very high membrane potential, event two ions difference can raise potential about 200 mV. In your case, I suppose 500 mV is not enough to separate all ions in a PBC box. https://www.mpibpc.mpg.de/grubmueller/compel Harutyun Sahakyan Senior Assistant at Laboratory of? Computational Modeling of Biological Processes,? Institute of Molecular Biology, NAS, Armenia, Yerevan Tel: +374 93 323990 h_sahakyan at mb.sci.am sahakyanhk at gmail.com February 13, 2020 2:07 AM, "Live King" wrote: > Dear all, > > I am running a simple test case with a lipid bilayer (DMPC), water, and > ions (150mM KCL) under the influence of a constant electric field ( 300mV, > 500mV, and 700mV). *I expected positive and negative ions to separate in > the presence of an external electric field*. However, I am not observing > such behavior despite running the all-atom simulation for 400ns in any > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui > production with electric field option. > > for example 500mV electric field in Z-direction : > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = > 500 mV * > > Are there any settings to run the electric field simulation that I miss? > Any help will be greatly appreciated. > > 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 ph.marwaabdelkader at gmail.com Thu Feb 13 19:33:18 2020 From: ph.marwaabdelkader at gmail.com (Marwa Abd El Kader) Date: Thu, 13 Feb 2020 18:33:18 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated Message-ID: Dear gmx-users mailing list team, I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trjconv after creating an index file having a specific residue(s) on the interface between the 2 chains, but nothing is working. I fixed this issue before but when there was only one chain, now with 2 chains, I don't know how to rejoin them together again. Can you suggest me any solution, please?! *N.B: the 2 chains are considered as one when selected in VMD Regards, Marwa From sadafrani6 at gmail.com Thu Feb 13 21:19:20 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 13 Feb 2020 20:19:20 -0000 Subject: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics Message-ID: Dear Gromacs users I am doing free energy calculation of a ligand with protein. When I do gmx bar it gives me the following error:- Temperature: 298.15 K Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0 1 3.29 0.06 1.28 0.10 1.37 0.08 1.54 0.09 1 2 1.41 0.04 0.47 0.05 0.31 0.05 0.77 0.03 2 3 0.88 0.06 0.09 0.02 0.06 0.01 0.41 0.06 3 4 0.67 0.03 -0.01 0.03 -0.01 0.03 0.25 0.01 4 5 0.50 0.01 0.11 0.00 0.10 0.00 0.22 0.01 5 6 0.33 0.01 -0.04 0.01 -0.07 0.03 0.21 0.03 6 7 0.27 0.02 0.07 0.04 0.04 0.02 0.22 0.03 7 8 0.11 0.03 0.05 0.02 0.04 0.01 0.16 0.01 8 9 0.11 0.01 -0.09 0.02 -0.10 0.02 0.17 0.01 9 10 0.08 0.02 0.12 0.01 0.12 0.01 0.20 0.00 10 11 -0.04 0.03 -0.01 0.03 -0.01 0.03 0.18 0.01 11 12 -0.09 0.03 0.06 0.03 0.05 0.03 0.19 0.02 12 13 -0.02 0.03 -0.12 0.03 -0.12 0.03 0.23 0.01 13 14 -0.01 0.03 0.17 0.03 0.16 0.03 0.28 0.02 14 15 -0.06 0.03 -0.09 0.03 -0.09 0.03 0.25 0.01 15 16 -0.04 0.03 0.13 0.04 0.13 0.04 0.29 0.01 16 17 -0.15 0.03 0.04 0.01 0.04 0.01 0.24 0.01 17 18 -0.14 0.03 0.01 0.02 0.01 0.02 0.25 0.01 18 19 -0.07 0.03 -0.01 0.01 -0.08 0.02 0.27 0.01 19 20 -0.05 0.01 0.18 0.00 0.09 0.00 0.28 0.00 WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. Final results in kJ/mol: point 0 - 1, DG 8.14 +/- 0.14 point 1 - 2, DG 3.50 +/- 0.09 point 2 - 3, DG 2.19 +/- 0.14 point 3 - 4, DG 1.66 +/- 0.07 point 4 - 5, DG 1.24 +/- 0.02 point 5 - 6, DG 0.83 +/- 0.02 point 6 - 7, DG 0.66 +/- 0.06 point 7 - 8, DG 0.28 +/- 0.08 point 8 - 9, DG 0.28 +/- 0.03 point 9 - 10, DG 0.19 +/- 0.05 point 10 - 11, DG -0.10 +/- 0.08 point 11 - 12, DG -0.22 +/- 0.07 point 12 - 13, DG -0.05 +/- 0.08 point 13 - 14, DG -0.03 +/- 0.08 point 14 - 15, DG -0.16 +/- 0.07 point 15 - 16, DG -0.10 +/- 0.07 point 16 - 17, DG -0.37 +/- 0.07 point 17 - 18, DG -0.35 +/- 0.08 point 18 - 19, DG -0.17 +/- 0.06 point 19 - 20, DG -0.13 +/- 0.02 total 0 - 20, DG 17.29 +/- 0.47 I have read in the link that I should not have negative entropy values in my simulation https://www.mail-archive.com/gmx-users at gromacs.org/msg55772.html. Can anyone please suggest me what could be wrong during my simulation and how should I fix it? Thank you Sadaf Rani Ph.D. visiting student Lancaster University Uk From jalemkul at vt.edu Fri Feb 14 03:30:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 02:30:05 -0000 Subject: [gmx-users] genion without stdin In-Reply-To: References: <7a73144291464ca48809ebc4f00a3aef@iwm.fraunhofer.de> Message-ID: On 2/13/20 5:59 AM, Christian Blau wrote: > Hello Matthias, > > > yes, if you use an indexfile with exactly one index group inside, this > index group will be automatically picked. > > > (like > > [ solvent ] > > 1001 1002 1003 1004 1005 1006 1007 1008 1009? ... > > and nothing else > It's even easier than that: echo "SOL" | gmx genion ... -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 Feb 14 03:31:04 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 02:31:04 -0000 Subject: [gmx-users] grompp error : Atomtype HC not found In-Reply-To: References: Message-ID: <85eb3eef-3329-dec1-51d8-2f0fea481201@vt.edu> On 2/13/20 8:56 AM, Atila Petrosian wrote: > Hi gromacs users, > > I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + > water molecules) using gromacs 2019. > > I used ATB for drug molecules and Tieleman's web site for lipid molecules. ATB uses a custom version of GROMOS96 that uses new atom types. You need to use their force field files. > --------------------------------------- > My topology file is as follows: > --------------------------------------- > #include "ffgmx.itp" There is no reason to use this totally obsolete force field. -Justin > #include "lipid.itp" > #include "dppc.itp" > #include "lig.itp" > > #ifdef POSRES_LIG > #include "lig_posre.itp" > #endif > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > [ system ] > ; name > dppc/lig/lig/sol > > [ molecules ] > ; Compound #mols > DPP 128 > LIG 2 > SOL 7173 > --------------------------------------- > My lig.itp file is as follows: > --------------------------------------- > . > . > . > . > ; > [ moleculetype ] > ; Name nrexcl > LIG 3 > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 HC 1 LIG H27 1 0.131 1.0080 > 2 CAro 1 LIG C24 2 -0.130 12.0110 > 3 CAro 1 LIG C23 3 -0.130 12.0110 > 4 HC 1 LIG H26 4 0.131 1.0080 > 5 CAro 1 LIG C22 5 -0.119 12.0110 > 6 HC 1 LIG H25 6 0.135 1.0080 > 7 CAro 1 LIG C21 7 -0.039 12.0110 > 8 CAro 1 LIG C26 8 -0.119 12.0110 > 9 HC 1 LIG H29 9 0.135 1.0080 > 10 CAro 1 LIG C25 10 -0.130 12.0110 > 11 HC 1 LIG H28 11 0.131 1.0080 > 12 C 1 LIG C18 12 -0.051 12.0110 > 13 CH2 1 LIG C19 13 0.055 14.0270 > 14 CH3 1 LIG C20 14 0.020 15.0350 > 15 CAro 1 LIG C11 15 -0.025 12.0110 > 16 CAro 1 LIG C12 16 -0.040 12.0110 > 17 CAro 1 LIG C13 17 -0.117 12.0110 > 18 HC 1 LIG H15 18 0.137 1.0080 > 19 CAro 1 LIG C14 19 -0.133 12.0110 > 20 HC 1 LIG H16 20 0.131 1.0080 > 21 CAro 1 LIG C15 21 -0.129 12.0110 > 22 HC 1 LIG H17 22 0.131 1.0080 > 23 CAro 1 LIG C16 23 -0.133 12.0110 > 24 HC 1 LIG H18 24 0.131 1.0080 > 25 CAro 1 LIG C17 25 -0.117 12.0110 > 26 HC 1 LIG H19 26 0.137 1.0080 > 27 CAro 1 LIG C8 27 -0.076 12.0110 > 28 CAro 1 LIG C7 28 -0.079 12.0110 > 29 HC 1 LIG H12 29 0.139 1.0080 > 30 CAro 1 LIG C6 30 -0.184 12.0110 > 31 HC 1 LIG H11 31 0.143 1.0080 > 32 CAro 1 LIG C5 32 0.087 12.0110 > 33 CAro 1 LIG C10 33 -0.184 12.0110 > 34 HC 1 LIG H14 34 0.143 1.0080 > 35 CAro 1 LIG C9 35 -0.079 12.0110 > 36 HC 1 LIG H13 36 0.139 1.0080 > 37 OE 1 LIG O1 37 -0.219 15.9994 > 38 CH2 1 LIG C4 38 0.149 14.0270 > 39 CH2 1 LIG C3 39 0.101 14.0270 > 40 NTer 1 LIG N1 40 -0.267 14.0067 > 41 CH3 1 LIG C1 41 0.097 15.0350 > 42 CH3 1 LIG C2 42 0.097 15.0350 > ; total charge of the molecule: 0.000 > [ bonds ] > ; ai aj funct c0 c1 > 1 2 2 0.1090 1.2300e+07 > 2 3 2 0.1390 8.6600e+06 > . > . > . > . > . > --------------------------------------- > After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top > -o system.gro, I encountered with the following error: > --------------------------------------- > ERROR 1 [file lig.itp, line 65]: > Atomtype HC not found > --------------------------------------- > > How to resole it? > > Best, > Atila -- ================================================== 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 Feb 14 03:31:24 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 02:31:24 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: References: Message-ID: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: > Dear gmx-users mailing list team, > I want to know how to fix the separation of 2 chains after the production > run. I'm trying different combinations of trjconv after creating an index > file having a specific residue(s) on the interface between the 2 chains, > but nothing is working. I fixed this issue before but when there was only > one chain, now with 2 chains, I don't know how to rejoin them together > again. Can you suggest me any solution, please?! > *N.B: the 2 chains are considered as one when selected in VMD Center on a single chain rather than trying to work with the interface residues. -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 nt2614888 at gmail.com Fri Feb 14 06:05:46 2020 From: nt2614888 at gmail.com (Neha Tiwari) Date: Fri, 14 Feb 2020 05:05:46 -0000 Subject: [gmx-users] (no subject) Message-ID: Dear Gromacs experts, I have generated topology files(.itp) of the ligand from the ATB server and everything goes well, but when it comes to generating ions.tpr file, I am getting following error. $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr :-) GROMACS - gmx grompp, 2018.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ya/Desktop/Neha/fecA/gromos Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' NOTE 1 [file ions.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 49113858 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type '4JCP' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file topol.top, line 45350]: System has non-zero total charge: -14.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet ERROR 1 [file topol.top, line 45350]: atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 2 [file topol.top, line 45350]: atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 3 [file topol.top, line 45350]: atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 4 [file topol.top, line 45350]: atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 5 [file topol.top, line 45350]: atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 6 [file topol.top, line 45350]: atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 7 [file topol.top, line 45350]: atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 8 [file topol.top, line 45350]: atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 9 [file topol.top, line 45350]: atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 10 [file topol.top, line 45350]: atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 11 [file topol.top, line 45350]: atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 12 [file topol.top, line 45350]: atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 13 [file topol.top, line 45350]: atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 14 [file topol.top, line 45350]: atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 15 [file topol.top, line 45350]: atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) There were 2 notes ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137) Fatal error: There were 15 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help. Thanks in advance. Regards, Neha. From paul.bauer.q at gmail.com Fri Feb 14 08:32:41 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Fri, 14 Feb 2020 07:32:41 -0000 Subject: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics In-Reply-To: References: Message-ID: <022dd565-f3d4-2ef4-33c4-8a854d67a8a9@gmail.com> Hello, you'll need to check if you are properly sampling the different states in your simulations,? which should be possible by analyzing the histograms you can get from gmx bar -oh Otherwise you'll need to check if your simulation parameters are realistic, as the program warns you :) Cheers Paul On 13/02/2020 21:19, Sadaf Rani wrote: > Dear Gromacs users > > I am doing free energy calculation of a ligand with protein. When I do gmx > bar it gives me the following error:- > > Temperature: 298.15 K > > Detailed results in kT (see help for explanation): > > lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- > 0 1 3.29 0.06 1.28 0.10 1.37 0.08 1.54 0.09 > 1 2 1.41 0.04 0.47 0.05 0.31 0.05 0.77 0.03 > 2 3 0.88 0.06 0.09 0.02 0.06 0.01 0.41 0.06 > 3 4 0.67 0.03 -0.01 0.03 -0.01 0.03 0.25 0.01 > 4 5 0.50 0.01 0.11 0.00 0.10 0.00 0.22 0.01 > 5 6 0.33 0.01 -0.04 0.01 -0.07 0.03 0.21 0.03 > 6 7 0.27 0.02 0.07 0.04 0.04 0.02 0.22 0.03 > 7 8 0.11 0.03 0.05 0.02 0.04 0.01 0.16 0.01 > 8 9 0.11 0.01 -0.09 0.02 -0.10 0.02 0.17 0.01 > 9 10 0.08 0.02 0.12 0.01 0.12 0.01 0.20 0.00 > 10 11 -0.04 0.03 -0.01 0.03 -0.01 0.03 0.18 0.01 > 11 12 -0.09 0.03 0.06 0.03 0.05 0.03 0.19 0.02 > 12 13 -0.02 0.03 -0.12 0.03 -0.12 0.03 0.23 0.01 > 13 14 -0.01 0.03 0.17 0.03 0.16 0.03 0.28 0.02 > 14 15 -0.06 0.03 -0.09 0.03 -0.09 0.03 0.25 0.01 > 15 16 -0.04 0.03 0.13 0.04 0.13 0.04 0.29 0.01 > 16 17 -0.15 0.03 0.04 0.01 0.04 0.01 0.24 0.01 > 17 18 -0.14 0.03 0.01 0.02 0.01 0.02 0.25 0.01 > 18 19 -0.07 0.03 -0.01 0.01 -0.08 0.02 0.27 0.01 > 19 20 -0.05 0.01 0.18 0.00 0.09 0.00 0.28 0.00 > > WARNING: Some of these results violate the Second Law of Thermodynamics: > This is can be the result of severe undersampling, or (more likely) > there is something wrong with the simulations. > > > Final results in kJ/mol: > > point 0 - 1, DG 8.14 +/- 0.14 > point 1 - 2, DG 3.50 +/- 0.09 > point 2 - 3, DG 2.19 +/- 0.14 > point 3 - 4, DG 1.66 +/- 0.07 > point 4 - 5, DG 1.24 +/- 0.02 > point 5 - 6, DG 0.83 +/- 0.02 > point 6 - 7, DG 0.66 +/- 0.06 > point 7 - 8, DG 0.28 +/- 0.08 > point 8 - 9, DG 0.28 +/- 0.03 > point 9 - 10, DG 0.19 +/- 0.05 > point 10 - 11, DG -0.10 +/- 0.08 > point 11 - 12, DG -0.22 +/- 0.07 > point 12 - 13, DG -0.05 +/- 0.08 > point 13 - 14, DG -0.03 +/- 0.08 > point 14 - 15, DG -0.16 +/- 0.07 > point 15 - 16, DG -0.10 +/- 0.07 > point 16 - 17, DG -0.37 +/- 0.07 > point 17 - 18, DG -0.35 +/- 0.08 > point 18 - 19, DG -0.17 +/- 0.06 > point 19 - 20, DG -0.13 +/- 0.02 > > total 0 - 20, DG 17.29 +/- 0.47 > > > I have read in the link that I should not have negative entropy values in > my simulation > https://www.mail-archive.com/gmx-users at gromacs.org/msg55772.html. > Can anyone please suggest me what could be wrong during my simulation and > how should I fix it? > > Thank you > Sadaf Rani > Ph.D. visiting student > Lancaster University > Uk -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From ph.marwaabdelkader at gmail.com Fri Feb 14 08:48:55 2020 From: ph.marwaabdelkader at gmail.com (Marwa Abd El Kader) Date: Fri, 14 Feb 2020 07:48:55 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> References: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> Message-ID: Dear Justin, Would you please tell me how, give me an example code, because I'm a novice? Thanks in advance, Marwa On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: > > > On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: > > Dear gmx-users mailing list team, > > I want to know how to fix the separation of 2 chains after the production > > run. I'm trying different combinations of trjconv after creating an index > > file having a specific residue(s) on the interface between the 2 chains, > > but nothing is working. I fixed this issue before but when there was only > > one chain, now with 2 chains, I don't know how to rejoin them together > > again. Can you suggest me any solution, please?! > > *N.B: the 2 chains are considered as one when selected in VMD > > Center on a single chain rather than trying to work with the interface > residues. > > -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 vikasdubey1008 at gmail.com Fri Feb 14 10:37:33 2020 From: vikasdubey1008 at gmail.com (Live King) Date: Fri, 14 Feb 2020 09:37:33 -0000 Subject: [gmx-users] Can't observe ion separation under the influence of electric field In-Reply-To: <8e8f67eddbe432be57f7fcc0785fabb4@mb.sci.am> References: <8e8f67eddbe432be57f7fcc0785fabb4@mb.sci.am> Message-ID: Dear David and Harutyun, Thanks for your reply. Density plots were the first check I did. They show a very minor difference. I imagined that the electric field is not sufficient, however, presence of high electric field ( > 1 V or 1000mV)* disrupts the membrane and my simulation crashes*. Is there any solution to this problem? I will have a look at compel. On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan wrote: > You can use compel and build a double bilayer system to separate ions. > However, if you separate positive and negative ions, you will have very > high membrane potential, event two ions difference can raise potential > about 200 mV. In your case, I suppose 500 mV is not enough to separate all > ions in a PBC box. > > https://www.mpibpc.mpg.de/grubmueller/compel > > > > Harutyun Sahakyan > Senior Assistant at Laboratory of > Computational Modeling of Biological Processes, > Institute of Molecular Biology, NAS, Armenia, Yerevan > Tel: +374 93 323990 > h_sahakyan at mb.sci.am > sahakyanhk at gmail.com > > February 13, 2020 2:07 AM, "Live King" wrote: > > > Dear all, > > > > I am running a simple test case with a lipid bilayer (DMPC), water, and > > ions (150mM KCL) under the influence of a constant electric field ( > 300mV, > > 500mV, and 700mV). *I expected positive and negative ions to separate in > > the presence of an external electric field*. However, I am not observing > > such behavior despite running the all-atom simulation for 400ns in any > > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui > > production with electric field option. > > > > for example 500mV electric field in Z-direction : > > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = > > 500 mV * > > > > Are there any settings to run the electric field simulation that I miss? > > Any help will be greatly appreciated. > > > > 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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 prinebula23 at gmail.com Fri Feb 14 11:20:54 2020 From: prinebula23 at gmail.com (Priyanka Singh) Date: Fri, 14 Feb 2020 10:20:54 -0000 Subject: [gmx-users] RNA md simulation Message-ID: Hi can anyone help with the problem of terminal end notation for charmm36 ff for RNA molecule to generate .gro file usind gromac-2019.3 Thanks all. looking forward for help. From atila.petrosian at gmail.com Fri Feb 14 12:09:46 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Fri, 14 Feb 2020 11:09:46 -0000 Subject: [gmx-users] grompp error : Atomtype HC not found Message-ID: Dear Justin, Thanks for answer. You said " There is no reason to use this totally obsolete force field (ffgmx.itp)". I used ffgmx.itp, because there was a example.top file in Tieleman's web site: ------------------------------------------------------- ; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion ; alm.itp can be made in a straightforward manner with pdb2gmx, starting ; with a pdb file of alamethicin. ; make sure lipid.itp, popc.itp and alm.itp are in a location where ; grompp can find them (GMXLIB, current directory, or directory given in ; the .mdp file with the include option. #include "ffgmx.itp" #include "lipid.itp" #include "popc.itp" #include "alm.itp" #include "ions.itp" #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Alm on surf + relaxed popc [ molecules ] ; name number Protein 1 POPC 128 SOL 3552 Na 1 ------------------------------------------------------- Based on your suggestion, I used following in my topology file (I deleted ffgmx.itp): #include "lipid.itp" #include "dppc.itp" #include "lig.itp" ------------------------------------------------------- But I encountered with: ------------------------------------------------------- Fatal error: Syntax error - File lipid.itp, line 11 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes ------------------------------------------------------- lipid.itp file from Tieleman's web site is as follows: ------------------------------------------------------- ;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS ;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et ;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are ;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters, ;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as ;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS. [ defaults ] 1 1 [ atomtypes ] ;name mass charge ptype c6 c12 ; LO 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS LC 12.0110 0.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS LH1 13.0190 0.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS LH2 14.0270 0.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS LP 30.9738 0.000 A 9.16000e-03 2.50700e-05 ;phosphor, OPLS LOS 15.9994 0.000 A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS LP2 14.0270 0.000 A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ LP3 15.0350 0.000 A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ LC3 15.0350 0.000 A 9.35700e-03 3.60900e-05 ;CH3, OPLS LC2 14.0270 0.000 A 5.94700e-03 1.79000e-05 ;CH2, OPLS ------------------------------------------------------- How to resolve that? Best, Atila From jalemkul at vt.edu Fri Feb 14 14:58:46 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 13:58:46 -0000 Subject: [gmx-users] (no subject) In-Reply-To: References: Message-ID: <9c2d91bd-bd54-bb46-1fb5-686be21de949@vt.edu> On 2/14/20 12:05 AM, Neha Tiwari wrote: > Dear Gromacs experts, > I have generated topology files(.itp) of the ligand from the ATB server and > everything goes well, but when it comes to generating ions.tpr file, I am > getting following error. > > > $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > :-) GROMACS - gmx grompp, 2018.1 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra > > Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru > > Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus > > > Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl > > Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola > > Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov > > Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen > > Christian Wennberg Maarten Wolf > > and the project leaders: > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2017, The GROMACS development team at > > Uppsala University, Stockholm University and > > the Royal Institute of Technology, Sweden. > > check out http://www.gromacs.org for more information. > > > > GROMACS is free software; you can redistribute it and/or modify it > > under the terms of the GNU Lesser General Public License > > as published by the Free Software Foundation; either version 2.1 > > of the License, or (at your option) any later version. > > > > GROMACS: gmx grompp, version 2018.1 > > Executable: /usr/bin/gmx > > Data prefix: /usr > > Working dir: /home/ya/Desktop/Neha/fecA/gromos > > Command line: > > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > > > Ignoring obsolete mdp entry 'title' > > > > NOTE 1 [file ions.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 49113858 > > Generated 165 of the 1596 non-bonded parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein' > > Excluding 3 bonded neighbours molecule type '4JCP' > > Excluding 2 bonded neighbours molecule type 'SOL' > > > > NOTE 2 [file topol.top, line 45350]: > > System has non-zero total charge: -14.000000 > > Total charge should normally be an integer. See > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > for discussion on how close it should be to an integer. > > > > > > > > Removing all charge groups because cutoff-scheme=Verlet > > > > ERROR 1 [file topol.top, line 45350]: > > atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 2 [file topol.top, line 45350]: > > atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 3 [file topol.top, line 45350]: > > atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 4 [file topol.top, line 45350]: > > atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 5 [file topol.top, line 45350]: > > atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 6 [file topol.top, line 45350]: > > atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 7 [file topol.top, line 45350]: > > atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 8 [file topol.top, line 45350]: > > atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 9 [file topol.top, line 45350]: > > atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 10 [file topol.top, line 45350]: > > atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 11 [file topol.top, line 45350]: > > atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 12 [file topol.top, line 45350]: > > atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 13 [file topol.top, line 45350]: > > atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 14 [file topol.top, line 45350]: > > atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > ERROR 15 [file topol.top, line 45350]: > > atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) > > > > > > > > There were 2 notes > > > > ------------------------------------------------------- > > Program: gmx grompp, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137) > > > > Fatal error: > > There were 15 errors in input file(s) > Likely the format/contents of those topology lines are wrong if grompp finds zero mass. -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 Feb 14 14:59:20 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 13:59:20 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: References: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> Message-ID: <61b779df-7e13-f15a-7fa9-6a1764154a0f@vt.edu> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: > Dear Justin, > Would you please tell me how, give me an example code, because I'm a novice? The same thing you did before but instead of trying to select interfacial residues, make an index group of one of the protein chains and select it for the centering group. -Justin > Thanks in advance, > Marwa > > On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: > >> >> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: >>> Dear gmx-users mailing list team, >>> I want to know how to fix the separation of 2 chains after the production >>> run. I'm trying different combinations of trjconv after creating an index >>> file having a specific residue(s) on the interface between the 2 chains, >>> but nothing is working. I fixed this issue before but when there was only >>> one chain, now with 2 chains, I don't know how to rejoin them together >>> again. Can you suggest me any solution, please?! >>> *N.B: the 2 chains are considered as one when selected in VMD >> Center on a single chain rather than trying to work with the interface >> residues. >> >> -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 Feb 14 14:59:59 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 13:59:59 -0000 Subject: [gmx-users] RNA md simulation In-Reply-To: References: Message-ID: <9ec947f0-2b7c-8f05-88ec-28638b1b373e@vt.edu> On 2/14/20 5:20 AM, Priyanka Singh wrote: > Hi can anyone help with the problem of terminal end notation for charmm36 > ff for RNA molecule to generate .gro file usind gromac-2019.3 The standard 5'-OH and 3'-OH are 5TER and 3TER. -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 Feb 14 15:01:54 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 14:01:54 -0000 Subject: [gmx-users] grompp error : Atomtype HC not found In-Reply-To: References: Message-ID: <66f5c8fb-908b-ecbe-e39f-dbe2725c0718@vt.edu> On 2/14/20 6:09 AM, Atila Petrosian wrote: > Dear Justin, > Thanks for answer. > > You said " There is no reason to use this totally obsolete force field > (ffgmx.itp)". > I used ffgmx.itp, because there was a example.top file in Tieleman's web > site: That example is almost as old as I am :) It reproduces published work but no longer reflects the state of the art. ffgmx (the "GROMACS force field," which is a terrible name for a hacked/partially undocumented GROMOS87) is no longer acceptable for modern simulations. Please see a more updated approach that uses GROMOS96 at http://www.mdtutorials.com/gmx/membrane_protein/index.html though I will note that the Berger parameters that are distributed by Tieleman and used in that tutorial are also not as high-quality as other more modern parameter sets like Slipids and CHARMM36. -Justin > ------------------------------------------------------- > ; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion > ; alm.itp can be made in a straightforward manner with pdb2gmx, starting > ; with a pdb file of alamethicin. > ; make sure lipid.itp, popc.itp and alm.itp are in a location where > ; grompp can find them (GMXLIB, current directory, or directory given in > ; the .mdp file with the include option. > #include "ffgmx.itp" > #include "lipid.itp" > #include "popc.itp" > #include "alm.itp" > #include "ions.itp" > > #ifdef FLEX_SPC > #include "flexspc.itp" > #else > #include "spc.itp" > #endif > > [ system ] > ; name > Alm on surf + relaxed popc > > [ molecules ] > ; name number > Protein 1 > POPC 128 > SOL 3552 > Na 1 > ------------------------------------------------------- > Based on your suggestion, I used following in my topology file (I deleted > ffgmx.itp): > > #include "lipid.itp" > #include "dppc.itp" > #include "lig.itp" > ------------------------------------------------------- > But I encountered with: > ------------------------------------------------------- > Fatal error: > Syntax error - File lipid.itp, line 11 > Last line read: > '[ atomtypes ]' > Invalid order for directive atomtypes > ------------------------------------------------------- > lipid.itp file from Tieleman's web site is as follows: > ------------------------------------------------------- > ;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS > ;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et > ;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are > ;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters, > ;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as > ;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS. > > [ defaults ] > 1 1 > > [ atomtypes ] > ;name mass charge ptype c6 c12 > ; > LO 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS > LOM 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS > LNL 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS > LC 12.0110 0.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS > LH1 13.0190 0.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS > LH2 14.0270 0.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS > LP 30.9738 0.000 A 9.16000e-03 2.50700e-05 ;phosphor, OPLS > LOS 15.9994 0.000 A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS > LP2 14.0270 0.000 A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ > LP3 15.0350 0.000 A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ > LC3 15.0350 0.000 A 9.35700e-03 3.60900e-05 ;CH3, OPLS > LC2 14.0270 0.000 A 5.94700e-03 1.79000e-05 ;CH2, OPLS > ------------------------------------------------------- > > How to resolve that? > > Best, > Atila -- ================================================== 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 mhviet at ifpan.edu.pl Fri Feb 14 16:24:58 2020 From: mhviet at ifpan.edu.pl (Man Hoang Viet) Date: Fri, 14 Feb 2020 15:24:58 -0000 Subject: [gmx-users] Can't observe ion separation under the influence of electric field In-Reply-To: References: Message-ID: <132dc1e78ccd79bbfd4fe8dc82a16572.squirrel@webmail.ifpan.edu.pl> Hi Live King, I think the temperature coupling strongly effect on your observation since the velocity of atoms (ions) will be rescale after every tau-t value. It means the movement direction of ion under EEF will be mostly canceled for every tau-t (ps). If you set tau-t to be larger than default value (.i.e 10, 100 or 1000) you can see the effect of EEF on your system. Viet Man, University of Pittsburgh School of Pharmacy > > Dear David and Harutyun, > > Thanks for your reply. Density plots were the first check I did. They show > a very minor difference. I imagined that the electric field is not > sufficient, however, presence of high electric field ( > 1 V or 1000mV)* > disrupts the membrane and my simulation crashes*. Is there any solution to > this problem? I will have a look at compel. > > On Thu, Feb 13, 2020 at 6:21 PM Harutyun Sahakyan > wrote: > >> You can use compel and build a double bilayer system to separate ions. >> However, if you separate positive and negative ions, you will have very >> high membrane potential, event two ions difference can raise potential >> about 200 mV. In your case, I suppose 500 mV is not enough to separate >> all >> ions in a PBC box. >> >> https://www.mpibpc.mpg.de/grubmueller/compel >> >> >> >> Harutyun Sahakyan >> Senior Assistant at Laboratory of >> Computational Modeling of Biological Processes, >> Institute of Molecular Biology, NAS, Armenia, Yerevan >> Tel: +374 93 323990 >> h_sahakyan at mb.sci.am >> sahakyanhk at gmail.com >> >> February 13, 2020 2:07 AM, "Live King" wrote: >> >> > Dear all, >> > >> > I am running a simple test case with a lipid bilayer (DMPC), water, >> and >> > ions (150mM KCL) under the influence of a constant electric field ( >> 300mV, >> > 500mV, and 700mV). *I expected positive and negative ions to separate >> in >> > the presence of an external electric field*. However, I am not >> observing >> > such behavior despite running the all-atom simulation for 400ns in any >> > case. I am using gromacs 2018.2, my mdp file is standard charmm-gui >> > production with electric field option. >> > >> > for example 500mV electric field in Z-direction : >> > electric-field-z = 0.060 0 0 0 ; *500**mv = 8.25nm* 0.060 = >> > 500 mV * >> > >> > Are there any settings to run the electric field simulation that I >> miss? >> > Any help will be greatly appreciated. >> > >> > Thank you, From andrew.bostick1 at gmail.com Fri Feb 14 17:13:57 2020 From: andrew.bostick1 at gmail.com (Andrew Bostick) Date: Fri, 14 Feb 2020 16:13:57 -0000 Subject: [gmx-users] Ligand in PRODRG server is protonated. Why? Message-ID: Dear gromacs users, I am doing MD simulation of protein-ligand complex. For ligand, I used PRODRG server. My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In PRODRG outputs, ligand is protonated on N atom and has 1 atom more than original structure (58 atoms). I don't want this output. My aim is studying unprotonated structure of Tamoxifen. How to resolve that. Best, Andrew From ali.khodayari at student.kuleuven.be Fri Feb 14 17:16:46 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Fri, 14 Feb 2020 16:16:46 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: References: Message-ID: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> Thank you Alessandra. However, fixing the topology did not remove the error. It still stands as before: A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501 Anyone has any idea why it could be happening? My best, Ali -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: donderdag 13 februari 2020 16:28 To: gmx-users at gromacs.org; gromacs.org_gmx-users Subject: Re: [gmx-users] Tabulated potentials Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > Dear Gromacs users, > > I?ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through > the energy groups specified. But how can I refer each bond type to its table? > > I have derived coarse-grained potentials for a cellobiose-water system. > There are 11 beads (4 bead types) in each cellobiose molecule, and > each water molecule is coarse-grained as one bead. Overall, there are > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > types, and 2 dihedral potential tables for two types of dihedrals. The > tables are named as table_b1.xvg, table_b2.xvg, and so on. > Now my question is, how does gromacs recognise which table is regarding > which bonded term? The simulation crashes at the very beginning giving > me the following error: > > In topol.top one specifies which table is used for which interaction (bond, angle, dihedral). See the table below for the synthases http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file Best regards Alessandra > A tabulated bond interaction table number 1 is out of the table range: > r 0.511823, between table indices 511 and 512, table length 501 > > I believe this is caused due to high forces on atoms indeed, but it > might be also because tables are not specified to the correct bond type. > > > 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 jalemkul at vt.edu Fri Feb 14 18:56:10 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 14 Feb 2020 17:56:10 -0000 Subject: [gmx-users] Ligand in PRODRG server is protonated. Why? In-Reply-To: References: Message-ID: <5a81bc1b-47e6-0d96-e1ec-8b72b9cc3dd7@vt.edu> On 2/14/20 11:13 AM, Andrew Bostick wrote: > Dear gromacs users, > > I am doing MD simulation of protein-ligand complex. For ligand, I used > PRODRG server. > > My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of > Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In > PRODRG outputs, ligand is protonated on N atom and has 1 atom more than > original structure (58 atoms). I don't want this output. My aim is studying > unprotonated structure of Tamoxifen. > > How to resolve that. Protonation is addressed in their FAQ: http://prodrg1.dyndns.org/prodrg_faq.html I strongly discourage you from using PRODRG. Its topologies are of inadequate quality for MD simulations and were never intended to be used for such. -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 Feb 14 20:11:04 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Fri, 14 Feb 2020 19:11:04 -0000 Subject: [gmx-users] how to apply constraints in energy minimization Message-ID: Dear Gromacs users I am trying to run a protein-ligand free energy calculation in which I initially run MD for 3 ns without free energy calculation and took these coordinates for free energy in which I am doing two-step energy minimization. Firstly at steepest decent with force tolerance of 100 with 20000 nsteps which converges to in 7992 steps as mentioned below:- Energies (kJ/mol) Bond Restraint Pot. Angle Proper Dih. Improper Dih. 1.21424e+03 9.53698e+01 4.72990e+03 1.83362e+04 1.86005e+02 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 6.81666e+03 7.15551e+04 3.32691e+05 -6.56537e+03 -2.69738e+06 Coul. recip. Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.52484e+03 6.92787e+00 2.04511e+02 -2.26358e+06 0.00000e+00 Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.68131e+04 0.00000e+00 0.00000e+00 6.26922e+03 -1.62832e+03 dVrestraint/dl Constr. rmsd 0.00000e+00 2.65292e-06 *Steepest Descents converged to Fmax < 100 in 7992 stepsPotential Energy = -2.2635825e+06Maximum force = 9.0506676e+01 on atom 16669Norm of force = 3.6179803e+00* Step Time 2470 2470.00000 Energies (kJ/mol) Bond Restraint Pot. Angle Proper Dih. Improper Dih. 7.44151e+04 9.26252e+01 4.47510e+04 1.83016e+04 1.95586e+02 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 6.77053e+03 7.14269e+04 4.17453e+05 -6.56537e+03 -3.03191e+06 Coul. recip. Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.48733e+03 6.63779e+00 2.08432e+02 -2.40037e+06 0.00000e+00 Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -7.77641e+01 0.00000e+00 0.00000e+00 6.49503e+03 -1.88623e+03 dVrestraint/dl 0.00000e+00 For the second minimization, I am using l-bfgs integrator at force tolerance 10 with 50000 nsteps. I get the following message:- *Energy minimization has stopped, but the forces have not converged to therequested precision Fmax < 10 (which may not be possible for your system). * Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. Low-Memory BFGS Minimizer converged to machine precision in 2471 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.4003668e+06 Maximum force = 2.1663138e+02 on atom 1093 Norm of force = 3.8024703e+00 Performed 2565 energy evaluations in total. But my system crashes at nvt step generating different pdb structures. How should I solve this Any suggestions will really be appreciated. Thanks. Sadaf Rani Visiting Ph.D. student Lancaster University Uk From sadafrani6 at gmail.com Fri Feb 14 20:21:37 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Fri, 14 Feb 2020 19:21:37 -0000 Subject: [gmx-users] putting step wise constraints in energy minimization Message-ID: Dear Gromacs users I want to run energy minimization in steps first to remove clashes with ions, second keeping position of heavy atoms fixed and thirdly removing all constraints. How can I set this in mdp file for ions and protein atoms? Thanks Sadaf Rani Ph.D. visiting student Lancaster University UK From devargyachakraborty.kgp at gmail.com Sat Feb 15 10:50:41 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Sat, 15 Feb 2020 09:50:41 -0000 Subject: [gmx-users] problem while calculating order parameter Message-ID: i want to calculate the order prameter between two carbon atom namrd C01 and C03 in my topology file but while calculating, i am getting the following error. Taking z axis as normal to the membrane Reading file nvt.tpr, VERSION 2019.1 (single precision) Using following groups: Groupname: System First atomname: C01 First atomnr 0 Groupname: Other First atomname: C01 First atomnr 0 Groupname: EMI First atomname: C01 First atomnr 0 Groupname: NSC First atomname: NBT First atomnr 760 Groupname: Water First atomname: OW First atomnr 1360 Groupname: SOL First atomname: OW First atomnr 1360 Groupname: non-Water First atomname: C01 First atomnr 0 Groupname: C01 First atomname: C01 First atomnr 0 Groupname: C04 First atomname: C04 First atomnr 1 Groupname: C03 First atomname: C03 First atomnr 2 Groupname: H07 First atomname: H07 First atomnr 3 Groupname: H09 First atomname: H09 First atomnr 4 Groupname: H08 First atomname: H08 First atomnr 5 Groupname: C05 First atomname: C05 First atomnr 6 Groupname: H0B First atomname: H0B First atomnr 7 Groupname: H0C First atomname: H0C First atomnr 8 Groupname: H0D First atomname: H0D First atomnr 9 Groupname: N00 First atomname: N00 First atomnr 10 Groupname: C06 First atomname: C06 First atomnr 11 Groupname: H0F First atomname: H0F First atomnr 12 Groupname: C0N First atomname: C0N First atomnr 13 Groupname: H0O First atomname: H0O First atomnr 14 Groupname: H0P First atomname: H0P First atomnr 15 Groupname: H0Q First atomname: H0Q First atomnr 16 Groupname: N02 First atomname: N02 First atomnr 17 Groupname: H0E First atomname: H0E First atomnr 18 Groupname: NBT First atomname: NBT First atomnr 760 Groupname: SBT First atomname: SBT First atomnr 761 Groupname: OBT First atomname: OBT First atomnr 763 Groupname: CBT First atomname: CBT First atomnr 764 Groupname: F1 First atomname: F1 First atomnr 768 Reading frame 0 time 0.000 Number of elements in first group: 10360 ------------------------------------------------------- Program: gmx order, version 2019.1 Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) Fatal error: grp 1 does not have same number of elements as grp 1 can anybody help. Thanks From shakirashukoor1993 at gmail.com Sat Feb 15 13:16:58 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Sat, 15 Feb 2020 12:16:58 -0000 Subject: [gmx-users] problem while calculating order parameter In-Reply-To: References: Message-ID: I guess you have not made your index file correctly. It should contain only the group for which you will calculate the order parameter. On Sat, Feb 15, 2020 at 3:21 PM Devargya Chakraborty < devargyachakraborty.kgp at gmail.com> wrote: > i want to calculate the order prameter between two carbon atom namrd C01 > and C03 in my topology file but while calculating, i am getting the > following error. > > Taking z axis as normal to the membrane > Reading file nvt.tpr, VERSION 2019.1 (single precision) > Using following groups: > Groupname: System First atomname: C01 First atomnr 0 > Groupname: Other First atomname: C01 First atomnr 0 > Groupname: EMI First atomname: C01 First atomnr 0 > Groupname: NSC First atomname: NBT First atomnr 760 > Groupname: Water First atomname: OW First atomnr 1360 > Groupname: SOL First atomname: OW First atomnr 1360 > Groupname: non-Water First atomname: C01 First atomnr 0 > Groupname: C01 First atomname: C01 First atomnr 0 > Groupname: C04 First atomname: C04 First atomnr 1 > Groupname: C03 First atomname: C03 First atomnr 2 > Groupname: H07 First atomname: H07 First atomnr 3 > Groupname: H09 First atomname: H09 First atomnr 4 > Groupname: H08 First atomname: H08 First atomnr 5 > Groupname: C05 First atomname: C05 First atomnr 6 > Groupname: H0B First atomname: H0B First atomnr 7 > Groupname: H0C First atomname: H0C First atomnr 8 > Groupname: H0D First atomname: H0D First atomnr 9 > Groupname: N00 First atomname: N00 First atomnr 10 > Groupname: C06 First atomname: C06 First atomnr 11 > Groupname: H0F First atomname: H0F First atomnr 12 > Groupname: C0N First atomname: C0N First atomnr 13 > Groupname: H0O First atomname: H0O First atomnr 14 > Groupname: H0P First atomname: H0P First atomnr 15 > Groupname: H0Q First atomname: H0Q First atomnr 16 > Groupname: N02 First atomname: N02 First atomnr 17 > Groupname: H0E First atomname: H0E First atomnr 18 > Groupname: NBT First atomname: NBT First atomnr 760 > Groupname: SBT First atomname: SBT First atomnr 761 > Groupname: OBT First atomname: OBT First atomnr 763 > Groupname: CBT First atomname: CBT First atomnr 764 > Groupname: F1 First atomname: F1 First atomnr 768 > > Reading frame 0 time 0.000 Number of elements in first group: > 10360 > > ------------------------------------------------------- > Program: gmx order, version 2019.1 > Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) > > Fatal error: > grp 1 does not have same number of elements as grp 1 > > can anybody help. > > 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. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From jalemkul at vt.edu Sat Feb 15 15:28:52 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 15 Feb 2020 14:28:52 -0000 Subject: [gmx-users] putting step wise constraints in energy minimization In-Reply-To: References: Message-ID: On 2/14/20 2:21 PM, Sadaf Rani wrote: > Dear Gromacs users > I want to run energy minimization in steps > first to remove clashes with ions, second keeping position of heavy atoms > fixed and thirdly removing all constraints. How can I set this in mdp file > for ions and protein atoms? What you're referring to are restraints, not constraints. "define = -DPOSRES" restrains heavy atoms, so use that and then turn it off in the next round. -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 Sat Feb 15 15:30:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 15 Feb 2020 14:30:05 -0000 Subject: [gmx-users] problem while calculating order parameter In-Reply-To: References: Message-ID: <23e15586-3133-08fc-0086-2f0a455ddc71@vt.edu> On 2/15/20 4:50 AM, Devargya Chakraborty wrote: > i want to calculate the order prameter between two carbon atom namrd C01 > and C03 in my topology file but while calculating, i am getting the > following error. gmx order is designed to compute deuterium order parameters in alkyl chains. It requires special index groups that only contain the atoms of interest and those flanking them to define the local molecular axis. See http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an example. -Justin > Taking z axis as normal to the membrane > Reading file nvt.tpr, VERSION 2019.1 (single precision) > Using following groups: > Groupname: System First atomname: C01 First atomnr 0 > Groupname: Other First atomname: C01 First atomnr 0 > Groupname: EMI First atomname: C01 First atomnr 0 > Groupname: NSC First atomname: NBT First atomnr 760 > Groupname: Water First atomname: OW First atomnr 1360 > Groupname: SOL First atomname: OW First atomnr 1360 > Groupname: non-Water First atomname: C01 First atomnr 0 > Groupname: C01 First atomname: C01 First atomnr 0 > Groupname: C04 First atomname: C04 First atomnr 1 > Groupname: C03 First atomname: C03 First atomnr 2 > Groupname: H07 First atomname: H07 First atomnr 3 > Groupname: H09 First atomname: H09 First atomnr 4 > Groupname: H08 First atomname: H08 First atomnr 5 > Groupname: C05 First atomname: C05 First atomnr 6 > Groupname: H0B First atomname: H0B First atomnr 7 > Groupname: H0C First atomname: H0C First atomnr 8 > Groupname: H0D First atomname: H0D First atomnr 9 > Groupname: N00 First atomname: N00 First atomnr 10 > Groupname: C06 First atomname: C06 First atomnr 11 > Groupname: H0F First atomname: H0F First atomnr 12 > Groupname: C0N First atomname: C0N First atomnr 13 > Groupname: H0O First atomname: H0O First atomnr 14 > Groupname: H0P First atomname: H0P First atomnr 15 > Groupname: H0Q First atomname: H0Q First atomnr 16 > Groupname: N02 First atomname: N02 First atomnr 17 > Groupname: H0E First atomname: H0E First atomnr 18 > Groupname: NBT First atomname: NBT First atomnr 760 > Groupname: SBT First atomname: SBT First atomnr 761 > Groupname: OBT First atomname: OBT First atomnr 763 > Groupname: CBT First atomname: CBT First atomnr 764 > Groupname: F1 First atomname: F1 First atomnr 768 > > Reading frame 0 time 0.000 Number of elements in first group: > 10360 > > ------------------------------------------------------- > Program: gmx order, version 2019.1 > Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) > > Fatal error: > grp 1 does not have same number of elements as grp 1 > > can anybody help. > > Thanks -- ================================================== 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 ph.marwaabdelkader at gmail.com Sat Feb 15 15:52:27 2020 From: ph.marwaabdelkader at gmail.com (Marwa Abd El Kader) Date: Sat, 15 Feb 2020 14:52:27 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: <61b779df-7e13-f15a-7fa9-6a1764154a0f@vt.edu> References: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> <61b779df-7e13-f15a-7fa9-6a1764154a0f@vt.edu> Message-ID: Dear Justin, I 've tried centering on one chain and the same problem still exists, any suggestions? On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > > > On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: > > Dear Justin, > > Would you please tell me how, give me an example code, because I'm a > novice? > > The same thing you did before but instead of trying to select > interfacial residues, make an index group of one of the protein chains > and select it for the centering group. > > -Justin > > > Thanks in advance, > > Marwa > > > > On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: > > > >> > >> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: > >>> Dear gmx-users mailing list team, > >>> I want to know how to fix the separation of 2 chains after the > production > >>> run. I'm trying different combinations of trjconv after creating an > index > >>> file having a specific residue(s) on the interface between the 2 > chains, > >>> but nothing is working. I fixed this issue before but when there was > only > >>> one chain, now with 2 chains, I don't know how to rejoin them together > >>> again. Can you suggest me any solution, please?! > >>> *N.B: the 2 chains are considered as one when selected in VMD > >> Center on a single chain rather than trying to work with the interface > >> residues. > >> > >> -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 devargyachakraborty.kgp at gmail.com Sat Feb 15 16:41:53 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Sat, 15 Feb 2020 15:41:53 -0000 Subject: [gmx-users] problem while calculating order parameter In-Reply-To: <23e15586-3133-08fc-0086-2f0a455ddc71@vt.edu> References: <23e15586-3133-08fc-0086-2f0a455ddc71@vt.edu> Message-ID: Thanks On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul wrote: > > > On 2/15/20 4:50 AM, Devargya Chakraborty wrote: > > i want to calculate the order prameter between two carbon atom namrd C01 > > and C03 in my topology file but while calculating, i am getting the > > following error. > > gmx order is designed to compute deuterium order parameters in alkyl > chains. It requires special index groups that only contain the atoms of > interest and those flanking them to define the local molecular axis. See > http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an > example. > > -Justin > > > Taking z axis as normal to the membrane > > Reading file nvt.tpr, VERSION 2019.1 (single precision) > > Using following groups: > > Groupname: System First atomname: C01 First atomnr 0 > > Groupname: Other First atomname: C01 First atomnr 0 > > Groupname: EMI First atomname: C01 First atomnr 0 > > Groupname: NSC First atomname: NBT First atomnr 760 > > Groupname: Water First atomname: OW First atomnr 1360 > > Groupname: SOL First atomname: OW First atomnr 1360 > > Groupname: non-Water First atomname: C01 First atomnr 0 > > Groupname: C01 First atomname: C01 First atomnr 0 > > Groupname: C04 First atomname: C04 First atomnr 1 > > Groupname: C03 First atomname: C03 First atomnr 2 > > Groupname: H07 First atomname: H07 First atomnr 3 > > Groupname: H09 First atomname: H09 First atomnr 4 > > Groupname: H08 First atomname: H08 First atomnr 5 > > Groupname: C05 First atomname: C05 First atomnr 6 > > Groupname: H0B First atomname: H0B First atomnr 7 > > Groupname: H0C First atomname: H0C First atomnr 8 > > Groupname: H0D First atomname: H0D First atomnr 9 > > Groupname: N00 First atomname: N00 First atomnr 10 > > Groupname: C06 First atomname: C06 First atomnr 11 > > Groupname: H0F First atomname: H0F First atomnr 12 > > Groupname: C0N First atomname: C0N First atomnr 13 > > Groupname: H0O First atomname: H0O First atomnr 14 > > Groupname: H0P First atomname: H0P First atomnr 15 > > Groupname: H0Q First atomname: H0Q First atomnr 16 > > Groupname: N02 First atomname: N02 First atomnr 17 > > Groupname: H0E First atomname: H0E First atomnr 18 > > Groupname: NBT First atomname: NBT First atomnr 760 > > Groupname: SBT First atomname: SBT First atomnr 761 > > Groupname: OBT First atomname: OBT First atomnr 763 > > Groupname: CBT First atomname: CBT First atomnr 764 > > Groupname: F1 First atomname: F1 First atomnr 768 > > > > Reading frame 0 time 0.000 Number of elements in first group: > > 10360 > > > > ------------------------------------------------------- > > Program: gmx order, version 2019.1 > > Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) > > > > Fatal error: > > grp 1 does not have same number of elements as grp 1 > > > > can anybody help. > > > > Thanks > > -- > ================================================== > > 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 Feb 15 17:13:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 15 Feb 2020 16:13:05 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: References: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> <61b779df-7e13-f15a-7fa9-6a1764154a0f@vt.edu> Message-ID: <840fe62c-e72c-2c59-b6d5-24d07f7e1543@vt.edu> On 2/15/20 9:52 AM, Marwa Abd El Kader wrote: > Dear Justin, > I 've tried centering on one chain and the same problem still exists, any > suggestions? If centering on one chain via trjconv -center -pbc mol does not yield dimers, then I suspect the two chains are not actually associated and what you're observing is not actually a PBC issue, unless your box is too small and PBC jumps are unavoidable even if one species is properly centered. -Justin > On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > >> >> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: >>> Dear Justin, >>> Would you please tell me how, give me an example code, because I'm a >> novice? >> >> The same thing you did before but instead of trying to select >> interfacial residues, make an index group of one of the protein chains >> and select it for the centering group. >> >> -Justin >> >>> Thanks in advance, >>> Marwa >>> >>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: >>> >>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: >>>>> Dear gmx-users mailing list team, >>>>> I want to know how to fix the separation of 2 chains after the >> production >>>>> run. I'm trying different combinations of trjconv after creating an >> index >>>>> file having a specific residue(s) on the interface between the 2 >> chains, >>>>> but nothing is working. I fixed this issue before but when there was >> only >>>>> one chain, now with 2 chains, I don't know how to rejoin them together >>>>> again. Can you suggest me any solution, please?! >>>>> *N.B: the 2 chains are considered as one when selected in VMD >>>> Center on a single chain rather than trying to work with the interface >>>> residues. >>>> >>>> -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 neena.susaneappen at mail.utoronto.ca Sat Feb 15 17:44:42 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Sat, 15 Feb 2020 16:44:42 -0000 Subject: [gmx-users] Script for looping n simulations Message-ID: Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. Many thanks, Neena From jalemkul at vt.edu Sat Feb 15 17:56:10 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 15 Feb 2020 16:56:10 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: <87f8d8c6-7cf0-a27c-d0dd-dc64b0544043@vt.edu> On 2/15/20 11:44 AM, Neena Susan Eappen wrote: > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. It's the same logic as in http://www.mdtutorials.com/gmx/membrane_protein/Files/run_inflategro.sh - note that the script is more complicated than what you need; you just need to iterate over grompp and mdrun using a counter that reflects the current and previous simulation index. -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 Sat Feb 15 18:04:19 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 15 Feb 2020 17:04:19 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: <87f8d8c6-7cf0-a27c-d0dd-dc64b0544043@vt.edu> On 2/15/20 11:44 AM, Neena Susan Eappen wrote: > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. It's the same logic as in http://www.mdtutorials.com/gmx/membrane_protein/Files/run_inflategro.sh - note that the script is more complicated than what you need; you just need to iterate over grompp and mdrun using a counter that reflects the current and previous simulation index. -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 shihailong2019 at gmail.com Sat Feb 15 21:21:48 2020 From: shihailong2019 at gmail.com (Shi Hailong) Date: Sat, 15 Feb 2020 20:21:48 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 190, Issue 31 In-Reply-To: References: Message-ID: > On Feb 15, 2020, at 10:44 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: problem while calculating order parameter (Justin Lemkul) > 2. Re: Trajectory optimization - 2 chains are separated > (Marwa Abd El Kader) > 3. Re: problem while calculating order parameter > (Devargya Chakraborty) > 4. Re: Trajectory optimization - 2 chains are separated > (Justin Lemkul) > 5. Script for looping n simulations (Neena Susan Eappen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 15 Feb 2020 09:29:48 -0500 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] problem while calculating order parameter > Message-ID: <23e15586-3133-08fc-0086-2f0a455ddc71 at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 2/15/20 4:50 AM, Devargya Chakraborty wrote: >> i want to calculate the order prameter between two carbon atom namrd C01 >> and C03 in my topology file but while calculating, i am getting the >> following error. > > gmx order is designed to compute deuterium order parameters in alkyl > chains. It requires special index groups that only contain the atoms of > interest and those flanking them to define the local molecular axis. See > http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an > example. > > -Justin > >> Taking z axis as normal to the membrane >> Reading file nvt.tpr, VERSION 2019.1 (single precision) >> Using following groups: >> Groupname: System First atomname: C01 First atomnr 0 >> Groupname: Other First atomname: C01 First atomnr 0 >> Groupname: EMI First atomname: C01 First atomnr 0 >> Groupname: NSC First atomname: NBT First atomnr 760 >> Groupname: Water First atomname: OW First atomnr 1360 >> Groupname: SOL First atomname: OW First atomnr 1360 >> Groupname: non-Water First atomname: C01 First atomnr 0 >> Groupname: C01 First atomname: C01 First atomnr 0 >> Groupname: C04 First atomname: C04 First atomnr 1 >> Groupname: C03 First atomname: C03 First atomnr 2 >> Groupname: H07 First atomname: H07 First atomnr 3 >> Groupname: H09 First atomname: H09 First atomnr 4 >> Groupname: H08 First atomname: H08 First atomnr 5 >> Groupname: C05 First atomname: C05 First atomnr 6 >> Groupname: H0B First atomname: H0B First atomnr 7 >> Groupname: H0C First atomname: H0C First atomnr 8 >> Groupname: H0D First atomname: H0D First atomnr 9 >> Groupname: N00 First atomname: N00 First atomnr 10 >> Groupname: C06 First atomname: C06 First atomnr 11 >> Groupname: H0F First atomname: H0F First atomnr 12 >> Groupname: C0N First atomname: C0N First atomnr 13 >> Groupname: H0O First atomname: H0O First atomnr 14 >> Groupname: H0P First atomname: H0P First atomnr 15 >> Groupname: H0Q First atomname: H0Q First atomnr 16 >> Groupname: N02 First atomname: N02 First atomnr 17 >> Groupname: H0E First atomname: H0E First atomnr 18 >> Groupname: NBT First atomname: NBT First atomnr 760 >> Groupname: SBT First atomname: SBT First atomnr 761 >> Groupname: OBT First atomname: OBT First atomnr 763 >> Groupname: CBT First atomname: CBT First atomnr 764 >> Groupname: F1 First atomname: F1 First atomnr 768 >> >> Reading frame 0 time 0.000 Number of elements in first group: >> 10360 >> >> ------------------------------------------------------- >> Program: gmx order, version 2019.1 >> Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) >> >> Fatal error: >> grp 1 does not have same number of elements as grp 1 >> >> can anybody help. >> >> Thanks > > -- > ================================================== > > 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: 2 > Date: Sat, 15 Feb 2020 16:52:13 +0200 > From: Marwa Abd El Kader > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Trajectory optimization - 2 chains are > separated > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear Justin, > I 've tried centering on one chain and the same problem still exists, any > suggestions? > > On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > >> >> >> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: >>> Dear Justin, >>> Would you please tell me how, give me an example code, because I'm a >> novice? >> >> The same thing you did before but instead of trying to select >> interfacial residues, make an index group of one of the protein chains >> and select it for the centering group. >> >> -Justin >> >>> Thanks in advance, >>> Marwa >>> >>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: >>> >>>> >>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: >>>>> Dear gmx-users mailing list team, >>>>> I want to know how to fix the separation of 2 chains after the >> production >>>>> run. I'm trying different combinations of trjconv after creating an >> index >>>>> file having a specific residue(s) on the interface between the 2 >> chains, >>>>> but nothing is working. I fixed this issue before but when there was >> only >>>>> one chain, now with 2 chains, I don't know how to rejoin them together >>>>> again. Can you suggest me any solution, please?! >>>>> *N.B: the 2 chains are considered as one when selected in VMD >>>> Center on a single chain rather than trying to work with the interface >>>> residues. >>>> >>>> -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. >> > > > ------------------------------ > > Message: 3 > Date: Sat, 15 Feb 2020 21:11:20 +0530 > From: Devargya Chakraborty > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] problem while calculating order parameter > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Thanks > > On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul wrote: > >> >> >> On 2/15/20 4:50 AM, Devargya Chakraborty wrote: >>> i want to calculate the order prameter between two carbon atom namrd C01 >>> and C03 in my topology file but while calculating, i am getting the >>> following error. >> >> gmx order is designed to compute deuterium order parameters in alkyl >> chains. It requires special index groups that only contain the atoms of >> interest and those flanking them to define the local molecular axis. See >> http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an >> example. >> >> -Justin >> >>> Taking z axis as normal to the membrane >>> Reading file nvt.tpr, VERSION 2019.1 (single precision) >>> Using following groups: >>> Groupname: System First atomname: C01 First atomnr 0 >>> Groupname: Other First atomname: C01 First atomnr 0 >>> Groupname: EMI First atomname: C01 First atomnr 0 >>> Groupname: NSC First atomname: NBT First atomnr 760 >>> Groupname: Water First atomname: OW First atomnr 1360 >>> Groupname: SOL First atomname: OW First atomnr 1360 >>> Groupname: non-Water First atomname: C01 First atomnr 0 >>> Groupname: C01 First atomname: C01 First atomnr 0 >>> Groupname: C04 First atomname: C04 First atomnr 1 >>> Groupname: C03 First atomname: C03 First atomnr 2 >>> Groupname: H07 First atomname: H07 First atomnr 3 >>> Groupname: H09 First atomname: H09 First atomnr 4 >>> Groupname: H08 First atomname: H08 First atomnr 5 >>> Groupname: C05 First atomname: C05 First atomnr 6 >>> Groupname: H0B First atomname: H0B First atomnr 7 >>> Groupname: H0C First atomname: H0C First atomnr 8 >>> Groupname: H0D First atomname: H0D First atomnr 9 >>> Groupname: N00 First atomname: N00 First atomnr 10 >>> Groupname: C06 First atomname: C06 First atomnr 11 >>> Groupname: H0F First atomname: H0F First atomnr 12 >>> Groupname: C0N First atomname: C0N First atomnr 13 >>> Groupname: H0O First atomname: H0O First atomnr 14 >>> Groupname: H0P First atomname: H0P First atomnr 15 >>> Groupname: H0Q First atomname: H0Q First atomnr 16 >>> Groupname: N02 First atomname: N02 First atomnr 17 >>> Groupname: H0E First atomname: H0E First atomnr 18 >>> Groupname: NBT First atomname: NBT First atomnr 760 >>> Groupname: SBT First atomname: SBT First atomnr 761 >>> Groupname: OBT First atomname: OBT First atomnr 763 >>> Groupname: CBT First atomname: CBT First atomnr 764 >>> Groupname: F1 First atomname: F1 First atomnr 768 >>> >>> Reading frame 0 time 0.000 Number of elements in first group: >>> 10360 >>> >>> ------------------------------------------------------- >>> Program: gmx order, version 2019.1 >>> Source file: src/gromacs/gmxana/gmx_order.cpp (line 546) >>> >>> Fatal error: >>> grp 1 does not have same number of elements as grp 1 >>> >>> can anybody help. >>> >>> Thanks >> >> -- >> ================================================== >> >> 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. >> > > > ------------------------------ > > Message: 4 > Date: Sat, 15 Feb 2020 11:12:47 -0500 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Trajectory optimization - 2 chains are > separated > Message-ID: <840fe62c-e72c-2c59-b6d5-24d07f7e1543 at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 2/15/20 9:52 AM, Marwa Abd El Kader wrote: >> Dear Justin, >> I 've tried centering on one chain and the same problem still exists, any >> suggestions? > > If centering on one chain via trjconv -center -pbc mol does not yield > dimers, then I suspect the two chains are not actually associated and > what you're observing is not actually a PBC issue, unless your box is > too small and PBC jumps are unavoidable even if one species is properly > centered. > > -Justin > >> On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: >> >>> >>> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: >>>> Dear Justin, >>>> Would you please tell me how, give me an example code, because I'm a >>> novice? >>> >>> The same thing you did before but instead of trying to select >>> interfacial residues, make an index group of one of the protein chains >>> and select it for the centering group. >>> >>> -Justin >>> >>>> Thanks in advance, >>>> Marwa >>>> >>>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: >>>> >>>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: >>>>>> Dear gmx-users mailing list team, >>>>>> I want to know how to fix the separation of 2 chains after the >>> production >>>>>> run. I'm trying different combinations of trjconv after creating an >>> index >>>>>> file having a specific residue(s) on the interface between the 2 >>> chains, >>>>>> but nothing is working. I fixed this issue before but when there was >>> only >>>>>> one chain, now with 2 chains, I don't know how to rejoin them together >>>>>> again. Can you suggest me any solution, please?! >>>>>> *N.B: the 2 chains are considered as one when selected in VMD >>>>> Center on a single chain rather than trying to work with the interface >>>>> residues. >>>>> >>>>> -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 > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Sat, 15 Feb 2020 16:44:36 +0000 > From: Neena Susan Eappen > To: "gromacs.org_gmx-users at maillist.sys.kth.se" > > Subject: [gmx-users] Script for looping n simulations > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. > > Many thanks, > Neena > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 190, Issue 31 > ****************************************************** From shakirashukoor1993 at gmail.com Sun Feb 16 07:44:58 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Sun, 16 Feb 2020 06:44:58 -0000 Subject: [gmx-users] DEFORM option in gromacs Message-ID: Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From shakirashukoor1993 at gmail.com Sun Feb 16 12:12:27 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Sun, 16 Feb 2020 11:12:27 -0000 Subject: [gmx-users] (no subject) Message-ID: Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From jalemkul at vt.edu Sun Feb 16 14:10:45 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 16 Feb 2020 13:10:45 -0000 Subject: [gmx-users] DEFORM option in gromacs In-Reply-To: References: Message-ID: <8cc1820f-edf9-fc90-b9dd-a49c0d58610a@vt.edu> On 2/16/20 1:44 AM, shakira shukoor wrote: > Hi all > Can anyone help me with the DEFORM option in Gromacs to change the box > values? What are you trying to do and what problem are you encountering? Please don't repeatedly post the same question. It often takes time for people to see posts and have time to reply, especially on weekends. -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 shakirashukoor1993 at gmail.com Sun Feb 16 15:24:24 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Sun, 16 Feb 2020 14:24:24 -0000 Subject: [gmx-users] DEFORM option in gromacs In-Reply-To: <8cc1820f-edf9-fc90-b9dd-a49c0d58610a@vt.edu> References: <8cc1820f-edf9-fc90-b9dd-a49c0d58610a@vt.edu> Message-ID: I want to gradually decrease the box along xy direction in my simulation. I m confused what does this six values in the deform options mean? On Sun, Feb 16, 2020 at 6:41 PM Justin Lemkul wrote: > > > On 2/16/20 1:44 AM, shakira shukoor wrote: > > Hi all > > Can anyone help me with the DEFORM option in Gromacs to change the box > > values? > > What are you trying to do and what problem are you encountering? > > Please don't repeatedly post the same question. It often takes time for > people to see posts and have time to reply, especially on weekends. > > -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. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 From sadafrani6 at gmail.com Sun Feb 16 15:37:45 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 16 Feb 2020 14:37:45 -0000 Subject: [gmx-users] putting step wise constraints in energy minimization Message-ID: Thank you, Justin, I am still confused about constraints other than position restraints. As mentioned https://www.quora.com/q/gnvbdldrivyzzipw/Use-of-constraints-in-molecular-dynamics Should I use constraints also for my system to converge better? As I am doing energy minimization in two steps using steep emtol =100 and constraints= all-bonds, which converges in 9116 steps Step Time 9115 9115.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.35583e+03 4.93367e+03 1.88532e+04 2.36071e+02 6.91634e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 7.12823e+04 3.37615e+05 -6.30626e+03 -2.68202e+06 5.72973e+03 Potential Pres. DC (bar) Pressure (bar) -2.24140e+06 0.00000e+00 -2.56682e+04 Steepest Descents converged to Fmax < 100 in 9116 steps Potential Energy = -2.2414020e+06 Maximum force = 9.0994179e+01 on atom 76219 Norm of force = 3.3411843e+00 But the second minimization which I am doing in using steep integrator and emtol= 10 and constraints=none shows that:- Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 315 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.2420480e+06 Maximum force = 2.9302316e+02 on atom 4379 Norm of force = 3.5330992e+00 Finished mdrun on rank 0 Sun Feb 16 14:28:08 2020 How should I set the minimization energy of my system as it crashes after some steps of nvt equilibration? Thanks Sadaf Rani Ph.D. visiting student Lancaster university Uk From prathegreat2204 at gmail.com Sun Feb 16 17:33:13 2020 From: prathegreat2204 at gmail.com (Pranav BVN) Date: Sun, 16 Feb 2020 16:33:13 -0000 Subject: [gmx-users] Parametrization of Mn(ii) in charmm force field Message-ID: Greetings, I'm searching for a method to use Mn(ii) ions in a protein ligand simulation using charmm-36 ff in gromacs. But I donot seem to get any entry in ffnonbonded.itp in the charmm36-all-atom-ff directory. Is there any way to run the simulation with Mn using charmm36? Is there any way to achieve my goal? From sadafrani6 at gmail.com Sun Feb 16 18:05:51 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sun, 16 Feb 2020 17:05:51 -0000 Subject: [gmx-users] How to fix restraints in free energy calculation? Message-ID: Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some of my lamda windows, the residue restrained with ligand crashes and generates different PDB structures. It crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows 3,5,6,10, 14,15,19,20 it works well. My restraint section in topology is as below:- ; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 3437 7908 10 0.474 0.474 10.0 0.0 0.474 0.474 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 3437 7908 7905 7908 1 110.00 0.0 1 110.00 41.840 1 7908 3437 3439 3437 1 152.5 0.0 1 152.5 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7905 7908 3437 3439 1 140.19 0.0 0.0 140.19 0.0 41.840 7909 7908 3437 3439 1 -167.75 0.0 0.0 -69.05 0.0 41.840 7909 7908 3437 3433 1 -172.77 0.0 0.0 -172.77 0.0 41.840 Can anyone please suggest me how should I fix this? or where I am doing wrong? I will be really grateful. Thanks Sadaf Rani P.hD. visiting scholar Lancaster University Uk From jalemkul at vt.edu Sun Feb 16 18:32:43 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 16 Feb 2020 17:32:43 -0000 Subject: [gmx-users] DEFORM option in gromacs In-Reply-To: References: <8cc1820f-edf9-fc90-b9dd-a49c0d58610a@vt.edu> Message-ID: <39e45023-ace5-860a-a4df-f9a9100414c6@vt.edu> On 2/16/20 9:24 AM, shakira shukoor wrote: > I want to gradually decrease the box along xy direction in my simulation. I > m confused what does this six values in the deform options mean? http://manual.gromacs.org/current/user-guide/mdp-options.html#non-equilibrium-md They are the velocities at which the diagonal and off-diagonal terms (half matrix) of the full box tensor are changed. -Justin > On Sun, Feb 16, 2020 at 6:41 PM Justin Lemkul wrote: > >> >> On 2/16/20 1:44 AM, shakira shukoor wrote: >>> Hi all >>> Can anyone help me with the DEFORM option in Gromacs to change the box >>> values? >> What are you trying to do and what problem are you encountering? >> >> Please don't repeatedly post the same question. It often takes time for >> people to see posts and have time to reply, especially on weekends. >> >> -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 Sun Feb 16 18:34:34 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 16 Feb 2020 17:34:34 -0000 Subject: [gmx-users] putting step wise constraints in energy minimization In-Reply-To: References: Message-ID: <39caba54-dca1-3091-b30a-b1eb29e442dc@vt.edu> On 2/16/20 9:37 AM, Sadaf Rani wrote: > Thank you, Justin, > > I am still confused about constraints other than position restraints. As > mentioned > https://www.quora.com/q/gnvbdldrivyzzipw/Use-of-constraints-in-molecular-dynamics > > Should I use constraints also for my system to converge better? > As I am doing energy minimization in two steps using steep emtol =100 and > constraints= all-bonds, which converges in 9116 steps Constraints should be employed in a manner consistent with the force field parametrization strategy. Some force fields constrain all bonds (GROMOS) while others constrain only bonds to H (all the others). Use what the force field requires. If you don't use the appropriate constraints during minimization, your initial state may fail due to incompatibility of the geometry with the chosen (necessary) constraints. > Step Time > 9115 9115.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Improper Dih. LJ-14 > 1.35583e+03 4.93367e+03 1.88532e+04 2.36071e+02 6.91634e+03 > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > 7.12823e+04 3.37615e+05 -6.30626e+03 -2.68202e+06 5.72973e+03 > Potential Pres. DC (bar) Pressure (bar) > -2.24140e+06 0.00000e+00 -2.56682e+04 > > > Steepest Descents converged to Fmax < 100 in 9116 steps > Potential Energy = -2.2414020e+06 > Maximum force = 9.0994179e+01 on atom 76219 > Norm of force = 3.3411843e+00 > > But the second minimization which I am doing in using steep integrator and > emtol= 10 and constraints=none shows that:- > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 10 (which may not be possible for your system). > It > stopped because the algorithm tried to make a new step whose size was too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy or turn > off constraints altogether (set constraints = none in mdp file) > > Steepest Descents converged to machine precision in 315 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -2.2420480e+06 > Maximum force = 2.9302316e+02 on atom 4379 > Norm of force = 3.5330992e+00 > Finished mdrun on rank 0 Sun Feb 16 14:28:08 2020 > > How should I set the minimization energy of my system as it crashes after > some steps of nvt equilibration? There are many reasons for systems to crash; see http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up -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 Feb 16 18:36:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 16 Feb 2020 17:36:57 -0000 Subject: [gmx-users] Parametrization of Mn(ii) in charmm force field In-Reply-To: References: Message-ID: <4293f565-90d1-c46e-b32f-e888d3ebb4aa@vt.edu> On 2/16/20 11:32 AM, Pranav BVN wrote: > Greetings, > I'm searching for a method to use Mn(ii) ions in a protein ligand > simulation using charmm-36 ff in gromacs. But I donot seem to get any entry > in ffnonbonded.itp in the charmm36-all-atom-ff directory. Is there any way > to run the simulation with Mn using charmm36? Is there any way to > achieve my goal? Nonbonded (LJ) parameters can be found here: dx.doi.org/10.1021/jp309150r Parameters for covalent linkage to His can be found here (in the SI): https://aac.asm.org/content/61/11/e01572-17 -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 dallas.warren at monash.edu Sun Feb 16 22:13:57 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Sun, 16 Feb 2020 21:13:57 -0000 Subject: [gmx-users] Trajectory optimization - 2 chains are separated In-Reply-To: References: <3ca0a2cf-db5a-0389-1df8-83509d7dbf1b@vt.edu> <61b779df-7e13-f15a-7fa9-6a1764154a0f@vt.edu> Message-ID: Provide the command lines and images showing what is happening, that might help provide some insight for those trying to help. 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 Sun, 16 Feb 2020 at 01:52, Marwa Abd El Kader < ph.marwaabdelkader at gmail.com> wrote: > Dear Justin, > I 've tried centering on one chain and the same problem still exists, any > suggestions? > > On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > > > > > > > On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: > > > Dear Justin, > > > Would you please tell me how, give me an example code, because I'm a > > novice? > > > > The same thing you did before but instead of trying to select > > interfacial residues, make an index group of one of the protein chains > > and select it for the centering group. > > > > -Justin > > > > > Thanks in advance, > > > Marwa > > > > > > On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul wrote: > > > > > >> > > >> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote: > > >>> Dear gmx-users mailing list team, > > >>> I want to know how to fix the separation of 2 chains after the > > production > > >>> run. I'm trying different combinations of trjconv after creating an > > index > > >>> file having a specific residue(s) on the interface between the 2 > > chains, > > >>> but nothing is working. I fixed this issue before but when there was > > only > > >>> one chain, now with 2 chains, I don't know how to rejoin them > together > > >>> again. Can you suggest me any solution, please?! > > >>> *N.B: the 2 chains are considered as one when selected in VMD > > >> Center on a single chain rather than trying to work with the interface > > >> residues. > > >> > > >> -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 grx1985 at qq.com Mon Feb 17 00:42:19 2020 From: grx1985 at qq.com (=?gb18030?B?wejOtLfn?=) Date: Sun, 16 Feb 2020 23:42:19 -0000 Subject: [gmx-users] LJ interactions in gromacs Message-ID: Hi, I have a technique problem I would like to ask for suggestions. I would like to include some dumb atoms in my simulations. These dumb atoms only have LJ interactions with some atoms in the system (e.g., the lipid tails ), but do not interact with the other atoms (e.g., protein, waters). Is this possible in gromacs? If so, how could I do that? The reason I want to do so is that, I am simulating a membrane protein in a bilayer, and the lipids sometimes come into a cavity of the protein (which is what we do not want to happen). I want to fill the cavity with dumb atoms, so that the lipids will not come in. I am really appreciate for any suggestions. Thanks in advance for your help. With my best regards, RXG From kevin.boyd at uconn.edu Mon Feb 17 06:48:46 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Mon, 17 Feb 2020 05:48:46 -0000 Subject: [gmx-users] LJ interactions in gromacs In-Reply-To: References: Message-ID: Hi, A few groups have done things like this to shape membranes. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700167/ and https://pubs.acs.org/doi/10.1021/acs.jctc.8b00765 I was involved in the second publication, so feel free to contact me about implementation details if they're unclear. However, I'm not sure that this approach is reasonable for excluding lipids from a protein cavity. What else is supposed to occupy that cavity? A vacuum is unphysical, and if it's a part of the protein that's embedded in the membrane you don't want it filled with water. It also seems like this could lead to perturbations of the annular lipid shell, which may or may not be important. Kevin On Sun, Feb 16, 2020 at 3:42 PM ??? wrote: > Hi, > > > > I have a technique problem I would like to ask for suggestions. > > > > I would like to include some dumb atoms in my simulations. These dumb > atoms only have LJ interactions with some atoms in the system (e.g., the > lipid tails ), but do not interact with the other atoms (e.g., protein, > waters). Is this possible in gromacs? If so, how could I do that? > > > The reason I want to do so is that, I am simulating a membrane protein in > a bilayer, and the lipids sometimes come into a cavity of the protein > (which is what we do not want to happen). I want to fill the cavity with > dumb atoms, so that the lipids will not come in. > > > > I am really appreciate for any suggestions. Thanks in advance for your > help. > > > > With my best regards, > > RXG > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 cy16f01.dilip at nitk.edu.in Mon Feb 17 07:48:21 2020 From: cy16f01.dilip at nitk.edu.in (Dilip.H.N) Date: Mon, 17 Feb 2020 06:48:21 -0000 Subject: [gmx-users] Cannot flush logfile - maybe you are out of disk space? Message-ID: Dear all, I have extended a simulation (extension for 50 ns) and after some time i get the following error "Cannot flush logfile - maybe you are out of disk space?" and now the simulation has stopped running. The log file of the simulation is stopped at say 83ns- Step Time 41566000 83132.00000 Now i have made the disk-free and still, the simulation is still struck. So now may i know how can i proceed..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] Sender notified by Mailtrack 17/02/20, 12:14:16 From alessandra.villa.biosim at gmail.com Mon Feb 17 09:33:49 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 17 Feb 2020 08:33:49 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> References: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> Message-ID: Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table number 4 is out of the table range: r > 0.575410, between table indices 575 and 576, table length 501 > > Where exactly did you get this error? It looks like that your table is not covering all the request values (that means that it is too short) or the file is missing same values. Best regards Alessandra > Anyone has any idea why it could be happening? > > My best, > Ali > > > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: donderdag 13 februari 2020 16:28 > To: gmx-users at gromacs.org; gromacs.org_gmx-users < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > ali.khodayari at student.kuleuven.be> wrote: > > > Dear Gromacs users, > > > > I?ve got a question regarding the tabulated potentials for bonded > > interactions. > > > > Gromacs recognises and reads the non-bonded potential tables through > > the energy groups specified. But how can I refer each bond type to its > table? > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > each water molecule is coarse-grained as one bead. Overall, there are > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > types, and 2 dihedral potential tables for two types of dihedrals. The > > tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > Now my question is, how does gromacs recognise which table is regarding > > which bonded term? The simulation crashes at the very beginning giving > > me the following error: > > > > > In topol.top one specifies which table is used for which interaction > (bond, angle, dihedral). See the table below for the synthases > > > http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file > > Best regards > Alessandra > > > > > A tabulated bond interaction table number 1 is out of the table range: > > r 0.511823, between table indices 511 and 512, table length 501 > > > > I believe this is caused due to high forces on atoms indeed, but it > > might be also because tables are not specified to the correct bond type. > > > > > > 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. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Mon Feb 17 09:42:41 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 17 Feb 2020 08:42:41 -0000 Subject: [gmx-users] Cannot flush logfile - maybe you are out of disk space? In-Reply-To: References: Message-ID: Hi, On Mon, Feb 17, 2020 at 7:48 AM Dilip.H.N wrote: > Dear all, > I have extended a simulation (extension for 50 ns) and after some time i > get the following error "Cannot flush logfile - maybe you are out of disk > space?" and now the simulation has stopped running. The log file of the > simulation is stopped at say 83ns- > Step Time > 41566000 83132.00000 > > Now i have made the disk-free and still, the simulation is still struck. So > now may i know how can i proceed..?? > > You can use the checkpoint file to re-start your simulation. (see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mdrun.html?highlight=gmx%20mdrun ) If the old process is still active, better kill it. Best regards Alessandra > Any suggestions are highly appreciated. > > Thank you. > --- > With Best Regards, > > > *Dilip.H.N* > Ph.D Student. > > [image: Mailtrack] > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > Sender > notified by > Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > 17/02/20, > 12:14:16 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Mon Feb 17 09:50:18 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 17 Feb 2020 08:50:18 -0000 Subject: [gmx-users] Cannot flush logfile - maybe you are out of disk space? In-Reply-To: References: Message-ID: Hi, On Mon, Feb 17, 2020 at 7:48 AM Dilip.H.N wrote: > Dear all, > I have extended a simulation (extension for 50 ns) and after some time i > get the following error "Cannot flush logfile - maybe you are out of disk > space?" and now the simulation has stopped running. The log file of the > simulation is stopped at say 83ns- > Step Time > 41566000 83132.00000 > > Now i have made the disk-free and still, the simulation is still struck. So > now may i know how can i proceed..?? > > You can use the checkpoint file to re-start your simulation. (see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-mdrun.html?highlight=gmx%20mdrun ) If the old process is still active, better kill it. Best regards Alessandra > Any suggestions are highly appreciated. > > Thank you. > --- > With Best Regards, > > > *Dilip.H.N* > Ph.D Student. > > [image: Mailtrack] > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > Sender > notified by > Mailtrack > < > https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5& > > > 17/02/20, > 12:14:16 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 harry.greenblatt at weizmann.ac.il Mon Feb 17 10:07:30 2020 From: harry.greenblatt at weizmann.ac.il (Harry Mark Greenblatt) Date: Mon, 17 Feb 2020 09:07:30 -0000 Subject: [gmx-users] syntax error in GMXRC.csh in Gromacs2020 Message-ID: BS?D Seems that a bash formatted line has made it into the csh version of the GMXRC file: setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake The ?=? should be a space. Harry -------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt at weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-6340 234 Herzl St. Facsimile: 972-8-934-3361 Rehovot, 7610001 Israel From alessandra.villa.biosim at gmail.com Mon Feb 17 10:14:23 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 17 Feb 2020 09:14:23 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> Message-ID: Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including 1-4 interaction) is not trivial and involved different parameters, I would suggest to check if your change in topology are doing what to desire by looking at http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20 with particular attention to values of gen-pairs, nrexcl, [pairs]. Best regards Alessandra On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. wrote: > Anyone has advice/feedback? > > ?On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se > on behalf of Luirink, R.A." < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of > r.a.luirink at vu.nl> wrote: > > Here some output to illustrate what I mean. This is what you would > expect and what I also get for standard atom-atom interactions, not 1-4 and > not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 > (kJ/mol) > LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 > (kJ/mol) > Coul-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > LJ-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > > This is what you would expect for 1-4 interactions (which I get for > standard 1-4 interactions, but not the ones I specified) not LJ-SR and not > Coul-SR but LJ-14 and Coul-14: > Coul-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > LJ-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 > -1.69012e-05 (kJ/mol) > LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 > -7.03428e-05 (kJ/mol) > > And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR > as LJ-14 and Coul-14: > Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 > (kJ/mol) > LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 > (kJ/mol) > Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 > (kJ/mol) > LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 > (kJ/mol) > > It seems like a bug to me, or I have overlooked something.. > > On 06/02/2020, 14:44, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > Gromacs version 2018.6 btw. > > On 06/02/2020, 13:54, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > What I have tried is, instead of adding them to the [ pairs ] > block, is change the epsilon value manually via the [ nonbon_params ] > block. However, I can?t manually change the electrostatic interactions to > account for the fudgeQQ (0.8333) for these specific pairs (or at least, I > haven?t found a way to do so). > > > From: "Luirink, R.A." > Date: Thursday, 6 February 2020 at 11:49 > To: "gmx-users at gromacs.org" > Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 > as energy output > > Hello, > I try to specify a pair of atoms to be treated as a 1-4 > interaction (I replaced a covalent bond to a soft core restraint for free > energy calculation purposes, and now gromacs does not recognize it anymore > as 1-4 interaction, but it should still be treated as such). > I added the pair to the [ pairs ] block in the topology. I did > the same for 1-3 interactions, where I set the parameters to 0 for LJ > interactions. > > When I check the energy between these pairs of atoms, I > indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and > exactly twice the average value of LJ_14, where I have a fudge of 0.5). How > can I fix this issue? > Best, > Rosa > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Mon Feb 17 10:14:24 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 17 Feb 2020 09:14:24 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> Message-ID: Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including 1-4 interaction) is not trivial and involved different parameters, I would suggest to check if your change in topology are doing what to desire by looking at http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20 with particular attention to values of gen-pairs, nrexcl, [pairs]. Best regards Alessandra On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. wrote: > Anyone has advice/feedback? > > ?On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se > on behalf of Luirink, R.A." < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of > r.a.luirink at vu.nl> wrote: > > Here some output to illustrate what I mean. This is what you would > expect and what I also get for standard atom-atom interactions, not 1-4 and > not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 > (kJ/mol) > LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 > (kJ/mol) > Coul-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > LJ-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > > This is what you would expect for 1-4 interactions (which I get for > standard 1-4 interactions, but not the ones I specified) not LJ-SR and not > Coul-SR but LJ-14 and Coul-14: > Coul-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > LJ-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 > -1.69012e-05 (kJ/mol) > LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 > -7.03428e-05 (kJ/mol) > > And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR > as LJ-14 and Coul-14: > Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 > (kJ/mol) > LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 > (kJ/mol) > Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 > (kJ/mol) > LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 > (kJ/mol) > > It seems like a bug to me, or I have overlooked something.. > > On 06/02/2020, 14:44, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > Gromacs version 2018.6 btw. > > On 06/02/2020, 13:54, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > What I have tried is, instead of adding them to the [ pairs ] > block, is change the epsilon value manually via the [ nonbon_params ] > block. However, I can?t manually change the electrostatic interactions to > account for the fudgeQQ (0.8333) for these specific pairs (or at least, I > haven?t found a way to do so). > > > From: "Luirink, R.A." > Date: Thursday, 6 February 2020 at 11:49 > To: "gmx-users at gromacs.org" > Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 > as energy output > > Hello, > I try to specify a pair of atoms to be treated as a 1-4 > interaction (I replaced a covalent bond to a soft core restraint for free > energy calculation purposes, and now gromacs does not recognize it anymore > as 1-4 interaction, but it should still be treated as such). > I added the pair to the [ pairs ] block in the topology. I did > the same for 1-3 interactions, where I set the parameters to 0 for LJ > interactions. > > When I check the energy between these pairs of atoms, I > indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and > exactly twice the average value of LJ_14, where I have a fudge of 0.5). How > can I fix this issue? > Best, > Rosa > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 paul.bauer.q at gmail.com Mon Feb 17 10:59:04 2020 From: paul.bauer.q at gmail.com (Paul Bauer) Date: Mon, 17 Feb 2020 09:59:04 -0000 Subject: [gmx-users] syntax error in GMXRC.csh in Gromacs2020 In-Reply-To: References: Message-ID: Hello, Please open an issue on redmine for this. Cheers Paul On Mon, 17 Feb 2020, 10:07 Harry Mark Greenblatt, < harry.greenblatt at weizmann.ac.il> wrote: > BS?D > > Seems that a bash formatted line has made it into the csh version of the > GMXRC file: > > setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake > > The ?=? should be a space. > > Harry > > > > > -------------------------------------------------------------------- > Harry M. Greenblatt > Associate Staff Scientist > Dept of Structural Biology harry.greenblatt at weizmann.ac.il > > Weizmann Institute of Science Phone: 972-8-934-6340 > 234 Herzl St. Facsimile: 972-8-934-3361 > Rehovot, 7610001 > Israel > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Mon Feb 17 11:11:06 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Mon, 17 Feb 2020 10:11:06 -0000 Subject: [gmx-users] Increase Graphene sheet size Message-ID: Hello All, I want to create a graphene sheet with a specific dimensions (10*15*0.284) nm. I created a .gro file as below ( as mentioned in this website https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ ) GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring 4 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 0.245951 0.426000 0.284000 Now I don't know how to use genconf to repeat it until it gives me the required dimensions. As using genconf -nbox will repeat the above into a specific number of boxes but I can't get a sheet with accurate dimensions of (10*15*0.284 nm). I tried to generate a sheet using gencong and then use editconf to change the dimensions to the required ones, but the problem is that using editconf will put the graphene sheet in an empty box but will not change the dimension as I want. Another option is to divide the 10 (the required dimension) nm by 0.245951 (the dimension in the above .gro file) and to use the genconf with the result but it will be a lot of decimals and I am not sure if it will also give me the accurate dimension. Can anybody help me or guide me how to solve that problem. Thanks, Mohamed From peter.mawanga.lagos at gmail.com Mon Feb 17 13:19:11 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Mon, 17 Feb 2020 12:19:11 -0000 Subject: [gmx-users] Protein-Ligand Interaction calculation Message-ID: Hello everyone I used the CHARMM-GUI Membrane Builder to build a bilayer around my protein-ligand complex. However, unfortunately the ligand was not mentioned separately in the index (.ndx) file although it was mentioned in the topology (.top) file. Hence I am not able to calculate the energy between the protein and ligand using the energy (.edr) file. Please let me know if there is any workaround for this. It would be difficult to repeat the simulations again. -- Cheers Peter From alashkov83 at gmail.com Mon Feb 17 13:21:31 2020 From: alashkov83 at gmail.com (=?UTF-8?B?0JDQu9C10LrRgdCw0L3QtNGAINCb0LDRiNC60L7Qsg==?=) Date: Mon, 17 Feb 2020 12:21:31 -0000 Subject: [gmx-users] Protein-Ligand Interaction calculation In-Reply-To: References: Message-ID: You can rebuild index file using gmx make_ndx gromacs util. Alex ??, 17 ????. 2020 ?. ? 15:19, Peter Mawanga : > Hello everyone > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > protein-ligand complex. > > However, unfortunately the ligand was not mentioned separately in the index > (.ndx) file although it was mentioned in the topology (.top) file. Hence I > am not able to calculate the energy between the protein and ligand using > the energy (.edr) file. > > Please let me know if there is any workaround for this. It would be > difficult to repeat the simulations again. > > > -- > Cheers > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 177cy500.bratin at nitk.edu.in Mon Feb 17 13:45:07 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Mon, 17 Feb 2020 12:45:07 -0000 Subject: [gmx-users] Protein-Ligand Interaction calculation In-Reply-To: References: Message-ID: Hi.. You have to specify energy groups in .mdp option..then rerun the simulation..and analyse with gmx energy command On Mon 17 Feb, 2020, 5:52 PM ????????? ??????, wrote: > You can rebuild index file using gmx make_ndx gromacs util. > Alex > > ??, 17 ????. 2020 ?. ? 15:19, Peter Mawanga >: > > > Hello everyone > > > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > > protein-ligand complex. > > > > However, unfortunately the ligand was not mentioned separately in the > index > > (.ndx) file although it was mentioned in the topology (.top) file. Hence > I > > am not able to calculate the energy between the protein and ligand using > > the energy (.edr) file. > > > > Please let me know if there is any workaround for this. It would be > > difficult to repeat the simulations again. > > > > > > -- > > Cheers > > Peter > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 Feb 17 14:26:13 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 17 Feb 2020 13:26:13 -0000 Subject: [gmx-users] Protein-Ligand Interaction calculation In-Reply-To: References: Message-ID: <8687cf0d-328b-b81f-c84c-fb08139fd0cf@vt.edu> On 2/17/20 7:18 AM, Peter Mawanga wrote: > Hello everyone > > I used the CHARMM-GUI Membrane Builder to build a bilayer around my > protein-ligand complex. > > However, unfortunately the ligand was not mentioned separately in the index > (.ndx) file although it was mentioned in the topology (.top) file. Hence I > am not able to calculate the energy between the protein and ligand using > the energy (.edr) file. > > Please let me know if there is any workaround for this. It would be > difficult to repeat the simulations again. > > Computing interaction energy is a post-processing task. You should not specify energygrps in your .mdp file for the actual simulation because (1) it slows the simulation down and (2) it's not compatible with GPUs. All you need to do is generate a new .tpr file with the desired energygrps (you don't even need a special index file because all non-standard [moleculetype] entries are by default assigned to their own index groups) and use mdrun -rerun on the existing trajectory and the new .tpr file with energygrps. -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 pall.szilard at gmail.com Mon Feb 17 15:11:38 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 17 Feb 2020 14:11:38 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: Hi, If I understand correctly your jobs stall, what is in the log output? What about the console? Does this happen without PLUMED? -- Szil?rd On Tue, Feb 11, 2020 at 7:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point that it generates trajectory files but it never gives any > error either. > > I have switched from a large TREMD with 72 replicas to the Plumed > Hamiltonian method with only 6 replicas. Everything is now on one node and > each replica has 6 cores. I've turned off the dynamic load balancing on > this attempt per the recommendation from the Plumed site. > > Any ideas on how to troubleshoot? > > Thank you, > > Dan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 navneetcdl at gmail.com Mon Feb 17 15:14:03 2020 From: navneetcdl at gmail.com (Navneet Kumar) Date: Mon, 17 Feb 2020 14:14:03 -0000 Subject: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU Message-ID: Hello Everyone! I have currently installed GROMACS 2018.8 and using it. But for some of my previous work, I want to use the older version of GROMACS i.e 5.x. I have installed the GROMACS using this method >sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DCMAKE_C_COMPILER=/usr/bin/gcc-6 -DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8 > everytime when I use GROMACS I start with command- "source /usr/local/gromacs/bin/GMXRC" How can I install some other version of gromacs and use simultaneously? -- Thanks & Regards _______________________________________________________ [image: photo] *NAVNEET KUMAR* Doctoral Student Dept. of Pharmacoinformatics National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar - 160062, Punjab (INDIA) P +918017967647 <+918017967647> | E navneetcdl at gmail.com Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy. From blau at kth.se Mon Feb 17 15:29:58 2020 From: blau at kth.se (Christian Blau) Date: Mon, 17 Feb 2020 14:29:58 -0000 Subject: [gmx-users] (no subject) In-Reply-To: References: Message-ID: Hi Shakkira, The simulation box deformation is described by six parameters that describe three basis box vectors with the following contraints, ?- the first box vector is aligned along the x-axis, with coordinates thus has coordinates (xx,0,0) ?- the second box vector is aligned in the x-y plane with coordinates (yx,yy,0) ?- the third box vector is free (zx,zy,zz) The six parameters that you give in .mdp files are in the following order xx, yy, zz, yx, zx, zy The corrent box is then calculated as box(t_start)+(t-t_start)*deform For more information have a look at the gromacs manual mdp parameter description: http://manual.gromacs.org/current/user-guide/mdp-options.html under non-equilibrium MD: ?? (0 0 0 0 0 0) [nm ps\ :sup:`-1`] ?? The velocities of deformation for the box elements: a(x) b(y) c(z) ?? b(x) c(x) c(y). Each step the box elements for which :mdp:`deform` ?? is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal ?? elements are corrected for periodicity. The coordinates are ?? transformed accordingly. Frozen degrees of freedom are (purposely) ?? also transformed. The time ts is set to t at the first step and at ?? steps at which x and v are written to trajectory to ensure exact ?? restarts. Deformation can be used together with semiisotropic or ?? anisotropic pressure coupling when the appropriate ?? compressibilities are set to zero. The diagonal elements can be ?? used to strain a solid. The off-diagonal elements can be used to ?? shear a solid or a liquid. Best, Christian On 2020-02-16 12:12, shakira shukoor wrote: > Hi all > Can anyone help me with the DEFORM option in Gromacs to change the box > values? > > From shakirashukoor1993 at gmail.com Mon Feb 17 15:34:01 2020 From: shakirashukoor1993 at gmail.com (shakira shukoor) Date: Mon, 17 Feb 2020 14:34:01 -0000 Subject: [gmx-users] (no subject) In-Reply-To: References: Message-ID: Thanks christian for the detailed description. On Mon, Feb 17, 2020 at 8:00 PM Christian Blau wrote: > Hi Shakkira, > > > The simulation box deformation is described by six parameters that > describe three basis box vectors with the following > contraints, > > - the first box vector is aligned along the x-axis, with coordinates > thus has coordinates (xx,0,0) > > - the second box vector is aligned in the x-y plane with coordinates > (yx,yy,0) > > - the third box vector is free (zx,zy,zz) > > > The six parameters that you give in .mdp files are in the following order > > xx, yy, zz, yx, zx, zy > > > The corrent box is then calculated as > > box(t_start)+(t-t_start)*deform > > > For more information have a look at the gromacs manual mdp parameter > description: > > http://manual.gromacs.org/current/user-guide/mdp-options.html > > under non-equilibrium MD: > > (0 0 0 0 0 0) [nm ps\ :sup:`-1`] > The velocities of deformation for the box elements: a(x) b(y) c(z) > b(x) c(x) c(y). Each step the box elements for which :mdp:`deform` > is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal > elements are corrected for periodicity. The coordinates are > transformed accordingly. Frozen degrees of freedom are (purposely) > also transformed. The time ts is set to t at the first step and at > steps at which x and v are written to trajectory to ensure exact > restarts. Deformation can be used together with semiisotropic or > anisotropic pressure coupling when the appropriate > compressibilities are set to zero. The diagonal elements can be > used to strain a solid. The off-diagonal elements can be used to > shear a solid or a liquid. > > > Best, > > Christian > > On 2020-02-16 12:12, shakira shukoor wrote: > > Hi all > > Can anyone help me with the DEFORM option in Gromacs to change the box > > values? > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 adarsh_p130085bt at nitc.ac.in Mon Feb 17 15:37:48 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Mon, 17 Feb 2020 14:37:48 -0000 Subject: [gmx-users] CGENFF validation / optimization Message-ID: Dear all, While suing CGENFF server for " *.str " file generation, Few of the penalties were found to higher than 50. How to do validation/optimization.? Is there any recommended softwares / servers available for * " extensive validation / optimization." or any standard procedure available to do validation / optimization ?The *.str file also contains the following message.* ------------------------------------------------------------------------------------------------------------ ! "penalty" is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. ------------------------------------------------------------------------------------------------------------- From blau at kth.se Mon Feb 17 15:45:47 2020 From: blau at kth.se (Christian Blau) Date: Mon, 17 Feb 2020 14:45:47 -0000 Subject: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU In-Reply-To: References: Message-ID: <54ccc79a-775d-b25a-5733-c50865f23582@kth.se> Hi Navneet, This is achieved by setting the installation directory with cmake for the respective source code that you downloaded, then sourcing different GMXRC. Install different GROMACS builds fromt the source code into seperate folders using something like -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2019.6 and for another version -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2020 Then, "source /home/navneet/local/gromacs-2020/bin/GMXRC" will give you GROMACS 2020, while "source /home/navneet/local/gromacs-2019.6/bin/GMXRC" will give you GROMACS2019.6. Best, Christian On 2020-02-17 15:15, Navneet Kumar wrote: > Hello Everyone! > > I have currently installed GROMACS 2018.8 and using it. But for some of my > previous work, I want to use the older version of GROMACS i.e 5.x. > I have installed the GROMACS using this method > >> sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF > -DCMAKE_C_COMPILER=/usr/bin/gcc-6 > -DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8 >> everytime when I use GROMACS I start with command- > "source /usr/local/gromacs/bin/GMXRC" > How can I install some other version of gromacs and use simultaneously? > > > / From dburns at iastate.edu Mon Feb 17 15:55:42 2020 From: dburns at iastate.edu (Daniel Burns) Date: Mon, 17 Feb 2020 14:55:42 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: HI Szilard, I've deleted all my output but all the writing to the log and console stops around the step noting the domain decomposition (or other preliminary task). It is the same with or without Plumed - the TREMD with Gromacs only was the first thing to present this issue. I've discovered that if each replica is assigned its own node, the simulations proceed. If I try to run several replicas on each node (divided evenly), the simulations stall out before any trajectories get written. I have tried many different -np and -ntomp options as well as several slurm job submission scripts with node/ thread configurations but multiple simulations per node will not work. I need to be able to run several replicas on the same node to get enough data since it's hard to get more than 8 nodes (and as a result, replicas). Thanks for your reply. -Dan On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > Hi, > > I continue to have trouble getting an REMD job to run. It never makes it > to the point that it generates trajectory files but it never gives any > error either. > > I have switched from a large TREMD with 72 replicas to the Plumed > Hamiltonian method with only 6 replicas. Everything is now on one node and > each replica has 6 cores. I've turned off the dynamic load balancing on > this attempt per the recommendation from the Plumed site. > > Any ideas on how to troubleshoot? > > Thank you, > > Dan > From pall.szilard at gmail.com Mon Feb 17 16:07:21 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 17 Feb 2020 15:07:21 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: Hi Dan, What you describe in not an expected behaviro and it is something we should look into. What GROMACS version were you using? One thing that may help diagnosing the issue is: try to disable replica exchange and run -multidir that way. Does the simulation proceed? Can you please open an issue on redmine.gromacs.org and upload the necessary input files to reproduce, logs of your runs that reproduced the issue. Cheers, -- Szil?rd On Mon, Feb 17, 2020 at 3:56 PM Daniel Burns wrote: > HI Szilard, > > I've deleted all my output but all the writing to the log and console stops > around the step noting the domain decomposition (or other preliminary > task). It is the same with or without Plumed - the TREMD with Gromacs only > was the first thing to present this issue. > > I've discovered that if each replica is assigned its own node, the > simulations proceed. If I try to run several replicas on each node > (divided evenly), the simulations stall out before any trajectories get > written. > > I have tried many different -np and -ntomp options as well as several slurm > job submission scripts with node/ thread configurations but multiple > simulations per node will not work. I need to be able to run several > replicas on the same node to get enough data since it's hard to get more > than 8 nodes (and as a result, replicas). > > Thanks for your reply. > > -Dan > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > > > Hi, > > > > I continue to have trouble getting an REMD job to run. It never makes it > > to the point that it generates trajectory files but it never gives any > > error either. > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > Hamiltonian method with only 6 replicas. Everything is now on one node > and > > each replica has 6 cores. I've turned off the dynamic load balancing on > > this attempt per the recommendation from the Plumed site. > > > > Any ideas on how to troubleshoot? > > > > Thank you, > > > > Dan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Mon Feb 17 16:08:15 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 17 Feb 2020 15:08:15 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: Hi, That could be caused by configuration of the parallel file system or MPI on your cluster. If only one file descriptor is available per node to an MPI job, then your symptoms are explained. Some kinds of compute jobs follow such a model, so maybe someone optimized something for that. Mark On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > HI Szilard, > > I've deleted all my output but all the writing to the log and console stops > around the step noting the domain decomposition (or other preliminary > task). It is the same with or without Plumed - the TREMD with Gromacs only > was the first thing to present this issue. > > I've discovered that if each replica is assigned its own node, the > simulations proceed. If I try to run several replicas on each node > (divided evenly), the simulations stall out before any trajectories get > written. > > I have tried many different -np and -ntomp options as well as several slurm > job submission scripts with node/ thread configurations but multiple > simulations per node will not work. I need to be able to run several > replicas on the same node to get enough data since it's hard to get more > than 8 nodes (and as a result, replicas). > > Thanks for your reply. > > -Dan > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns wrote: > > > Hi, > > > > I continue to have trouble getting an REMD job to run. It never makes it > > to the point that it generates trajectory files but it never gives any > > error either. > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > Hamiltonian method with only 6 replicas. Everything is now on one node > and > > each replica has 6 cores. I've turned off the dynamic load balancing on > > this attempt per the recommendation from the Plumed site. > > > > Any ideas on how to troubleshoot? > > > > Thank you, > > > > Dan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Mon Feb 17 16:17:29 2020 From: dburns at iastate.edu (Daniel Burns) Date: Mon, 17 Feb 2020 15:17:29 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: Thanks Mark and Szilard, I forwarded Mark's suggestion to IT. I'll see what they have to say and then I'll try the simulation again and open an issue on redime. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 Mon Feb 17 17:01:30 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 17 Feb 2020 16:01:30 -0000 Subject: [gmx-users] How to set restraints in free energy calculation? Message-ID: Dear Gromacs users I am doing a free energy calculation of the protein-ligand complex. During decoupling of the ligand vdw forces from protein, I have selected 21 different lambda windows between 0-1. I have put distance angle and dihedral restraints to keep the ligand in its position but in some of my lamda windows, the residue restrained with ligand crashes and generates different PDB structures. The residue of protein on which I put restraints for ligand brreaks apart and simulation crashes in lambda windows 0,1,2,4,8,9,11,12,13,17,18 however in windows 3,5,6,10, 14,15,19,20 it works well. My restraint section in topology is as below:- ; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 3437 7908 10 0.474 0.474 10.0 0.0 0.474 0.474 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 3437 7908 7905 7908 1 110.00 0.0 1 110.00 41.840 1 7908 3437 3439 3437 1 152.5 0.0 1 152.5 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7905 7908 3437 3439 1 140.19 0.0 0.0 140.19 0.0 41.840 7909 7908 3437 3439 1 -167.75 0.0 0.0 -69.05 0.0 41.840 7909 7908 3437 3433 1 -172.77 0.0 0.0 -172.77 0.0 41.840 Can anyone please suggest me how should I fix this? or where I am doing wrong? I will be really grateful. Thanks. Sadaf Rani P.hD. visiting scholar Lancaster University Uk From oliverdutton at me.com Mon Feb 17 19:58:24 2020 From: oliverdutton at me.com (Oliver Dutton) Date: Mon, 17 Feb 2020 18:58:24 -0000 Subject: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU References: <48822E54-F4AC-4ED8-90C5-053DD43CDA8F@me.com> Message-ID: Hello, I am trying to do the exact same as Michael in https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html but hit the exact same error of it not finding a simple header file. I?ve tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro 560 GPU. I?m using the apple inbuilt compiler, same flags and cmake options as Michael. Was this ever got working? Kind regards, Oliver From dallas.warren at monash.edu Mon Feb 17 23:47:32 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 17 Feb 2020 22:47:32 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: genconf will only stack the box that you have in the original box in integer values. i.e. -nbox 2 4 10 If want a specific dimension, then the box you are stacking has to be an integer fraction of the final dimensions. Also note that the final dimension also has to be possible with the inter-atomic distances for the carbon atoms that make up the sheet. 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 Mon, 17 Feb 2020 at 21:11, Mohamed Abdelaal wrote: > Hello All, > > I want to create a graphene sheet with a specific dimensions (10*15*0.284) > nm. > > I created a .gro file as below ( as mentioned in this website > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > ) > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > 4 > 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 > 0.245951 0.426000 0.284000 > > Now I don't know how to use genconf to repeat it until it gives me the > required dimensions. As using genconf -nbox will repeat the above into a > specific number of boxes but I can't get a sheet with accurate dimensions > of (10*15*0.284 nm). > > I tried to generate a sheet using gencong and then use editconf to change > the dimensions to the required ones, but the problem is that using editconf > will put the graphene sheet in an empty box but will not change the > dimension as I want. > > Another option is to divide the 10 (the required dimension) nm by 0.245951 > (the dimension in the above .gro file) and to use the genconf with the > result but it will be a lot of decimals and I am not sure if it will also > give me the accurate dimension. > > Can anybody help me or guide me how to solve that problem. > > 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 myunggi at pukyong.ac.kr Tue Feb 18 01:56:04 2020 From: myunggi at pukyong.ac.kr (Myunggi Yi) Date: Tue, 18 Feb 2020 00:56:04 -0000 Subject: [gmx-users] Is Gromos force fields not recommended? Message-ID: Dear users, As the same as the title, Are Gromos force fields not recommended in Gromacs? From bonjour899 at 126.com Tue Feb 18 03:13:48 2020 From: bonjour899 at 126.com (bonjour899) Date: Tue, 18 Feb 2020 02:13:48 -0000 Subject: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation Message-ID: Hello everyone, This email is asking for some suggestions. Actually I'd like to conduct a kind of steered molecular dynamics simulation like this: Fixing one end of a protein, pulling the other end for a certain distance ?x (can be for example 0.5 nm, 0.2 nm ...), relaxing the whole system for sufficient time and then repeating that. The method I can think of is still using COM pulling code pull-coord1-type=umbrella pull-coord1-geometry=diatance This is like applying a harmonic spring between the two ends of the protein with harmonic potential U=1/2*k*(r-r0)^2 and I think I should modify the parameter "pull-coord1-init" to extend the equilibrium length of the spring for ?x so that I can achieve pulling the protein for ?x (is "pull-coord1-init" like the r0 in the harmonic potential equation? Maybe my understanding of this parameter is wrong?). However, since I want to pull the protein for a long distance, I should gradually change the equilibrium length, and I have no idea how to dynamically change the "pull-coord1-init" during SMD simulation. Or do I have to restart the simulation with a new .mdp file with different "pull-coord1-init" for each step? Best regards, W From navneetcdl at gmail.com Tue Feb 18 07:14:20 2020 From: navneetcdl at gmail.com (Navneet Kumar) Date: Tue, 18 Feb 2020 06:14:20 -0000 Subject: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU In-Reply-To: <54ccc79a-775d-b25a-5733-c50865f23582@kth.se> References: <54ccc79a-775d-b25a-5733-c50865f23582@kth.se> Message-ID: Thank you, Sir! On Mon, Feb 17, 2020 at 8:16 PM Christian Blau wrote: > Hi Navneet, > > This is achieved by setting the installation directory with cmake for the > respective source code that you downloaded, then sourcing different GMXRC. > > Install different GROMACS builds fromt the source code into seperate > folders using something like > > -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2019.6 > > and for another version > > -DCMAKE_INSTALL_PREFIX=/home/navneet/local/gromacs-2020 > > Then, > > "source /home/navneet/local/gromacs-2020/bin/GMXRC" > > will give you GROMACS 2020, while > > "source /home/navneet/local/gromacs-2019.6/bin/GMXRC" > > will give you GROMACS2019.6. > > Best, > > Christian > > On 2020-02-17 15:15, Navneet Kumar wrote: > > Hello Everyone! > > > > I have currently installed GROMACS 2018.8 and using it. But for some of > my > > previous work, I want to use the older version of GROMACS i.e 5.x. > > I have installed the GROMACS using this method > > > >> sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF > > -DCMAKE_C_COMPILER=/usr/bin/gcc-6 > > -DREGRESSIONTEST_PATH=/home/nitttr/Downloads/regressiontests-2018.8 > >> everytime when I use GROMACS I start with command- > > "source /usr/local/gromacs/bin/GMXRC" > > How can I install some other version of gromacs and use simultaneously? > > > > > > / > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Thanks & Regards _______________________________________________________ [image: photo] *NAVNEET KUMAR* Doctoral Student Dept. of Pharmacoinformatics National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar - 160062, Punjab (INDIA) P +918017967647 <+918017967647> | E navneetcdl at gmail.com Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy. From mark.j.abraham at gmail.com Tue Feb 18 07:28:16 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Tue, 18 Feb 2020 06:28:16 -0000 Subject: [gmx-users] Is Gromos force fields not recommended? In-Reply-To: References: Message-ID: Hi, No. Why do you ask? Mark On Tue., 18 Feb. 2020, 01:57 Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force fields not recommended in Gromacs? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 177cy500.bratin at nitk.edu.in Tue Feb 18 07:32:01 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Tue, 18 Feb 2020 06:32:01 -0000 Subject: [gmx-users] Is Gromos force fields not recommended? In-Reply-To: References: Message-ID: It is not like that...gromos is not compatible with gromacs... decission need to be taken depending on what system you want to simulate and what you are expecting from the simulation. On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force fields not recommended in Gromacs? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 18 08:59:16 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 18 Feb 2020 07:59:16 -0000 Subject: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation In-Reply-To: References: Message-ID: HI However, since I want to pull the protein for a long distance, I should > gradually change the equilibrium length, and I have no idea how to > dynamically change the "pull-coord1-init" during SMD simulation. Or do I > have to restart the simulation with a new .mdp file with different > "pull-coord1-init" for each step? > > > To change the pulling coordination during the simulation you can apply a rate. pull-coord1-rate [nm/ps] is the rate of change of the reference position I suggest to combine with pull-coord1-init [nm] (that is the reference distance at t=0). (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=freeze%20groups#com-pulling ) This is also useful to generate starting configurations (at defined distance values) for the umbrella sampling windows. Best regards Alessandra > Best regards, > W > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 18 08:59:16 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 18 Feb 2020 07:59:16 -0000 Subject: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation In-Reply-To: References: Message-ID: HI However, since I want to pull the protein for a long distance, I should > gradually change the equilibrium length, and I have no idea how to > dynamically change the "pull-coord1-init" during SMD simulation. Or do I > have to restart the simulation with a new .mdp file with different > "pull-coord1-init" for each step? > > > To change the pulling coordination during the simulation you can apply a rate. pull-coord1-rate [nm/ps] is the rate of change of the reference position I suggest to combine with pull-coord1-init [nm] (that is the reference distance at t=0). (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=freeze%20groups#com-pulling ) This is also useful to generate starting configurations (at defined distance values) for the umbrella sampling windows. Best regards Alessandra > Best regards, > W > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Tue Feb 18 09:15:51 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 18 Feb 2020 08:15:51 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Hi On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal wrote: > Hello All, > > I want to create a graphene sheet with a specific dimensions (10*15*0.284) > nm. > > I created a .gro file as below ( as mentioned in this website > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > ) > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > 4 > 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 > 0.245951 0.426000 0.284000 > > Now I don't know how to use genconf to repeat it until it gives me the > required dimensions. As using genconf -nbox will repeat the above into a > specific number of boxes but I can't get a sheet with accurate dimensions > of (10*15*0.284 nm). > > I tried to generate a sheet using gencong and then use editconf to change > the dimensions to the required ones, but the problem is that using editconf > will put the graphene sheet in an empty box but will not change the > dimension as I want. > > Another option is to divide the 10 (the required dimension) nm by 0.245951 > (the dimension in the above .gro file) and to use the genconf with the > result but it will be a lot of decimals and I am not sure if it will also > give me the accurate dimension. > > Can anybody help me or guide me how to solve that problem. > > you could try gmx solvate. It is not elegant solution but it may work, the limitation is that you do not control on the orientation and other geometrical parameter that may be relevant for graphene sheet. 1) generate an empty box with the desired dimension (empty.gro) 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o or in alternative you can use -cs and -box for all the options see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate Best regards Alessandra > 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 alessandra.villa.biosim at gmail.com Tue Feb 18 09:15:51 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 18 Feb 2020 08:15:51 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Hi On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal wrote: > Hello All, > > I want to create a graphene sheet with a specific dimensions (10*15*0.284) > nm. > > I created a .gro file as below ( as mentioned in this website > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > ) > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > 4 > 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 > 0.245951 0.426000 0.284000 > > Now I don't know how to use genconf to repeat it until it gives me the > required dimensions. As using genconf -nbox will repeat the above into a > specific number of boxes but I can't get a sheet with accurate dimensions > of (10*15*0.284 nm). > > I tried to generate a sheet using gencong and then use editconf to change > the dimensions to the required ones, but the problem is that using editconf > will put the graphene sheet in an empty box but will not change the > dimension as I want. > > Another option is to divide the 10 (the required dimension) nm by 0.245951 > (the dimension in the above .gro file) and to use the genconf with the > result but it will be a lot of decimals and I am not sure if it will also > give me the accurate dimension. > > Can anybody help me or guide me how to solve that problem. > > you could try gmx solvate. It is not elegant solution but it may work, the limitation is that you do not control on the orientation and other geometrical parameter that may be relevant for graphene sheet. 1) generate an empty box with the desired dimension (empty.gro) 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o or in alternative you can use -cs and -box for all the options see http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate Best regards Alessandra > 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 gmx3 at hotmail.com Tue Feb 18 09:19:09 2020 From: gmx3 at hotmail.com (Berk Hess) Date: Tue, 18 Feb 2020 08:19:09 -0000 Subject: [gmx-users] Is Gromos force fields not recommended? In-Reply-To: References: , Message-ID: If the GROMOS force-field would clearly not be compatible with GROMACS, we would have removed it from the GROMACS distribution. There are two issues here, which both stem from the fact that the GROMOS force-field has been parametrized with a simulation setup that, for good reasons, can not be reproduced in GROMACS. One is that certain properties, such a densities of liquids can be off by a small amount. The other is that certain people in the GROMOS community have claimed that the GROMOS force-field is used incorrectly in GROMACS. Note that other people in GROMOS community seem to think differently. I do not want to go into that discussion here. But to avoid users blaming GROMACS, we have added a warning in grompp. /Berk ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Bratin Kumar Das <177cy500.bratin at nitk.edu.in> Sent: Tuesday, February 18, 2020 7:31 AM To: gmx-users at gromacs.org ; myunggi at pknu.ac.kr Subject: Re: [gmx-users] Is Gromos force fields not recommended? It is not like that...gromos is not compatible with gromacs... decission need to be taken depending on what system you want to simulate and what you are expecting from the simulation. On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force fields not recommended in Gromacs? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 myunggi at pukyong.ac.kr Tue Feb 18 10:08:01 2020 From: myunggi at pukyong.ac.kr (Myunggi Yi) Date: Tue, 18 Feb 2020 09:08:01 -0000 Subject: [gmx-users] Is Gromos force fields not recommended? In-Reply-To: References: Message-ID: This is the warning from Grompp. The GROMOS force fields have been parameterized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Check if molecules in your system are affected by such issues before proceeding. Further information may be available at https://redmine.gromacs.org/issues/2884. On Tue, Feb 18, 2020 at 5:19 PM Berk Hess wrote: > If the GROMOS force-field would clearly not be compatible with GROMACS, we > would have removed it from the GROMACS distribution. > There are two issues here, which both stem from the fact that the GROMOS > force-field has been parametrized with a simulation setup that, for good > reasons, can not be reproduced in GROMACS. One is that certain properties, > such a densities of liquids can be off by a small amount. The other is that > certain people in the GROMOS community have claimed that the GROMOS > force-field is used incorrectly in GROMACS. Note that other people in > GROMOS community seem to think differently. I do not want to go into that > discussion here. But to avoid users blaming GROMACS, we have added a > warning in grompp. > > /Berk > > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Bratin > Kumar Das <177cy500.bratin at nitk.edu.in> > Sent: Tuesday, February 18, 2020 7:31 AM > To: gmx-users at gromacs.org ; myunggi at pknu.ac.kr < > myunggi at pknu.ac.kr> > Subject: Re: [gmx-users] Is Gromos force fields not recommended? > > It is not like that...gromos is not compatible with gromacs... decission > need to be taken depending on what system you want to simulate and what you > are expecting from the simulation. > On Tue 18 Feb, 2020, 6:27 AM Myunggi Yi, wrote: > > > Dear users, > > > > As the same as the title, > > > > Are Gromos force fields not recommended in Gromacs? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 mariemghoula at gmail.com Tue Feb 18 12:06:59 2020 From: mariemghoula at gmail.com (Mariem Ghoula) Date: Tue, 18 Feb 2020 11:06:59 -0000 Subject: [gmx-users] Unexpected cudaStreamQuery failure: unspecified launch failure Message-ID: Hi, I had this error while I was performing a short (1 ns) simulation. It seems to be related to the Nvidia driver. Can anyone please help me understand why I'm having this error? My system is a Ubuntu 18.04.4 LTS with cuda-toolkit version 9.1.85, nvidia driver version 410.78. I had this error: Command line: gmx mdrun -v -deffnm nvt Reading file nvt.tpr, VERSION 2019.5 (single precision) Changing nstlist from 20 to 100, rlist from 1.219 to 1.338 Using 1 MPI thread Using 20 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU starting mdrun 'Protein in water' 500000 steps, 1000.0 ps. step 200: timed with pme grid 72 72 72, coulomb cutoff 1.200: 14224.2 M-cycles step 400: timed with pme grid 60 60 60, coulomb cutoff 1.369: 19270.5 M-cycles step 600: timed with pme grid 64 64 64, coulomb cutoff 1.283: 16957.3 M-cycles step 800: timed with pme grid 72 72 72, coulomb cutoff 1.200: 14246.1 M-cycles optimal pme grid 72 72 72, coulomb cutoff 1.200 step 75400, will finish Mon Feb 17 22:17:08 2020 ------------------------------------------------------- Program: gmx mdrun, version 2019.5 Source file: src/gromacs/gpu_utils/cudautils.cuh (line 251) Fatal error: Unexpected cudaStreamQuery failure: unspecified launch failure For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I opened the file cudautils.cuh (line 251) to see what kind of error it can be but I don't get it. /*! \brief Returns true if all tasks in \p s have completed. * * \param[in] s stream to check * * \returns True if all tasks enqueued in the stream \p s (at the time of this call) have completed. */ static inline bool haveStreamTasksCompleted(cudaStream_t s) { cudaError_t stat = cudaStreamQuery(s); if (stat == cudaErrorNotReady) { // work is still in progress in the stream return false; } GMX_ASSERT(stat != cudaErrorInvalidResourceHandle, "Stream idnetifier not valid"); // cudaSuccess and cudaErrorNotReady are the expected return values CU_RET_ERR(stat, "Unexpected cudaStreamQuery failure"); GMX_ASSERT(stat == cudaSuccess, "Values other than cudaSuccess should have been explicitly handled"); return true; } my mdp file is the following and I'm using the charmm36m ff: title = IDE NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps (1ns) dt = 0.002 ; 2 fs ; Output control nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps nstxout-compressed = 500 ; save coordinates every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighbor searching and vdW cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 20 ; largely irrelevant with Verlet rlist = 1.2 vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein non-Protein ; 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 pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction is not used for proteins with the C36 additive FF DispCorr = no ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Thank you in advance for your help, - Myriam From ali.khodayari at student.kuleuven.be Tue Feb 18 12:11:45 2020 From: ali.khodayari at student.kuleuven.be (Ali Khodayari) Date: Tue, 18 Feb 2020 11:11:45 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: References: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> Message-ID: <000401d5e64c$2ca08d00$85e1a700$@student.kuleuven.be> So I am using Iterative Boltzmann Inversion to get the CG potentials for a cellobiose-water solution. During the first step of the simulation by gromacs, I get the error, which I think it might be due to some large forces, causing the distance between the CG beads to increase to values more than the length of the table. The bonded tables have values in between 0 to 0.5 nm for r. My best, Ali -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: maandag 17 februari 2020 9:34 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Tabulated potentials Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table number 4 is out of the table range: > r 0.575410, between table indices 575 and 576, table length 501 > > Where exactly did you get this error? It looks like that your table is not covering all the request values (that means that it is too short) or the file is missing same values. Best regards Alessandra > Anyone has any idea why it could be happening? > > My best, > Ali > > > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: donderdag 13 februari 2020 16:28 > To: gmx-users at gromacs.org; gromacs.org_gmx-users < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > ali.khodayari at student.kuleuven.be> wrote: > > > Dear Gromacs users, > > > > I?ve got a question regarding the tabulated potentials for bonded > > interactions. > > > > Gromacs recognises and reads the non-bonded potential tables through > > the energy groups specified. But how can I refer each bond type to > > its > table? > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > each water molecule is coarse-grained as one bead. Overall, there > > are > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > types, and 2 dihedral potential tables for two types of dihedrals. > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > Now my question is, how does gromacs recognise which table is > regarding > > which bonded term? The simulation crashes at the very beginning > > giving me the following error: > > > > > In topol.top one specifies which table is used for which interaction > (bond, angle, dihedral). See the table below for the synthases > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > ogies/topology-file-formats.html#topology-file > > Best regards > Alessandra > > > > > A tabulated bond interaction table number 1 is out of the table range: > > r 0.511823, between table indices 511 and 512, table length 501 > > > > I believe this is caused due to high forces on atoms indeed, but it > > might be also because tables are not specified to the correct bond type. > > > > > > 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. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Tue Feb 18 13:11:14 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 18 Feb 2020 12:11:14 -0000 Subject: [gmx-users] Fwd: Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU In-Reply-To: References: <48822E54-F4AC-4ED8-90C5-053DD43CDA8F@me.com> Message-ID: Hi Oliver, Does this affect an installation of GROMACS? In previous reports we have observed that the issue is only present when running "make check" in the build tree, but not in the case of an installed version. Cheers, -- Szil?rd On Mon, Feb 17, 2020 at 7:58 PM Oliver Dutton wrote: > Hello, > > I am trying to do the exact same as Michael in > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html > < > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html > > > but hit the exact same error of it not finding a simple header file. I?ve > tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro > 560 GPU. > > I?m using the apple inbuilt compiler, same flags and cmake options as > Michael. Was this ever got working? > > Kind regards, > Oliver > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 subhomoy.bk at gmail.com Tue Feb 18 13:15:49 2020 From: subhomoy.bk at gmail.com (Subhomoi Borkotoky) Date: Tue, 18 Feb 2020 12:15:49 -0000 Subject: [gmx-users] Listing residues in gromacs Message-ID: Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -------------------------- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subhomoi at yahoo.com https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ From subhomoy.bk at gmail.com Tue Feb 18 13:19:41 2020 From: subhomoy.bk at gmail.com (Subhomoi Borkotoky) Date: Tue, 18 Feb 2020 12:19:41 -0000 Subject: [gmx-users] Listing residues in gromacs Message-ID: Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -------------------------- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subhomoi at yahoo.com https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ From blau at kth.se Tue Feb 18 14:28:14 2020 From: blau at kth.se (Christian Blau) Date: Tue, 18 Feb 2020 13:28:14 -0000 Subject: [gmx-users] Listing residues in gromacs In-Reply-To: References: Message-ID: <286b11ad-d7bc-ac3a-434a-9d61ca409282@kth.se> Hi Subhomoi, Yes, gmx select can do that (see http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) For what you want to do, it's beneficial to have a look at the selection syntax here http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html Best, Christian On 2020-02-18 13:14, Subhomoi Borkotoky wrote: > Hi, > > Is there any option in gromacs to list residues/atoms around a reference > group? I have checked trjorder , but it only gives number of molecules. > > Thanks & Regards, > -------------------------- > *Subhomoi Borkotoky, Ph. D.* > Kusuma School of Biological Sciences, > Indian Institute of Technology Delhi, > New Delhi-110016, > India. > > Alternate E-mail : subhomoi at yahoo.com > > https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ From r.a.luirink at vu.nl Tue Feb 18 14:31:24 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Tue, 18 Feb 2020 13:31:24 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> Message-ID: <24DEFDEB-45BC-4BA2-B2DB-7491F49C5C8B@vu.nl> Thank you Alessandra, They are indeed averaged over the simulation time, but the SR values should be zero for these specific pairs of interactions. I managed to "hack" it by defining a bond between them with a force constant of zero. It works! Best, Rosa ?Op 17-02-20 10:15 heeft gromacs.org_gmx-users-bounces at maillist.sys.kth.se namens Alessandra Villa geschreven: Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including 1-4 interaction) is not trivial and involved different parameters, I would suggest to check if your change in topology are doing what to desire by looking at http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20 with particular attention to values of gen-pairs, nrexcl, [pairs]. Best regards Alessandra On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. wrote: > Anyone has advice/feedback? > > On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se > on behalf of Luirink, R.A." < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of > r.a.luirink at vu.nl> wrote: > > Here some output to illustrate what I mean. This is what you would > expect and what I also get for standard atom-atom interactions, not 1-4 and > not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 > (kJ/mol) > LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 > (kJ/mol) > Coul-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > LJ-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > > This is what you would expect for 1-4 interactions (which I get for > standard 1-4 interactions, but not the ones I specified) not LJ-SR and not > Coul-SR but LJ-14 and Coul-14: > Coul-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > LJ-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 > -1.69012e-05 (kJ/mol) > LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 > -7.03428e-05 (kJ/mol) > > And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR > as LJ-14 and Coul-14: > Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 > (kJ/mol) > LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 > (kJ/mol) > Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 > (kJ/mol) > LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 > (kJ/mol) > > It seems like a bug to me, or I have overlooked something.. > > On 06/02/2020, 14:44, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > Gromacs version 2018.6 btw. > > On 06/02/2020, 13:54, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > What I have tried is, instead of adding them to the [ pairs ] > block, is change the epsilon value manually via the [ nonbon_params ] > block. However, I can?t manually change the electrostatic interactions to > account for the fudgeQQ (0.8333) for these specific pairs (or at least, I > haven?t found a way to do so). > > > From: "Luirink, R.A." > Date: Thursday, 6 February 2020 at 11:49 > To: "gmx-users at gromacs.org" > Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 > as energy output > > Hello, > I try to specify a pair of atoms to be treated as a 1-4 > interaction (I replaced a covalent bond to a soft core restraint for free > energy calculation purposes, and now gromacs does not recognize it anymore > as 1-4 interaction, but it should still be treated as such). > I added the pair to the [ pairs ] block in the topology. I did > the same for 1-3 interactions, where I set the parameters to 0 for LJ > interactions. > > When I check the energy between these pairs of atoms, I > indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and > exactly twice the average value of LJ_14, where I have a fudge of 0.5). How > can I fix this issue? > Best, > Rosa > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 r.a.luirink at vu.nl Tue Feb 18 14:36:28 2020 From: r.a.luirink at vu.nl (Luirink, R.A.) Date: Tue, 18 Feb 2020 13:36:28 -0000 Subject: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output In-Reply-To: References: <3638CA15-C3F5-452B-9D63-3E56E187F37E@vu.nl> <01F5A231-E378-4F9F-8C93-45757ABEAB8A@vu.nl> <98CD74F4-C864-4B60-95A4-B4802A86A36C@vu.nl> <6E0CB3EF-5CC8-4137-97D4-6D23F9540BC7@vu.nl> Message-ID: <24DEFDEB-45BC-4BA2-B2DB-7491F49C5C8B@vu.nl> Thank you Alessandra, They are indeed averaged over the simulation time, but the SR values should be zero for these specific pairs of interactions. I managed to "hack" it by defining a bond between them with a force constant of zero. It works! Best, Rosa ?Op 17-02-20 10:15 heeft gromacs.org_gmx-users-bounces at maillist.sys.kth.se namens Alessandra Villa geschreven: Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including 1-4 interaction) is not trivial and involved different parameters, I would suggest to check if your change in topology are doing what to desire by looking at http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20 with particular attention to values of gen-pairs, nrexcl, [pairs]. Best regards Alessandra On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. wrote: > Anyone has advice/feedback? > > On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se > on behalf of Luirink, R.A." < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of > r.a.luirink at vu.nl> wrote: > > Here some output to illustrate what I mean. This is what you would > expect and what I also get for standard atom-atom interactions, not 1-4 and > not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 > (kJ/mol) > LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 > (kJ/mol) > Coul-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > LJ-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > > This is what you would expect for 1-4 interactions (which I get for > standard 1-4 interactions, but not the ones I specified) not LJ-SR and not > Coul-SR but LJ-14 and Coul-14: > Coul-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > LJ-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 > -1.69012e-05 (kJ/mol) > LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 > -7.03428e-05 (kJ/mol) > > And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR > as LJ-14 and Coul-14: > Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 > (kJ/mol) > LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 > (kJ/mol) > Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 > (kJ/mol) > LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 > (kJ/mol) > > It seems like a bug to me, or I have overlooked something.. > > On 06/02/2020, 14:44, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > Gromacs version 2018.6 btw. > > On 06/02/2020, 13:54, " > gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, > R.A." r.a.luirink at vu.nl> wrote: > > What I have tried is, instead of adding them to the [ pairs ] > block, is change the epsilon value manually via the [ nonbon_params ] > block. However, I can?t manually change the electrostatic interactions to > account for the fudgeQQ (0.8333) for these specific pairs (or at least, I > haven?t found a way to do so). > > > From: "Luirink, R.A." > Date: Thursday, 6 February 2020 at 11:49 > To: "gmx-users at gromacs.org" > Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 > as energy output > > Hello, > I try to specify a pair of atoms to be treated as a 1-4 > interaction (I replaced a covalent bond to a soft core restraint for free > energy calculation purposes, and now gromacs does not recognize it anymore > as 1-4 interaction, but it should still be treated as such). > I added the pair to the [ pairs ] block in the topology. I did > the same for 1-3 interactions, where I set the parameters to 0 for LJ > interactions. > > When I check the energy between these pairs of atoms, I > indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and > exactly twice the average value of LJ_14, where I have a fudge of 0.5). How > can I fix this issue? > Best, > Rosa > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 robert.cordina at strath.ac.uk Tue Feb 18 15:13:03 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Tue, 18 Feb 2020 14:13:03 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 Message-ID: Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride system, however I?m not entirely sure that I?m setting up the equilibration parameters in the mdp file correctly as I?m getting different simulation results from others who have published papers using this force field. All the bonding and non-bonding interactions have been typed up in the respective force-field files, and assuming those are correct (I?ve checked and re-checked them multiple times), the only thing I can think that is not correct are the mdp parameters. The Sum et al. paper, and another paper (Pizzirusso et al. J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from Sum paper in italics, text from Pizzirusso paper in bold, what I?ve put in the mdp file in regular font) Both NVT and NPT calculations were performed using 40 molecules in a cubic box with periodic boundary conditions pbc = xyz Interactions were truncated and shifted at rc = 11 ? with energies shifted at this distance rcoulomb = 1.1 (am I missing something here?) The system evolved with a leapfrog algorithm using a 2 fs timestep integrator = md dt = 0.002 Constant temperature and constant pressure simulations were maintained with the Berendsen?s thermostat and barostat, respectively, by uniform scaling of the atomic velocities (temperature) and by uniform scaling of the atomic positions and box length (pressure) Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, temperature and pressure were kept constant using a Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 bar-1, and anisotropic pressure coupling was used in the MD simulations. tcoupl = Berendsen tau-t = 1.0 tc-grps = XXX ref-t = 350 pcoupl = Berendsen pcoupltype = anisotropic compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 tau-p = 10 ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 1.01325 For all the calculations, a reaction-field correction was applied with continuum dielectric ?RF to correct for long-range interactions due to electrostatics cutoff-scheme = Verlet coulombtype = Reaction-Field epsilon-rf = a.bcd (I used actual numbers here of course) In addition I am using gen-vel = yes gen-temp = 350 gen-seed = -1 continuation = no Should I be adding anything with respect to vdw? In the forcefield.itp file I?m setting the following nbfunc = 1 comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot combining rule for the LJ parameters) gen-pairs = yes fudgeLJ = 1 fudgeQQ = 1 In ffbonded.itp bondtypes func = 1 angletypes func = 1 dihedraltypes func = 5 Thanks in advance for your help. Robert From adarsh_p130085bt at nitc.ac.in Tue Feb 18 15:18:57 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Tue, 18 Feb 2020 14:18:57 -0000 Subject: [gmx-users] CGENFF validation / optimization In-Reply-To: References: Message-ID: Dear all, While suing CGENFF server for " *.str " file generation, Few of the penalties were found to be higher than 50. How to do validation/optimization.? Is there any recommended softwares / servers available for * " extensive validation / optimization." or any standard procedure available to do validation / optimization ?The *.str file also contains the following message.* ------------------------------------------------------------------------------------------------------------ ! "penalty" is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. ------------------------------------------------------------------------------------------------------------- From hairul.ikmal at gmail.com Tue Feb 18 15:20:48 2020 From: hairul.ikmal at gmail.com (hairul.ikmal at gmail.com) Date: Tue, 18 Feb 2020 14:20:48 -0000 Subject: [gmx-users] GPU considerations for GROMACS Message-ID: Hello, Previously, I have helped building a workstation for my fellow researcher who heavily uses GROMACS for his MD simulations, with the following base specs: -CPU: 8 cores (Xeon E2278G) -RAM: 32GB -GPU: 1x RTX2080Ti With this setup, he managed to shrink down each simulation runtime to, say approximately 12 hours, compared to previous system (purely CPU only, no GPU support), which took days to complete. 1) Based on the current progress, we plan to build another system (which will also run GROMACS most of the time) using the existing workstation as reference. But currently we are unsure which setup (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, when running the same set of GROMACS simulation : Option 1: Retain same CPU, RAM and GPU specs (1x RTX2080Ti) Option 2: Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead of 1x RTX2080Ti 2) Besides building another system, we are considering to upgrade the existing system, too. For example, assuming the system has the expansion capability (enough PCI-e 16x slots, power supply), will adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) into existing setup will significantly cut down current runtime? If yes, by how much time reduction can we expect generally with this upgrade? Appreciate if someone can share their thoughts and experience. Thank you! -Hairul From sadafrani6 at gmail.com Tue Feb 18 16:30:03 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Tue, 18 Feb 2020 15:30:03 -0000 Subject: [gmx-users] How to cap a single residue in gromacs Message-ID: Dear Gromacs users I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand when I run pdb2gmx it gives me error:- Fatal error: In the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I added ACE and NME terminals as below in the gro file:- 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 However, it still claims the same error. How should I add this in force field file? How can I use -ter command that it can add N and C termini itself to the residue? I would really thankful for your suggestions. Thanks. Sadaf From catjmc at gmail.com Tue Feb 18 17:11:28 2020 From: catjmc at gmail.com (Jimmy Chen) Date: Tue, 18 Feb 2020 16:11:28 -0000 Subject: [gmx-users] Regarding to pme on gpu Message-ID: Hi, When set -pme gpu in mdrun, only one rank can be set for pme, -npme 1. What is the reason about only one rank for pme if use gpu to offload. Is it the limitation or somehow? I am interesting in any performance improvement is still doable and any improved plan for gpu kernel of pme and pp. there is no too much different in pme and pp between 2019.3 and 2020. Thanks, Jimmy From alexanderwien2k at gmail.com Tue Feb 18 21:23:46 2020 From: alexanderwien2k at gmail.com (Alex) Date: Tue, 18 Feb 2020 20:23:46 -0000 Subject: [gmx-users] Annealing Message-ID: Hi all, Using the last frame of a 300ns simulated at 298.1K and it's CPT file I would like to start an annealing simulation, so, I used gmx gromp -t case.cpt and here is a part of output of gromp: Simulated annealing for group Other: Single, 6 timepoints Time (ps) Temperature (K) 000000.0 298.1 ----------->>> *A* 300000.0 298.1 ----------->>> *B* 312000.0 433.1 462000.0 433.1 502000.0 298.1 600000.0- 298.1 Will read whole trajectory Last frame -1 time 300000.000 Using frame at t = 300000 ps Starting time for run is 0 ps So, according to above, I am confused if the simulation would start from A or B pointed out above? I like it to start from B, and considering the CPT file, but later I don't want to append in mdrun. Thank you Alex From sadafrani6 at gmail.com Tue Feb 18 21:58:12 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Tue, 18 Feb 2020 20:58:12 -0000 Subject: [gmx-users] Problem in energy minimization and domain decomposition Message-ID: Dear Gromacs users I am getting the following message while running an energy minimization:- There is no domain decomposition for 32 ranks that is compatible with the given box and a minimum cell size of 1.85723 nm I am not using any distance restraint, and selecting box size by the following command : gmx editconf -f rescloselig.gro -o rescloseligbox.gro -bt cubic -d 1.2 Can you please suggest me how should I fix it. Thanks. Sadaf From bjoern at cellmicrocosmos.org Wed Feb 19 01:36:00 2020 From: bjoern at cellmicrocosmos.org (=?UTF-8?Q?Bj=c3=b6rn_Sommer?=) Date: Wed, 19 Feb 2020 00:36:00 -0000 Subject: [gmx-users] MolVA 2020 Deadline Extension (February 29th) - EuroVis 2020 Workshop on Molecular Graphics and Visual Analysis of Molecular Data In-Reply-To: References: Message-ID: <31ffcbf9-ca74-567a-9c3f-48f9c89113e1@cellmicrocosmos.org> Dear colleagues, We would like to inform you about the extended deadlineforfull papers as well as short papers to:************************************************************************ Workshop on Molecular Graphics and Visual Analysis of Molecular Data (co-located with EuroVis & Eurographics 2020), May 25th, 2020, Norrk?ping, Sweden Important Dates (NEW) ************************************************************************ Paper Submission Deadline:? February 29, 2020 Notification of Acceptance: ? ? April 3, 2020 Camera-ready Deadline:? ? ? ? April 17, 2020 Workshop Date:? ? ? ? ? ? ? ? ? ? ? May 25, 2020 ? Molecular visualization and graphics belong among the oldest branches of scientific visualization, which has been developing for over 50 years. Due to the continuous advances in both computational biology and computer graphics techniques, molecular graphics and visualization are very active areas of research. Not only the ever-increasing dataset sizes yield a constant challenge for visual analysis, but also new technologies like advances in web-based graphics or augmented and virtual reality open new possibilities. This half-day multidisciplinary workshop - which is held in conjunction with EuroVis for the third time and with Eurographics for the first time - brings together visualization and computer graphics researchers working with molecular data.?? Whereas molecular graphics is an established topic for many years, the hybrid-dimensional visual analysis of molecular structures is still a quite new research field with a lot of potential. We would like to encourage submissions especially using new technologies, such as immersive analytics or ML-related approaches. We invite short papers as well as full papers (2-4 pages for short and up to 8 pages for full papers, both with an additional page reserved for references). All papers will undergo a single-stage, double-blind peer review process. Accepted papers will be published in the EG digital library. The workshop will be held in Norrk?ping, Sweden, May 25th, 2020, as part of EuroVis & Eurographics 2020. ?? Suggested topics include, but are not limited to: - Molecular Graphics & Rendering - Web-based Molecular Graphics & Visualization - Immersive Analytics approaches using, e.g., VR/AR technologies - Visual Analysis of Molecular Data (e.g., molecular structures, biological networks, and pathways, or omics data) - Visualization of Dynamic Molecular Data & Large Molecular Systems - Tools papers describing new molecular visualization tools or novel features in existing tools? ? More info: https://tinyurl.com/molva ? Organizers and Contact ************************************************************************ - Jan Byska, Masaryk University, Czech Republic - Michael Krone, University of T?bingen, Germany - Bjorn Sommer, Royal College of Art, UK ? If you have any questions, please contact us: mailto: molva.eurovis at gmail.com ? ? Submission ************************************************************************ Please submit your short and full papers via PCS (Deadline: February 29, 2020): https://new.precisionconference.com/(EuroVis & Eurographics 2020 MolVA Workshop)?? Please follow the EG guidelines for writing the paper. You can find more info and templates in the links below. Web: https://tinyurl.com/molvaLaTeX template: https://tinyurl.com/MolVA2020-zip Best regards, ???Jan By?ka, Michael Krone, Bjorn Sommer ???MolVA 2020 Organizing Committee From catjmc at gmail.com Wed Feb 19 04:38:11 2020 From: catjmc at gmail.com (Jimmy Chen) Date: Wed, 19 Feb 2020 03:38:11 -0000 Subject: [gmx-users] Regarding to pme on gpu In-Reply-To: References: Message-ID: Hi, When set -pme gpu in mdrun, only one rank can be set for pme, -npme 1. What is the reason about only one rank for pme if use gpu to offload. Is it the limitation or somehow? I am interesting in any performance improvement is still doable and any improved plan for gpu kernel of pme and pp. there is no too much different in pme and pp between 2019.3 and 2020. Thanks, Jimmy > From alessandra.villa.biosim at gmail.com Wed Feb 19 09:12:38 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:12:38 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: <000401d5e64c$2ca08d00$85e1a700$@student.kuleuven.be> References: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> <000401d5e64c$2ca08d00$85e1a700$@student.kuleuven.be> Message-ID: Hi, On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > So I am using Iterative Boltzmann Inversion to get the CG potentials for a > cellobiose-water solution. During the first step of the simulation by > gromacs, I get the error, which I think it might be due to some large > forces, causing the distance between the CG beads to increase to values > more than the length of the table. The bonded tables have values in > between 0 to 0.5 nm for r. > As far as I recall the error messages that you got was something like "A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501" Your table is up to the 0.5 (501 lines), but the program is looking for a values of 0.575410 nm, that it is out of the range of the values for your table. Could it be that one of cellobiose-water distances is 0.575410 nm in the first frames? The errors seems to indicate that you need a longer table at least up 0.58 nm or more (even if it corresponds to high potential values). Note that if your table is for non-bonded interactions, then also the mdp parameters set requirement on the table lengths (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=table#tables ) Best regards Alessandra > My best, > Ali > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: maandag 17 februari 2020 9:34 > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < > ali.khodayari at student.kuleuven.be> wrote: > > > Thank you Alessandra. However, fixing the topology did not remove the > > error. It still stands as before: > > > > A tabulated bond interaction table number 4 is out of the table range: > > r 0.575410, between table indices 575 and 576, table length 501 > > > > > Where exactly did you get this error? > > It looks like that your table is not covering all the request values (that > means that it is too short) or the file is missing same values. > > Best regards > Alessandra > > > > > Anyone has any idea why it could be happening? > > > > My best, > > Ali > > > > > > > > -----Original Message----- > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > > Alessandra Villa > > Sent: donderdag 13 februari 2020 16:28 > > To: gmx-users at gromacs.org; gromacs.org_gmx-users < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Subject: Re: [gmx-users] Tabulated potentials > > > > Hi, > > > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > > ali.khodayari at student.kuleuven.be> wrote: > > > > > Dear Gromacs users, > > > > > > I?ve got a question regarding the tabulated potentials for bonded > > > interactions. > > > > > > Gromacs recognises and reads the non-bonded potential tables through > > > the energy groups specified. But how can I refer each bond type to > > > its > > table? > > > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > > each water molecule is coarse-grained as one bead. Overall, there > > > are > > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > > types, and 2 dihedral potential tables for two types of dihedrals. > > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > > > Now my question is, how does gromacs recognise which table is > > regarding > > > which bonded term? The simulation crashes at the very beginning > > > giving me the following error: > > > > > > > > In topol.top one specifies which table is used for which interaction > > (bond, angle, dihedral). See the table below for the synthases > > > > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > > ogies/topology-file-formats.html#topology-file > > > > Best regards > > Alessandra > > > > > > > > > A tabulated bond interaction table number 1 is out of the table range: > > > r 0.511823, between table indices 511 and 512, table length 501 > > > > > > I believe this is caused due to high forces on atoms indeed, but it > > > might be also because tables are not specified to the correct bond > type. > > > > > > > > > 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. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 09:12:39 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:12:39 -0000 Subject: [gmx-users] Tabulated potentials In-Reply-To: <000401d5e64c$2ca08d00$85e1a700$@student.kuleuven.be> References: <000501d5e352$2161f930$6425eb90$@student.kuleuven.be> <000401d5e64c$2ca08d00$85e1a700$@student.kuleuven.be> Message-ID: Hi, On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari < ali.khodayari at student.kuleuven.be> wrote: > So I am using Iterative Boltzmann Inversion to get the CG potentials for a > cellobiose-water solution. During the first step of the simulation by > gromacs, I get the error, which I think it might be due to some large > forces, causing the distance between the CG beads to increase to values > more than the length of the table. The bonded tables have values in > between 0 to 0.5 nm for r. > As far as I recall the error messages that you got was something like "A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501" Your table is up to the 0.5 (501 lines), but the program is looking for a values of 0.575410 nm, that it is out of the range of the values for your table. Could it be that one of cellobiose-water distances is 0.575410 nm in the first frames? The errors seems to indicate that you need a longer table at least up 0.58 nm or more (even if it corresponds to high potential values). Note that if your table is for non-bonded interactions, then also the mdp parameters set requirement on the table lengths (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=table#tables ) Best regards Alessandra > My best, > Ali > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: maandag 17 februari 2020 9:34 > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < > ali.khodayari at student.kuleuven.be> wrote: > > > Thank you Alessandra. However, fixing the topology did not remove the > > error. It still stands as before: > > > > A tabulated bond interaction table number 4 is out of the table range: > > r 0.575410, between table indices 575 and 576, table length 501 > > > > > Where exactly did you get this error? > > It looks like that your table is not covering all the request values (that > means that it is too short) or the file is missing same values. > > Best regards > Alessandra > > > > > Anyone has any idea why it could be happening? > > > > My best, > > Ali > > > > > > > > -----Original Message----- > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > > Alessandra Villa > > Sent: donderdag 13 februari 2020 16:28 > > To: gmx-users at gromacs.org; gromacs.org_gmx-users < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Subject: Re: [gmx-users] Tabulated potentials > > > > Hi, > > > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > > ali.khodayari at student.kuleuven.be> wrote: > > > > > Dear Gromacs users, > > > > > > I?ve got a question regarding the tabulated potentials for bonded > > > interactions. > > > > > > Gromacs recognises and reads the non-bonded potential tables through > > > the energy groups specified. But how can I refer each bond type to > > > its > > table? > > > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > > each water molecule is coarse-grained as one bead. Overall, there > > > are > > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > > types, and 2 dihedral potential tables for two types of dihedrals. > > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > > > Now my question is, how does gromacs recognise which table is > > regarding > > > which bonded term? The simulation crashes at the very beginning > > > giving me the following error: > > > > > > > > In topol.top one specifies which table is used for which interaction > > (bond, angle, dihedral). See the table below for the synthases > > > > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > > ogies/topology-file-formats.html#topology-file > > > > Best regards > > Alessandra > > > > > > > > > A tabulated bond interaction table number 1 is out of the table range: > > > r 0.511823, between table indices 511 and 512, table length 501 > > > > > > I believe this is caused due to high forces on atoms indeed, but it > > > might be also because tables are not specified to the correct bond > type. > > > > > > > > > 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. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 09:23:46 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:23:46 -0000 Subject: [gmx-users] How to cap a single residue in gromacs In-Reply-To: References: Message-ID: Hi On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > Dear Gromacs users > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > when I run pdb2gmx it gives me error:- > Fatal error: > In the chosen force field there is no residue type for 'PHE' as a > standalone > (starting & ending) residue > > I added ACE and NME terminals as below in the gro file:- > > 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 > 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 > > NOTE that several atoms in the above gro file have the same (0. 0. 0.) coordinate/position. That may cause a crash when you start the simulation > However, it still claims the same error. > How should I add this in force field file? How can I use -ter command that > it can add N and C termini itself to the residue? > Yes the first thing I will do is to try is -ter. Different force fields have different termini definition (maybe the force field has already ACE and NME) Best regards Alessandra > I would really thankful for your suggestions. > 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 alessandra.villa.biosim at gmail.com Wed Feb 19 09:23:46 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:23:46 -0000 Subject: [gmx-users] How to cap a single residue in gromacs In-Reply-To: References: Message-ID: Hi On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > Dear Gromacs users > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > when I run pdb2gmx it gives me error:- > Fatal error: > In the chosen force field there is no residue type for 'PHE' as a > standalone > (starting & ending) residue > > I added ACE and NME terminals as below in the gro file:- > > 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 > 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 > > NOTE that several atoms in the above gro file have the same (0. 0. 0.) coordinate/position. That may cause a crash when you start the simulation > However, it still claims the same error. > How should I add this in force field file? How can I use -ter command that > it can add N and C termini itself to the residue? > Yes the first thing I will do is to try is -ter. Different force fields have different termini definition (maybe the force field has already ACE and NME) Best regards Alessandra > I would really thankful for your suggestions. > 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 alessandra.villa.biosim at gmail.com Wed Feb 19 09:46:51 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:46:51 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the equilibration > parameters in the mdp file correctly as I?m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I?ve checked > and re-checked them multiple times), the only thing I can think that is not > correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from Sum > paper in italics, text from Pizzirusso paper in bold, what I?ve put in the > mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a cubic > box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 ? with energies shifted > at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling of > the atomic positions and box length (pressure) > Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In > this ensemble, temperature and pressure were kept constant using a > Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 bar-1, > and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics > cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > check that nrexcl in topol.top is in line with the force field. > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > Best regards Alessandra > > Thanks in advance for your help. > > 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. On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the equilibration > parameters in the mdp file correctly as I?m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I?ve checked > and re-checked them multiple times), the only thing I can think that is not > correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from Sum > paper in italics, text from Pizzirusso paper in bold, what I?ve put in the > mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a cubic > box with periodic boundary conditions > pbc = xyz > > Interactions were truncated and shifted at rc = 11 ? with energies shifted > at this distance > rcoulomb = 1.1 (am I missing something here?) > > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling of > the atomic positions and box length (pressure) > Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In > this ensemble, temperature and pressure were kept constant using a > Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 bar-1, > and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics > cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > > Thanks in advance for your help. > > 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 alessandra.villa.biosim at gmail.com Wed Feb 19 09:46:51 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 08:46:51 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the equilibration > parameters in the mdp file correctly as I?m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I?ve checked > and re-checked them multiple times), the only thing I can think that is not > correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from Sum > paper in italics, text from Pizzirusso paper in bold, what I?ve put in the > mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a cubic > box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 ? with energies shifted > at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling of > the atomic positions and box length (pressure) > Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In > this ensemble, temperature and pressure were kept constant using a > Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 bar-1, > and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics > cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > check that nrexcl in topol.top is in line with the force field. > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > Best regards Alessandra > > Thanks in advance for your help. > > 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. On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the equilibration > parameters in the mdp file correctly as I?m getting different simulation > results from others who have published papers using this force field. All > the bonding and non-bonding interactions have been typed up in the > respective force-field files, and assuming those are correct (I?ve checked > and re-checked them multiple times), the only thing I can think that is not > correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from Sum > paper in italics, text from Pizzirusso paper in bold, what I?ve put in the > mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a cubic > box with periodic boundary conditions > pbc = xyz > > Interactions were truncated and shifted at rc = 11 ? with energies shifted > at this distance > rcoulomb = 1.1 (am I missing something here?) > > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling of > the atomic positions and box length (pressure) > Atomistic MD was performed using GROMACS 4.5 under an NPT ensemble. In > this ensemble, temperature and pressure were kept constant using a > Berendsen thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 bar-1, > and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics > cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > > Thanks in advance for your help. > > 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 m.b.abdelaal at gmail.com Wed Feb 19 10:30:58 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 19 Feb 2020 09:30:58 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong. I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do that :) ? Thanks, Mohamed On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > Hi > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal > wrote: > > > Hello All, > > > > I want to create a graphene sheet with a specific dimensions > (10*15*0.284) > > nm. > > > > I created a .gro file as below ( as mentioned in this website > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > ) > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > 4 > > 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 > > 0.245951 0.426000 0.284000 > > > > Now I don't know how to use genconf to repeat it until it gives me the > > required dimensions. As using genconf -nbox will repeat the above into a > > specific number of boxes but I can't get a sheet with accurate dimensions > > of (10*15*0.284 nm). > > > > I tried to generate a sheet using gencong and then use editconf to change > > the dimensions to the required ones, but the problem is that using > editconf > > will put the graphene sheet in an empty box but will not change the > > dimension as I want. > > > > Another option is to divide the 10 (the required dimension) nm by > 0.245951 > > (the dimension in the above .gro file) and to use the genconf with the > > result but it will be a lot of decimals and I am not sure if it will also > > give me the accurate dimension. > > > > Can anybody help me or guide me how to solve that problem. > > > > > you could try gmx solvate. It is not elegant solution but it may work, the > limitation is that you do not control on the orientation and other > geometrical parameter that may be relevant for graphene sheet. > > 1) generate an empty box with the desired dimension (empty.gro) > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > or in alternative you can use -cs and -box > for all the options see > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > Best regards > Alessandra > > > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Feb 19 10:31:00 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 19 Feb 2020 09:31:00 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong. I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do that :) ? Thanks, Mohamed On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > Hi > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal > wrote: > > > Hello All, > > > > I want to create a graphene sheet with a specific dimensions > (10*15*0.284) > > nm. > > > > I created a .gro file as below ( as mentioned in this website > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > ) > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > 4 > > 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 > > 0.245951 0.426000 0.284000 > > > > Now I don't know how to use genconf to repeat it until it gives me the > > required dimensions. As using genconf -nbox will repeat the above into a > > specific number of boxes but I can't get a sheet with accurate dimensions > > of (10*15*0.284 nm). > > > > I tried to generate a sheet using gencong and then use editconf to change > > the dimensions to the required ones, but the problem is that using > editconf > > will put the graphene sheet in an empty box but will not change the > > dimension as I want. > > > > Another option is to divide the 10 (the required dimension) nm by > 0.245951 > > (the dimension in the above .gro file) and to use the genconf with the > > result but it will be a lot of decimals and I am not sure if it will also > > give me the accurate dimension. > > > > Can anybody help me or guide me how to solve that problem. > > > > > you could try gmx solvate. It is not elegant solution but it may work, the > limitation is that you do not control on the orientation and other > geometrical parameter that may be relevant for graphene sheet. > > 1) generate an empty box with the desired dimension (empty.gro) > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > or in alternative you can use -cs and -box > for all the options see > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > Best regards > Alessandra > > > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Wed Feb 19 11:05:34 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Wed, 19 Feb 2020 10:05:34 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: Dear Alessandra, Many thanks for your reply. Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that "In the NERD force field, atoms/sites within a molecule that do not interact by any other intramolecular potential are also allowed to interact though the Lennard-Jones potential". In the paper all bond stretching, bond bending and torsion angle parameters are given, so is nrexcl = 3 correct? LJ potentials are 1-4 interactions, so this looks the right way to do it to me, but I stand to be corrected. Re compressibility, that was a typo from my part in the email, it's correctly set at 0.00001. Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section multiple times but I'm still not sure how to translate the description in the Sum paper to these settings. Any suggestions as to what "Interactions were truncated and shifted at rc = 11 ? with energies shifted at this distance" would mean for these settings? cutoff-scheme = Verlet rcoulomb = 1.1 coulombtype = Reaction-Field (I have to use this because I'm using the epsilon-rf setting too right?) epsilon-rf = a.bcd vdwtype = Cut-Off (?) vdw-modifier = Potential-shift-Verlet or Potential-switch (?) rvdw-switch = 0 (?) rvdw = 1.1 (will this just be the same as rcoulomb?) Thanks again for your help. Best regards, Robert -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: 19 February 2020 08:47 To: gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the > equilibration parameters in the mdp file correctly as I?m getting > different simulation results from others who have published papers > using this force field. All the bonding and non-bonding interactions > have been typed up in the respective force-field files, and assuming > those are correct (I?ve checked and re-checked them multiple times), > the only thing I can think that is not correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > put in the mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a > cubic box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 ? with energies > shifted at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling > of the atomic positions and box length (pressure) Atomistic MD was > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > temperature and pressure were kept constant using a Berendsen > thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > bar-1, and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > check that nrexcl in topol.top is in line with the force field. > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > Best regards Alessandra > > Thanks in advance for your help. > > 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. On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the > equilibration parameters in the mdp file correctly as I?m getting > different simulation results from others who have published papers > using this force field. All the bonding and non-bonding interactions > have been typed up in the respective force-field files, and assuming > those are correct (I?ve checked and re-checked them multiple times), > the only thing I can think that is not correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > put in the mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a > cubic box with periodic boundary conditions > pbc = xyz > > Interactions were truncated and shifted at rc = 11 ? with energies > shifted at this distance > rcoulomb = 1.1 (am I missing something here?) > > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling > of the atomic positions and box length (pressure) Atomistic MD was > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > temperature and pressure were kept constant using a Berendsen > thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > bar-1, and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > > Thanks in advance for your help. > > 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 Wed Feb 19 11:05:34 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Wed, 19 Feb 2020 10:05:34 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: Dear Alessandra, Many thanks for your reply. Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that "In the NERD force field, atoms/sites within a molecule that do not interact by any other intramolecular potential are also allowed to interact though the Lennard-Jones potential". In the paper all bond stretching, bond bending and torsion angle parameters are given, so is nrexcl = 3 correct? LJ potentials are 1-4 interactions, so this looks the right way to do it to me, but I stand to be corrected. Re compressibility, that was a typo from my part in the email, it's correctly set at 0.00001. Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section multiple times but I'm still not sure how to translate the description in the Sum paper to these settings. Any suggestions as to what "Interactions were truncated and shifted at rc = 11 ? with energies shifted at this distance" would mean for these settings? cutoff-scheme = Verlet rcoulomb = 1.1 coulombtype = Reaction-Field (I have to use this because I'm using the epsilon-rf setting too right?) epsilon-rf = a.bcd vdwtype = Cut-Off (?) vdw-modifier = Potential-shift-Verlet or Potential-switch (?) rvdw-switch = 0 (?) rvdw = 1.1 (will this just be the same as rcoulomb?) Thanks again for your help. Best regards, Robert -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: 19 February 2020 08:47 To: gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the > equilibration parameters in the mdp file correctly as I?m getting > different simulation results from others who have published papers > using this force field. All the bonding and non-bonding interactions > have been typed up in the respective force-field files, and assuming > those are correct (I?ve checked and re-checked them multiple times), > the only thing I can think that is not correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > put in the mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a > cubic box with periodic boundary conditions > pbc = xyz > > If you do not have a pre-built structure, your equilibration time may be longer that in the original paper, the best is to ask the authors the coordinate of pre-equilibrated system. > Interactions were truncated and shifted at rc = 11 ? with energies > shifted at this distance > rcoulomb = 1.1 (am I missing something here?) > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw (see for definition: http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van ) > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling > of the atomic positions and box length (pressure) Atomistic MD was > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > temperature and pressure were kept constant using a Berendsen > thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > bar-1, and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > system > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > compressibility is 10-5 bar-1 tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > check that nrexcl in topol.top is in line with the force field. > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > Best regards Alessandra > > Thanks in advance for your help. > > 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. On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > system, however I?m not entirely sure that I?m setting up the > equilibration parameters in the mdp file correctly as I?m getting > different simulation results from others who have published papers > using this force field. All the bonding and non-bonding interactions > have been typed up in the respective force-field files, and assuming > those are correct (I?ve checked and re-checked them multiple times), > the only thing I can think that is not correct are the mdp parameters. > > The Sum et al. paper, and another paper (Pizzirusso et al. > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > put in the mdp file in regular font) > > Both NVT and NPT calculations were performed using 40 molecules in a > cubic box with periodic boundary conditions > pbc = xyz > > Interactions were truncated and shifted at rc = 11 ? with energies > shifted at this distance > rcoulomb = 1.1 (am I missing something here?) > > The system evolved with a leapfrog algorithm using a 2 fs timestep > integrator = md > dt = 0.002 > > Constant temperature and constant pressure simulations were maintained > with the Berendsen?s thermostat and barostat, respectively, by uniform > scaling of the atomic velocities (temperature) and by uniform scaling > of the atomic positions and box length (pressure) Atomistic MD was > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > temperature and pressure were kept constant using a Berendsen > thermostat/barostat. Temperature and pressure couplings of 1 and > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > bar-1, and anisotropic pressure coupling was used in the MD simulations. > tcoupl = Berendsen > tau-t = 1.0 > tc-grps = XXX > ref-t = 350 > > pcoupl = Berendsen > pcoupltype = anisotropic > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > tau-p = 10 > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > 1.01325 > > For all the calculations, a reaction-field correction was applied with > continuum dielectric ?RF to correct for long-range interactions due to > electrostatics cutoff-scheme = Verlet > coulombtype = Reaction-Field > epsilon-rf = a.bcd (I used actual numbers here of course) > > > In addition I am using > gen-vel = yes > gen-temp = 350 > gen-seed = -1 > continuation = no > > > Should I be adding anything with respect to vdw? > > > In the forcefield.itp file I?m setting the following > nbfunc = 1 > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > combining rule for the LJ parameters) > gen-pairs = yes > fudgeLJ = 1 > fudgeQQ = 1 > > In ffbonded.itp > bondtypes func = 1 > angletypes func = 1 > dihedraltypes func = 5 > > > > Thanks in advance for your help. > > 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 11:10:36 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 10:10:36 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: HI, On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal wrote: > Many thanks Alessandra for your reply :) > > gmx solvate will add water around my graphene sheet but will not increase > the graphene sheet itself. Please correct me if I am wrong. > > Yes/No, gmx solvate is normally used to add water or to build solvent box but my suggestion was to use gmx solvate tools for your aim. What I suggested was to use the tool to fill an empty box (of desidered dimension) with copies of your graphene pre-equilibrated (small) sheet. Best regards Alessandra > I already simulated the graphene sheet but I need to increase its dimension > to a certain dimensions. > > any Ideas how to do that :) ? > > Thanks, > Mohamed > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > alessandra.villa.biosim at gmail.com> wrote: > > > Hi > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > m.b.abdelaal at gmail.com> > > wrote: > > > > > Hello All, > > > > > > I want to create a graphene sheet with a specific dimensions > > (10*15*0.284) > > > nm. > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > ) > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > 4 > > > 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 > > > 0.245951 0.426000 0.284000 > > > > > > Now I don't know how to use genconf to repeat it until it gives me the > > > required dimensions. As using genconf -nbox will repeat the above into > a > > > specific number of boxes but I can't get a sheet with accurate > dimensions > > > of (10*15*0.284 nm). > > > > > > I tried to generate a sheet using gencong and then use editconf to > change > > > the dimensions to the required ones, but the problem is that using > > editconf > > > will put the graphene sheet in an empty box but will not change the > > > dimension as I want. > > > > > > Another option is to divide the 10 (the required dimension) nm by > > 0.245951 > > > (the dimension in the above .gro file) and to use the genconf with the > > > result but it will be a lot of decimals and I am not sure if it will > also > > > give me the accurate dimension. > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > the > > limitation is that you do not control on the orientation and other > > geometrical parameter that may be relevant for graphene sheet. > > > > 1) generate an empty box with the desired dimension (empty.gro) > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > > > or in alternative you can use -cs and -box > > for all the options see > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > Best regards > > Alessandra > > > > > > > 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 11:17:16 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 10:17:16 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: HI, On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal wrote: > Many thanks Alessandra for your reply :) > > gmx solvate will add water around my graphene sheet but will not increase > the graphene sheet itself. Please correct me if I am wrong. > > Yes/No, gmx solvate is normally used to add water or to build solvent box but my suggestion was to use gmx solvate tools for your aim. What I suggested was to use the tool to fill an empty box (of desidered dimension) with copies of your graphene pre-equilibrated (small) sheet. Best regards Alessandra > I already simulated the graphene sheet but I need to increase its dimension > to a certain dimensions. > > any Ideas how to do that :) ? > > Thanks, > Mohamed > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > alessandra.villa.biosim at gmail.com> wrote: > > > Hi > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > m.b.abdelaal at gmail.com> > > wrote: > > > > > Hello All, > > > > > > I want to create a graphene sheet with a specific dimensions > > (10*15*0.284) > > > nm. > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > ) > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > 4 > > > 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 > > > 0.245951 0.426000 0.284000 > > > > > > Now I don't know how to use genconf to repeat it until it gives me the > > > required dimensions. As using genconf -nbox will repeat the above into > a > > > specific number of boxes but I can't get a sheet with accurate > dimensions > > > of (10*15*0.284 nm). > > > > > > I tried to generate a sheet using gencong and then use editconf to > change > > > the dimensions to the required ones, but the problem is that using > > editconf > > > will put the graphene sheet in an empty box but will not change the > > > dimension as I want. > > > > > > Another option is to divide the 10 (the required dimension) nm by > > 0.245951 > > > (the dimension in the above .gro file) and to use the genconf with the > > > result but it will be a lot of decimals and I am not sure if it will > also > > > give me the accurate dimension. > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > the > > limitation is that you do not control on the orientation and other > > geometrical parameter that may be relevant for graphene sheet. > > > > 1) generate an empty box with the desired dimension (empty.gro) > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > > > or in alternative you can use -cs and -box > > for all the options see > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > Best regards > > Alessandra > > > > > > > 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 11:27:10 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 10:27:10 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: Hi, On Wed, Feb 19, 2020 at 11:06 AM Robert Cordina wrote: > Dear Alessandra, > > Many thanks for your reply. > Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that > "In the NERD force field, atoms/sites within a molecule that do not > interact by any other intramolecular potential are also allowed to interact > though the Lennard-Jones potential". In the paper all bond stretching, > bond bending and torsion angle parameters are given, so is nrexcl = 3 > correct? LJ potentials are 1-4 interactions, so this looks the right way > to do it to me, but I stand to be corrected. > Re compressibility, that was a typo from my part in the email, it's > correctly set at 0.00001. > Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section > multiple times but I'm still not sure how to translate the description in > the Sum paper to these settings. Any suggestions as to what "Interactions > were truncated and shifted at rc = 11 ? with energies shifted at this > distance" would mean for these settings? > > cutoff-scheme = Verlet > rcoulomb = 1.1 > coulombtype = Reaction-Field (I have to use this because I'm using the > epsilon-rf setting too right?) > epsilon-rf = a.bcd > > vdwtype = Cut-Off (?) > vdw-modifier = Potential-shift-Verlet or Potential-switch (?) > The sentence, you have reported, is not clear. It could be that the authors used vdwtype = cutoff vdw-modifier = Potential-shift (from mdp parameter of gromacs2020). rvdw = 1.1 But you should check with them, which treatment they use for the non-bonded interactions Best regards Alessandra rvdw-switch = 0 (?) > rvdw = 1.1 (will this just be the same as rcoulomb?) > > > Thanks again for your help. > > Best regards, > > Robert > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: 19 February 2020 08:47 > To: gmx-users at gromacs.org > Cc: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS > 2019.3 > > HI, > > Below some suggestions assuming that the energy terms are correctly > implemented (force field) > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cordina at strath.ac.uk> > wrote: > > > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > > system, however I?m not entirely sure that I?m setting up the > > equilibration parameters in the mdp file correctly as I?m getting > > different simulation results from others who have published papers > > using this force field. All the bonding and non-bonding interactions > > have been typed up in the respective force-field files, and assuming > > those are correct (I?ve checked and re-checked them multiple times), > > the only thing I can think that is not correct are the mdp parameters. > > > > The Sum et al. paper, and another paper (Pizzirusso et al. > > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > > put in the mdp file in regular font) > > > > Both NVT and NPT calculations were performed using 40 molecules in a > > cubic box with periodic boundary conditions > > pbc = xyz > > > > > If you do not have a pre-built structure, your equilibration time may be > longer that in the original paper, the best is to ask the authors the > coordinate of pre-equilibrated system. > > > > > Interactions were truncated and shifted at rc = 11 ? with energies > > shifted at this distance > > rcoulomb = 1.1 (am I missing something here?) > > > > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw > > (see for definition: > > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van > ) > > > > > The system evolved with a leapfrog algorithm using a 2 fs timestep > > integrator = md > > dt = 0.002 > > > > Constant temperature and constant pressure simulations were maintained > > with the Berendsen?s thermostat and barostat, respectively, by uniform > > scaling of the atomic velocities (temperature) and by uniform scaling > > of the atomic positions and box length (pressure) Atomistic MD was > > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > > temperature and pressure were kept constant using a Berendsen > > thermostat/barostat. Temperature and pressure couplings of 1 and > > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > > bar-1, and anisotropic pressure coupling was used in the MD simulations. > > tcoupl = Berendsen > > tau-t = 1.0 > > tc-grps = XXX > > > > system > > > ref-t = 350 > > > > pcoupl = Berendsen > > pcoupltype = anisotropic > > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > > > > compressibility is 10-5 bar-1 > > tau-p = 10 > > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > > 1.01325 > > > > For all the calculations, a reaction-field correction was applied with > > continuum dielectric ?RF to correct for long-range interactions due to > > electrostatics cutoff-scheme = Verlet > > coulombtype = Reaction-Field > > epsilon-rf = a.bcd (I used actual numbers here of course) > > > > > > In addition I am using > > gen-vel = yes > > gen-temp = 350 > > gen-seed = -1 > > continuation = no > > > > > > Should I be adding anything with respect to vdw? > > > > > > In the forcefield.itp file I?m setting the following > > nbfunc = 1 > > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > > combining rule for the LJ parameters) > > gen-pairs = yes > > fudgeLJ = 1 > > fudgeQQ = 1 > > > > > check that nrexcl in topol.top is in line with the force field. > > > > In ffbonded.itp > > bondtypes func = 1 > > angletypes func = 1 > > dihedraltypes func = 5 > > > > > > > Best regards > Alessandra > > > > > > > Thanks in advance for your help. > > > > 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. > > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cordina at strath.ac.uk> > wrote: > > > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > > system, however I?m not entirely sure that I?m setting up the > > equilibration parameters in the mdp file correctly as I?m getting > > different simulation results from others who have published papers > > using this force field. All the bonding and non-bonding interactions > > have been typed up in the respective force-field files, and assuming > > those are correct (I?ve checked and re-checked them multiple times), > > the only thing I can think that is not correct are the mdp parameters. > > > > The Sum et al. paper, and another paper (Pizzirusso et al. > > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > > put in the mdp file in regular font) > > > > Both NVT and NPT calculations were performed using 40 molecules in a > > cubic box with periodic boundary conditions > > pbc = xyz > > > > Interactions were truncated and shifted at rc = 11 ? with energies > > shifted at this distance > > rcoulomb = 1.1 (am I missing something here?) > > > > The system evolved with a leapfrog algorithm using a 2 fs timestep > > integrator = md > > dt = 0.002 > > > > Constant temperature and constant pressure simulations were maintained > > with the Berendsen?s thermostat and barostat, respectively, by uniform > > scaling of the atomic velocities (temperature) and by uniform scaling > > of the atomic positions and box length (pressure) Atomistic MD was > > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > > temperature and pressure were kept constant using a Berendsen > > thermostat/barostat. Temperature and pressure couplings of 1 and > > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > > bar-1, and anisotropic pressure coupling was used in the MD simulations. > > tcoupl = Berendsen > > tau-t = 1.0 > > tc-grps = XXX > > ref-t = 350 > > > > pcoupl = Berendsen > > pcoupltype = anisotropic > > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > > tau-p = 10 > > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > > 1.01325 > > > > For all the calculations, a reaction-field correction was applied with > > continuum dielectric ?RF to correct for long-range interactions due to > > electrostatics cutoff-scheme = Verlet > > coulombtype = Reaction-Field > > epsilon-rf = a.bcd (I used actual numbers here of course) > > > > > > In addition I am using > > gen-vel = yes > > gen-temp = 350 > > gen-seed = -1 > > continuation = no > > > > > > Should I be adding anything with respect to vdw? > > > > > > In the forcefield.itp file I?m setting the following > > nbfunc = 1 > > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > > combining rule for the LJ parameters) > > gen-pairs = yes > > fudgeLJ = 1 > > fudgeQQ = 1 > > > > In ffbonded.itp > > bondtypes func = 1 > > angletypes func = 1 > > dihedraltypes func = 5 > > > > > > > > Thanks in advance for your help. > > > > 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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 alessandra.villa.biosim at gmail.com Wed Feb 19 11:27:10 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 19 Feb 2020 10:27:10 -0000 Subject: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3 In-Reply-To: References: Message-ID: Hi, On Wed, Feb 19, 2020 at 11:06 AM Robert Cordina wrote: > Dear Alessandra, > > Many thanks for your reply. > Re comment on nrexcl, I'm using nrexcl = 3 as the Sum paper states that > "In the NERD force field, atoms/sites within a molecule that do not > interact by any other intramolecular potential are also allowed to interact > though the Lennard-Jones potential". In the paper all bond stretching, > bond bending and torsion angle parameters are given, so is nrexcl = 3 > correct? LJ potentials are 1-4 interactions, so this looks the right way > to do it to me, but I stand to be corrected. > Re compressibility, that was a typo from my part in the email, it's > correctly set at 0.00001. > Re vdwtype, vdw-modifier, rvdw-switch, rvdw... I have read this section > multiple times but I'm still not sure how to translate the description in > the Sum paper to these settings. Any suggestions as to what "Interactions > were truncated and shifted at rc = 11 ? with energies shifted at this > distance" would mean for these settings? > > cutoff-scheme = Verlet > rcoulomb = 1.1 > coulombtype = Reaction-Field (I have to use this because I'm using the > epsilon-rf setting too right?) > epsilon-rf = a.bcd > > vdwtype = Cut-Off (?) > vdw-modifier = Potential-shift-Verlet or Potential-switch (?) > The sentence, you have reported, is not clear. It could be that the authors used vdwtype = cutoff vdw-modifier = Potential-shift (from mdp parameter of gromacs2020). rvdw = 1.1 But you should check with them, which treatment they use for the non-bonded interactions Best regards Alessandra rvdw-switch = 0 (?) > rvdw = 1.1 (will this just be the same as rcoulomb?) > > > Thanks again for your help. > > Best regards, > > Robert > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: 19 February 2020 08:47 > To: gmx-users at gromacs.org > Cc: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] Implementing the NERD Force Field in GROMACS > 2019.3 > > HI, > > Below some suggestions assuming that the energy terms are correctly > implemented (force field) > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cordina at strath.ac.uk> > wrote: > > > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > > system, however I?m not entirely sure that I?m setting up the > > equilibration parameters in the mdp file correctly as I?m getting > > different simulation results from others who have published papers > > using this force field. All the bonding and non-bonding interactions > > have been typed up in the respective force-field files, and assuming > > those are correct (I?ve checked and re-checked them multiple times), > > the only thing I can think that is not correct are the mdp parameters. > > > > The Sum et al. paper, and another paper (Pizzirusso et al. > > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > > put in the mdp file in regular font) > > > > Both NVT and NPT calculations were performed using 40 molecules in a > > cubic box with periodic boundary conditions > > pbc = xyz > > > > > If you do not have a pre-built structure, your equilibration time may be > longer that in the original paper, the best is to ask the authors the > coordinate of pre-equilibrated system. > > > > > Interactions were truncated and shifted at rc = 11 ? with energies > > shifted at this distance > > rcoulomb = 1.1 (am I missing something here?) > > > > > here you miss the vdwtype; vdw-modifier; rvdw-switch?; rvdw > > (see for definition: > > http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=vdw#Van > ) > > > > > The system evolved with a leapfrog algorithm using a 2 fs timestep > > integrator = md > > dt = 0.002 > > > > Constant temperature and constant pressure simulations were maintained > > with the Berendsen?s thermostat and barostat, respectively, by uniform > > scaling of the atomic velocities (temperature) and by uniform scaling > > of the atomic positions and box length (pressure) Atomistic MD was > > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > > temperature and pressure were kept constant using a Berendsen > > thermostat/barostat. Temperature and pressure couplings of 1 and > > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > > bar-1, and anisotropic pressure coupling was used in the MD simulations. > > tcoupl = Berendsen > > tau-t = 1.0 > > tc-grps = XXX > > > > system > > > ref-t = 350 > > > > pcoupl = Berendsen > > pcoupltype = anisotropic > > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > > > > compressibility is 10-5 bar-1 > > tau-p = 10 > > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > > 1.01325 > > > > For all the calculations, a reaction-field correction was applied with > > continuum dielectric ?RF to correct for long-range interactions due to > > electrostatics cutoff-scheme = Verlet > > coulombtype = Reaction-Field > > epsilon-rf = a.bcd (I used actual numbers here of course) > > > > > > In addition I am using > > gen-vel = yes > > gen-temp = 350 > > gen-seed = -1 > > continuation = no > > > > > > Should I be adding anything with respect to vdw? > > > > > > In the forcefield.itp file I?m setting the following > > nbfunc = 1 > > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > > combining rule for the LJ parameters) > > gen-pairs = yes > > fudgeLJ = 1 > > fudgeQQ = 1 > > > > > check that nrexcl in topol.top is in line with the force field. > > > > In ffbonded.itp > > bondtypes func = 1 > > angletypes func = 1 > > dihedraltypes func = 5 > > > > > > > Best regards > Alessandra > > > > > > > Thanks in advance for your help. > > > > 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. > > > On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina < > robert.cordina at strath.ac.uk> > wrote: > > > Hi, I?m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure triacylglyceride > > system, however I?m not entirely sure that I?m setting up the > > equilibration parameters in the mdp file correctly as I?m getting > > different simulation results from others who have published papers > > using this force field. All the bonding and non-bonding interactions > > have been typed up in the respective force-field files, and assuming > > those are correct (I?ve checked and re-checked them multiple times), > > the only thing I can think that is not correct are the mdp parameters. > > > > The Sum et al. paper, and another paper (Pizzirusso et al. > > J.Am.Chem.Soc.2018, 140, 12405?12414) state the following (text from > > Sum paper in italics, text from Pizzirusso paper in bold, what I?ve > > put in the mdp file in regular font) > > > > Both NVT and NPT calculations were performed using 40 molecules in a > > cubic box with periodic boundary conditions > > pbc = xyz > > > > Interactions were truncated and shifted at rc = 11 ? with energies > > shifted at this distance > > rcoulomb = 1.1 (am I missing something here?) > > > > The system evolved with a leapfrog algorithm using a 2 fs timestep > > integrator = md > > dt = 0.002 > > > > Constant temperature and constant pressure simulations were maintained > > with the Berendsen?s thermostat and barostat, respectively, by uniform > > scaling of the atomic velocities (temperature) and by uniform scaling > > of the atomic positions and box length (pressure) Atomistic MD was > > performed using GROMACS 4.5 under an NPT ensemble. In this ensemble, > > temperature and pressure were kept constant using a Berendsen > > thermostat/barostat. Temperature and pressure couplings of 1 and > > 10 ps were used, respectively. Compressibility was fixed at 1 ? 10-5 > > bar-1, and anisotropic pressure coupling was used in the MD simulations. > > tcoupl = Berendsen > > tau-t = 1.0 > > tc-grps = XXX > > ref-t = 350 > > > > pcoupl = Berendsen > > pcoupltype = anisotropic > > compressibility = 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 > > tau-p = 10 > > ref-p = 1.01325 1.01325 1.01325 1.01325 1.01325 > > 1.01325 > > > > For all the calculations, a reaction-field correction was applied with > > continuum dielectric ?RF to correct for long-range interactions due to > > electrostatics cutoff-scheme = Verlet > > coulombtype = Reaction-Field > > epsilon-rf = a.bcd (I used actual numbers here of course) > > > > > > In addition I am using > > gen-vel = yes > > gen-temp = 350 > > gen-seed = -1 > > continuation = no > > > > > > Should I be adding anything with respect to vdw? > > > > > > In the forcefield.itp file I?m setting the following > > nbfunc = 1 > > comb-rule = 2 (Sum paper states that they use Lorentz-Berthelot > > combining rule for the LJ parameters) > > gen-pairs = yes > > fudgeLJ = 1 > > fudgeQQ = 1 > > > > In ffbonded.itp > > bondtypes func = 1 > > angletypes func = 1 > > dihedraltypes func = 5 > > > > > > > > Thanks in advance for your help. > > > > 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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Wed Feb 19 11:38:39 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 19 Feb 2020 10:38:39 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Hi Alessandra, Many thanks again for your help :) That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize it. now I have an additional part of the graphene sheet which is out of the box, How can I remove it. I want my simulation and visualization to be with a specific dimensions which is the dimensions of the box. I would appreciate if you can further clarify how can I do that. Thanks, Mohamed On Wed, Feb 19, 2020 at 10:10 Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > HI, > > > > On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal > wrote: > > > Many thanks Alessandra for your reply :) > > > > gmx solvate will add water around my graphene sheet but will not increase > > the graphene sheet itself. Please correct me if I am wrong. > > > > > Yes/No, gmx solvate is normally used to add water or to build solvent box > but my suggestion was to use gmx solvate tools for your aim. > What I suggested was to use the tool to fill an empty box (of desidered > dimension) with copies of your graphene pre-equilibrated (small) sheet. > > Best regards > Alessandra > > > > I already simulated the graphene sheet but I need to increase its > dimension > > to a certain dimensions. > > > > any Ideas how to do that :) ? > > > > Thanks, > > Mohamed > > > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > > alessandra.villa.biosim at gmail.com> wrote: > > > > > Hi > > > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > > m.b.abdelaal at gmail.com> > > > wrote: > > > > > > > Hello All, > > > > > > > > I want to create a graphene sheet with a specific dimensions > > > (10*15*0.284) > > > > nm. > > > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > > ) > > > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > > 4 > > > > 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 > > > > 0.245951 0.426000 0.284000 > > > > > > > > Now I don't know how to use genconf to repeat it until it gives me > the > > > > required dimensions. As using genconf -nbox will repeat the above > into > > a > > > > specific number of boxes but I can't get a sheet with accurate > > dimensions > > > > of (10*15*0.284 nm). > > > > > > > > I tried to generate a sheet using gencong and then use editconf to > > change > > > > the dimensions to the required ones, but the problem is that using > > > editconf > > > > will put the graphene sheet in an empty box but will not change the > > > > dimension as I want. > > > > > > > > Another option is to divide the 10 (the required dimension) nm by > > > 0.245951 > > > > (the dimension in the above .gro file) and to use the genconf with > the > > > > result but it will be a lot of decimals and I am not sure if it will > > also > > > > give me the accurate dimension. > > > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > > the > > > limitation is that you do not control on the orientation and other > > > geometrical parameter that may be relevant for graphene sheet. > > > > > > 1) generate an empty box with the desired dimension (empty.gro) > > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > > > > > or in alternative you can use -cs and -box > > > for all the options see > > > > > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > > > Best regards > > > Alessandra > > > > > > > > > > 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. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 Wed Feb 19 11:38:40 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 19 Feb 2020 10:38:40 -0000 Subject: [gmx-users] Increase Graphene sheet size In-Reply-To: References: Message-ID: Hi Alessandra, Many thanks again for your help :) That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize it. now I have an additional part of the graphene sheet which is out of the box, How can I remove it. I want my simulation and visualization to be with a specific dimensions which is the dimensions of the box. I would appreciate if you can further clarify how can I do that. Thanks, Mohamed On Wed, Feb 19, 2020 at 10:10 Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > HI, > > > > On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal > wrote: > > > Many thanks Alessandra for your reply :) > > > > gmx solvate will add water around my graphene sheet but will not increase > > the graphene sheet itself. Please correct me if I am wrong. > > > > > Yes/No, gmx solvate is normally used to add water or to build solvent box > but my suggestion was to use gmx solvate tools for your aim. > What I suggested was to use the tool to fill an empty box (of desidered > dimension) with copies of your graphene pre-equilibrated (small) sheet. > > Best regards > Alessandra > > > > I already simulated the graphene sheet but I need to increase its > dimension > > to a certain dimensions. > > > > any Ideas how to do that :) ? > > > > Thanks, > > Mohamed > > > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > > alessandra.villa.biosim at gmail.com> wrote: > > > > > Hi > > > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > > m.b.abdelaal at gmail.com> > > > wrote: > > > > > > > Hello All, > > > > > > > > I want to create a graphene sheet with a specific dimensions > > > (10*15*0.284) > > > > nm. > > > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > > ) > > > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > > 4 > > > > 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 > > > > 0.245951 0.426000 0.284000 > > > > > > > > Now I don't know how to use genconf to repeat it until it gives me > the > > > > required dimensions. As using genconf -nbox will repeat the above > into > > a > > > > specific number of boxes but I can't get a sheet with accurate > > dimensions > > > > of (10*15*0.284 nm). > > > > > > > > I tried to generate a sheet using gencong and then use editconf to > > change > > > > the dimensions to the required ones, but the problem is that using > > > editconf > > > > will put the graphene sheet in an empty box but will not change the > > > > dimension as I want. > > > > > > > > Another option is to divide the 10 (the required dimension) nm by > > > 0.245951 > > > > (the dimension in the above .gro file) and to use the genconf with > the > > > > result but it will be a lot of decimals and I am not sure if it will > > also > > > > give me the accurate dimension. > > > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > > the > > > limitation is that you do not control on the orientation and other > > > geometrical parameter that may be relevant for graphene sheet. > > > > > > 1) generate an empty box with the desired dimension (empty.gro) > > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro ..... -o > > > > > > or in alternative you can use -cs and -box > > > for all the options see > > > > > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > > > Best regards > > > Alessandra > > > > > > > > > > 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. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 Wed Feb 19 12:29:36 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Wed, 19 Feb 2020 11:29:36 -0000 Subject: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) Message-ID: Thank you, Alessandra, for your reply. I have tried TER in the PDB file but it doesn't work. It requires an N and C terminal for amino acid residue. I have prepared residue in avogadros and used these coordinates. ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00 N1+ ATOM 2 CA PHE A 1 1.462 0.000 0.000 1.00 0.00 C ATOM 3 C PHE A 1 1.902 0.000 1.473 1.00 0.00 C ATOM 4 O PHE A 1 1.105 0.000 2.411 1.00 0.00 O ATOM 5 CB PHE A 1 2.020 1.225 -0.743 1.00 0.00 C ATOM 6 CG PHE A 1 3.442 1.037 -1.219 1.00 0.00 C ATOM 7 CD2 PHE A 1 4.512 1.642 -0.547 1.00 0.00 C ATOM 8 CE2 PHE A 1 5.823 1.440 -0.982 1.00 0.00 C ATOM 9 CZ PHE A 1 6.074 0.642 -2.097 1.00 0.00 C ATOM 10 CE1 PHE A 1 5.015 0.044 -2.777 1.00 0.00 C ATOM 11 CD1 PHE A 1 3.705 0.238 -2.340 1.00 0.00 C ATOM 12 H PHE A 1 -0.467 0.280 0.859 1.00 0.00 H ATOM 13 HA PHE A 1 1.790 -0.939 -0.463 1.00 0.00 H ATOM 14 HB1 PHE A 1 1.956 2.118 -0.106 1.00 0.00 H ATOM 15 HB2 PHE A 1 1.405 1.454 -1.623 1.00 0.00 H ATOM 16 HD2 PHE A 1 4.334 2.273 0.322 1.00 0.00 H ATOM 17 HE2 PHE A 1 6.649 1.912 -0.456 1.00 0.00 H ATOM 18 HZ PHE A 1 7.094 0.492 -2.441 1.00 0.00 H ATOM 19 HE1 PHE A 1 5.208 -0.570 -3.654 1.00 0.00 H ATOM 20 HD1 PHE A 1 2.885 -0.231 -2.885 1.00 0.00 H ATOM 21 HN PHE A 1 -0.339 0.853 -0.435 1.00 0.00 H ATOM 22 2HN PHE A 1 -0.339 -0.853 -0.435 1.00 0.00 H ATOM 23 OXT PHE A 1 3.231 -0.000 1.717 1.00 0.00 O1- However, it claims that in the chosen force field there is no residue type for 'PHE' as a standalone (starting & ending) residue I am using AMBER99SB-ILDN force field for protein. I have looked into the force field both CPHE and NPHE are different as below:- [ CPHE ] [ atoms ] N N -0.38210 1 H H 0.26810 2 CA CT -0.18250 3 HA H1 0.10980 4 CB CT -0.09590 5 HB1 HC 0.04430 6 HB2 HC 0.04430 7 CG CA 0.05520 8 CD1 CA -0.13000 9 HD1 HA 0.14080 10 CE1 CA -0.18470 11 HE1 HA 0.14610 12 CZ CA -0.09440 13 HZ HA 0.12800 14 CE2 CA -0.18470 15 HE2 HA 0.14610 16 CD2 CA -0.13000 17 HD2 HA 0.14080 18 C C 0.76600 19 OC1 O2 -0.80260 20 OC2 O2 -0.80260 21 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ CZ HZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C OC1 C OC2 -C N [ impropers ] -C CA N H CA OC1 C OC2 CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2 CZ HZ CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB [ NPHE ] [ atoms ] N N3 0.17370 1 H1 H 0.19210 2 H2 H 0.19210 3 H3 H 0.19210 4 CA CT 0.07330 5 HA HP 0.10410 6 CB CT 0.03300 7 HB1 HC 0.01040 8 HB2 HC 0.01040 9 CG CA 0.00310 10 CD1 CA -0.13920 11 HD1 HA 0.13740 12 CE1 CA -0.16020 13 HE1 HA 0.14330 14 CZ CA -0.12080 15 HZ HA 0.13290 16 CE2 CA -0.16030 17 HE2 HA 0.14330 18 CD2 CA -0.13910 19 HD2 HA 0.13740 20 C C 0.61230 21 O O -0.57130 22 [ bonds ] N H1 N H2 N H3 N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ CZ HZ CZ CE2 CE2 HE2 CE2 CD2 CD2 HD2 C O C +N [ impropers ] CA +N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CE1 CE2 CZ HZ CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB How should I build it. Thanks. Sadaf From peter.mawanga.lagos at gmail.com Wed Feb 19 15:10:24 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Wed, 19 Feb 2020 14:10:24 -0000 Subject: [gmx-users] Selective RMSD calculation Message-ID: Hello everyone After fitting the protein-ligand system to the starting conformation, I would like to extract the RMSD information for the ligand only but cannot find such an option for a selective output. Please let me know if this can be achieved with the gmx tool, I couldn't find such an option with both the "rms" and "rmsd" commands. -- Thanks Peter From 177cy500.bratin at nitk.edu.in Wed Feb 19 15:47:33 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Wed, 19 Feb 2020 14:47:33 -0000 Subject: [gmx-users] Selective RMSD calculation In-Reply-To: References: Message-ID: Hi, You can calculate the rmsd by passing the index file of the ligand... gmx rms -h On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, wrote: > Hello everyone > > After fitting the protein-ligand system to the starting conformation, I > would like to extract the RMSD information for the ligand only but cannot > find such an option for a selective output. > > Please let me know if this can be achieved with the gmx tool, I couldn't > find such an option with both the "rms" and "rmsd" commands. > > -- > Thanks > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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.olagunju at fz-juelich.de Wed Feb 19 16:45:09 2020 From: m.olagunju at fz-juelich.de (Maryam) Date: Wed, 19 Feb 2020 15:45:09 -0000 Subject: [gmx-users] Converting Charmm to gmx format using cgenff Message-ID: <81ee07b7-b601-d63b-88dd-15ed0339a924@fz-juelich.de> Dear gmx users, I am trying to generate topology for small ligands using cgenff . I will like to confirm if the Charmm to gmx script available on the Mackerell website is compatible with all versions of charmm forcefield or can only be used with Charm36 forcefield. P.S. I have tried it with charm22* and did not get any error, I will just like to double check. Looking forward to your reply. Best regards, Maryam ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ From kevin.boyd at uconn.edu Wed Feb 19 17:45:48 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Wed, 19 Feb 2020 16:45:48 -0000 Subject: [gmx-users] GPU considerations for GROMACS In-Reply-To: References: Message-ID: Hi, A CPU:GPU ratio of 4:1 is fairly well balanced these days (depending on the quality of the hardware), so you should expect to roughly double your throughput adding a second GPU to your current system. However, that doesn't mean your single simulation performance will double - it's a lot more efficient to run multiple simulations in parallel with these setups, because multiple GPUs don't scale perfectly. We can't make absolute statements about the performance you should expect, it depends a lot on workload among other things. Have you seen the "More bang for your buck" paper?. https://arxiv.org/abs/1903.05918 Kevin On Tue, Feb 18, 2020 at 6:21 AM hairul.ikmal at gmail.com < hairul.ikmal at gmail.com> wrote: > Hello, > > Previously, I have helped building a workstation for my fellow > researcher who heavily uses GROMACS for his MD simulations, with the > following base specs: > > -CPU: 8 cores (Xeon E2278G) > -RAM: 32GB > -GPU: 1x RTX2080Ti > > > With this setup, he managed to shrink down each simulation runtime to, > say approximately 12 hours, compared to previous system (purely CPU > only, no GPU support), which took days to complete. > > > 1) Based on the current progress, we plan to build another system > (which will also run GROMACS most of the time) using the existing > workstation as reference. But currently we are unsure which setup > (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, > when running the same set of GROMACS simulation : > > > Option 1: > Retain same CPU, RAM and GPU specs (1x RTX2080Ti) > > > Option 2: > Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead > of 1x RTX2080Ti > > > 2) Besides building another system, we are considering to upgrade the > existing system, too. For example, assuming the system has the > expansion capability (enough PCI-e 16x slots, power supply), will > adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) > into existing setup will significantly cut down current runtime? If > yes, by how much time reduction can we expect generally with this > upgrade? > > > Appreciate if someone can share their thoughts and experience. > Thank you! > > > -Hairul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 jason.hogrefe at exxactcorp.com Wed Feb 19 18:41:22 2020 From: jason.hogrefe at exxactcorp.com (Jason Hogrefe) Date: Wed, 19 Feb 2020 17:41:22 -0000 Subject: [gmx-users] GPU considerations for GROMACS In-Reply-To: References: Message-ID: We recommend Intel Xeon if possible. You can see how we set up our GROMACS optimized workstations at https://www.exxactcorp.com/GROMACS-Certified-GPU-Systems If Xeon is not an option, at the very least use a high-end i7 or i9 9th/10th gen. With Memory the system should typically have 64GB to start, up to 128GB. For the GPU we typically start with RTX 2080 and go up from there. Can you explain a little more about your environment? What SSD? What dataset? What type of job are you running, etc? Thanks, Jason Hogrefe Exxact Corporation https://www.exxactcorp.com -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of hairul.ikmal at gmail.com Sent: Tuesday, February 18, 2020 6:21 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] GPU considerations for GROMACS [EXTERNAL] Hello, Previously, I have helped building a workstation for my fellow researcher who heavily uses GROMACS for his MD simulations, with the following base specs: -CPU: 8 cores (Xeon E2278G) -RAM: 32GB -GPU: 1x RTX2080Ti With this setup, he managed to shrink down each simulation runtime to, say approximately 12 hours, compared to previous system (purely CPU only, no GPU support), which took days to complete. 1) Based on the current progress, we plan to build another system (which will also run GROMACS most of the time) using the existing workstation as reference. But currently we are unsure which setup (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, when running the same set of GROMACS simulation : Option 1: Retain same CPU, RAM and GPU specs (1x RTX2080Ti) Option 2: Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead of 1x RTX2080Ti 2) Besides building another system, we are considering to upgrade the existing system, too. For example, assuming the system has the expansion capability (enough PCI-e 16x slots, power supply), will adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) into existing setup will significantly cut down current runtime? If yes, by how much time reduction can we expect generally with this upgrade? Appreciate if someone can share their thoughts and experience. Thank you! -Hairul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 Wed Feb 19 21:13:52 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Wed, 19 Feb 2020 20:13:52 -0000 Subject: [gmx-users] How to cap a single residue in gromacs In-Reply-To: References: Message-ID: Hi, Without saying about the physical meaning of your model because I don't know what you are doing. About technical point, I used your PHE coordinate and using pymol to cap with ACE, NME as you said then execute pdb2gmx using amber99sb forcefield in gromacs, it works well. What is the error that you say? On Wed, Feb 19, 2020, 09:25 Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > Hi > > On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > > > Dear Gromacs users > > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > > when I run pdb2gmx it gives me error:- > > Fatal error: > > In the chosen force field there is no residue type for 'PHE' as a > > standalone > > (starting & ending) residue > > > > I added ACE and NME terminals as below in the gro file:- > > > > 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > > 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > > 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > > 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > > 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > > 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > > 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > > 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > > 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > > 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > > 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > > 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > > 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > > 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 > > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > > 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > > 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > > 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > > 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > > 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > > 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > > 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > > 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 > > 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 > > > > NOTE that several atoms in the above gro file have the same (0. 0. 0.) > coordinate/position. > That may cause a crash when you start the simulation > > > > However, it still claims the same error. > > How should I add this in force field file? How can I use -ter command > that > > it can add N and C termini itself to the residue? > > > > Yes the first thing I will do is to try is -ter. > Different force fields have different termini definition > (maybe the force field has already ACE and NME) > > Best regards > Alessandra > > > > > I would really thankful for your suggestions. > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 lvqingjiejie at 163.com Thu Feb 20 02:58:09 2020 From: lvqingjiejie at 163.com (Qing Lv) Date: Thu, 20 Feb 2020 01:58:09 -0000 Subject: [gmx-users] How to deal with unexpected reactions in umbrella sampling? In-Reply-To: References: Message-ID: <50a75b94.1cdd.1706050f384.Coremail.lvqingjiejie@163.com> Dear Colleagues, I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only method I can think is to impose additional restraints to avoid this reaction, but the additional restraints will probably affect the umbrella sampling (although the additional restraints are not related to the reaction coordinate). Thanks, Qing From bonjour899 at 126.com Thu Feb 20 03:30:47 2020 From: bonjour899 at 126.com (bonjour899) Date: Thu, 20 Feb 2020 02:30:47 -0000 Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory Message-ID: <47a3d435.73ec.170606ec424.Coremail.bonjour899@126.com> Hello, I have encountered a weird problem. I've been using GROMACS with GPU on a server and always performance good. However when I just reran a job today and suddenly got this error: Command line: gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3? Back Off! I just backed up pull.log to ./#pull.log.1# ------------------------------------------------------- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) ? Fatal error: cudaFuncGetAttributes failed: out of memory ? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems the GPU is 0 occupied and I can run other apps with GPU, but I cannot run GROMACS mdrun anymore, even if doing energy minimization. From koyj2018 at kaist.ac.kr Thu Feb 20 06:34:53 2020 From: koyj2018 at kaist.ac.kr (=?UTF-8?B?6rOg7Jew7KO8?=) Date: Thu, 20 Feb 2020 05:34:53 -0000 Subject: [gmx-users] =?utf-8?q?gmx_trjconv_-force_option_doesn=27t_seem_to?= =?utf-8?q?_work=2E?= Message-ID: <5e4e1c133fda_@_imoxion.com> Hello! I have a question about gmx trjconv -force option because it seems to work at all. I'm using GROMACS-5.1.5 version and I want to extract forces using gmx trjconv command. So I tried. gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -novel -force yes -pbc mol -o test.gro ? However, the force was not obtained in test.gro. ? How do I get the force corresponding to specific coordinates. ? Thanks. ? Yeonju Go From vuqv.phys at gmail.com Thu Feb 20 11:43:57 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Thu, 20 Feb 2020 10:43:57 -0000 Subject: [gmx-users] How to deal with unexpected reactions in umbrella sampling? In-Reply-To: <50a75b94.1cdd.1706050f384.Coremail.lvqingjiejie@163.com> References: <50a75b94.1cdd.1706050f384.Coremail.lvqingjiejie@163.com> Message-ID: Hi, you can think about employed multi-dimensional umbrella sampling and used 3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone, P. M., Snow, C. D., Lucent, D., & Pande, V. S. (2008). Side-chain recognition and gating in the ribosome exit tunnel. *Proceedings of the National Academy of Sciences of the United States of America*, *105*(43), 16549?16554. https://doi.org/10.1073/pnas.0801795105 I don't know whether he delivered the code for 3D-WHAM or not Best, On Thu, Feb 20, 2020 at 2:58 AM Qing Lv wrote: > Dear Colleagues, > > > I am doing an umbrella sampling of an enzymatic reaction using QM/MM. > However, as the reaction coordinate exceeds a certain value, an unexpected > reaction, which is obviously unreasonable, often occurs during the umbrella > sampling. So, how to deal with such problem? The only method I can think is > to impose additional restraints to avoid this reaction, but the additional > restraints will probably affect the umbrella sampling (although the > additional restraints are not related to the reaction coordinate). > > > Thanks, > Qing > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 peter.mawanga.lagos at gmail.com Thu Feb 20 11:56:02 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Thu, 20 Feb 2020 10:56:02 -0000 Subject: [gmx-users] Selective RMSD calculation In-Reply-To: References: Message-ID: Thanks a lot Bratin for your help. It worked and I was able to get the RMSD values. However, there is no option to change the reference frame (from the input trajectory) for the RMSD calculation. As a workaround, I was thinking about extracting the different frames of the ligand as separate .gro files but couldn't figure out how to do that easily. Can this be achieved using "trjconv" but without supplying multiple text files for the frame index values? Please let me know. On Wed, Feb 19, 2020 at 3:48 PM Bratin Kumar Das < 177cy500.bratin at nitk.edu.in> wrote: > Hi, > You can calculate the rmsd by passing the index file of the ligand... > gmx rms -h > > On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, > > wrote: > > > Hello everyone > > > > After fitting the protein-ligand system to the starting conformation, I > > would like to extract the RMSD information for the ligand only but cannot > > find such an option for a selective output. > > > > Please let me know if this can be achieved with the gmx tool, I couldn't > > find such an option with both the "rms" and "rmsd" commands. > > > > -- > > Thanks > > Peter > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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. > -- Cheers Peter From lvqingjiejie at 163.com Thu Feb 20 12:16:08 2020 From: lvqingjiejie at 163.com (Qing Lv) Date: Thu, 20 Feb 2020 11:16:08 -0000 Subject: [gmx-users] How to deal with unexpected reactions in umbrella sampling? In-Reply-To: References: <50a75b94.1cdd.1706050f384.Coremail.lvqingjiejie@163.com> Message-ID: <127b20be.1b2e.1706241b4f1.Coremail.lvqingjiejie@163.com> Thank you, Quyen. I will look into this paper. Qing At 2020-02-20 18:45:58, "Quyen V. Vu" wrote: >Hi, >you can think about employed multi-dimensional umbrella sampling and used >3D-WHAM to derived the PMF as professor Pander did in this paper: Petrone, >P. M., Snow, C. D., Lucent, D., & Pande, V. S. (2008). Side-chain >recognition and gating in the ribosome exit tunnel. *Proceedings of the >National Academy of Sciences of the United States of America*, *105*(43), >16549?16554. https://doi.org/10.1073/pnas.0801795105 > >I don't know whether he delivered the code for 3D-WHAM or not > >Best, > >On Thu, Feb 20, 2020 at 2:58 AM Qing Lv wrote: > >> Dear Colleagues, >> >> >> I am doing an umbrella sampling of an enzymatic reaction using QM/MM. >> However, as the reaction coordinate exceeds a certain value, an unexpected >> reaction, which is obviously unreasonable, often occurs during the umbrella >> sampling. So, how to deal with such problem? The only method I can think is >> to impose additional restraints to avoid this reaction, but the additional >> restraints will probably affect the umbrella sampling (although the >> additional restraints are not related to the reaction coordinate). >> >> >> Thanks, >> Qing >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 177cy500.bratin at nitk.edu.in Thu Feb 20 14:00:31 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Thu, 20 Feb 2020 13:00:31 -0000 Subject: [gmx-users] Selective RMSD calculation In-Reply-To: References: Message-ID: Hi You have said correctly...you can use trjconv for that.. On Thu 20 Feb, 2020, 4:30 PM Peter Mawanga, wrote: > Thanks a lot Bratin for your help. > > It worked and I was able to get the RMSD values. However, there is no > option to change the reference frame (from the input trajectory) for the > RMSD calculation. > > As a workaround, I was thinking about extracting the different frames of > the ligand as separate .gro files but couldn't figure out how to do that > easily. Can this be achieved using "trjconv" but without supplying multiple > text files for the frame index values? Please let me know. > > On Wed, Feb 19, 2020 at 3:48 PM Bratin Kumar Das < > 177cy500.bratin at nitk.edu.in> wrote: > > > Hi, > > You can calculate the rmsd by passing the index file of the > ligand... > > gmx rms -h > > > > On Wed 19 Feb, 2020, 7:41 PM Peter Mawanga, < > peter.mawanga.lagos at gmail.com > > > > > wrote: > > > > > Hello everyone > > > > > > After fitting the protein-ligand system to the starting conformation, I > > > would like to extract the RMSD information for the ligand only but > cannot > > > find such an option for a selective output. > > > > > > Please let me know if this can be achieved with the gmx tool, I > couldn't > > > find such an option with both the "rms" and "rmsd" commands. > > > > > > -- > > > Thanks > > > Peter > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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. > > > > > -- > Cheers > Peter > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 ggroenh at gwdg.de Thu Feb 20 14:08:48 2020 From: ggroenh at gwdg.de (Groenhof, Gerrit) Date: Thu, 20 Feb 2020 13:08:48 -0000 Subject: [gmx-users] How to deal with unexpected reactions in umbrella sampling? In-Reply-To: References: Message-ID: <053BEFCE-9238-4741-8D2C-18A2F574A908@mpibpc.mpg.de> Hi, There is not much information to go with, but I can give some general remarks. Could this not suggest that either your reaction coordinate is not suited, driving the system into a region of very high potential energy, from where it can escape though the reaction you consider unreasonable. Before embarking on the QM/MM umbrella sampling, did you check whether the coordinate is suitable in isolation? Alternatively, the QM description may fail to capture the electronic structure along your coordinate. Has your QM method been validated for the reaction you?re studying? Best wishes & good luck with your simulations, Gerrit > > Dear Colleagues, > > > I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only method I can think is to impose additional restraints to avoid this reaction, but the additional restraints will probably affect the umbrella sampling (although the additional restraints are not related to the reaction coordinate). > > > Thanks, > Qing > > > - > From peter.mawanga.lagos at gmail.com Thu Feb 20 14:15:25 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Thu, 20 Feb 2020 13:15:25 -0000 Subject: [gmx-users] Output trajectory frames as separate coordinate files Message-ID: Hello everyone Is it possible to output different frames of a .trr trajectory as single .gro files without supplying an index (.ndx) file each time? In VMD this can be achieved with: set mol [molinfo top] set sel [atomselect $mol all] set n [molinfo $mol get numframes] for {set i 0} {$i < $n} {incr i} { $sel frame $i $sel update $sel writepdb $i.pdb } $sel delete I am searching for a similar command in Gromacs if feasible where just supplying the frame number would be fine or a workaround. Thank you for your assistance. -- Cheers Peter From peter.mawanga.lagos at gmail.com Thu Feb 20 14:31:00 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Thu, 20 Feb 2020 13:31:00 -0000 Subject: [gmx-users] Output trajectory frames as separate coordinate files In-Reply-To: References: Message-ID: My apologies, this can be achieved easily with the command below: gmx trjconv -s -f -n -split -o . On Thu, Feb 20, 2020 at 2:15 PM Peter Mawanga wrote: > Hello everyone > > Is it possible to output different frames of a .trr trajectory as single > .gro files without supplying an index (.ndx) file each time? > > In VMD this can be achieved with: > > set mol [molinfo top] > set sel [atomselect $mol all] > set n [molinfo $mol get numframes] > for {set i 0} {$i < $n} {incr i} { > $sel frame $i > $sel update > $sel writepdb $i.pdb > } > $sel delete > > I am searching for a similar command in Gromacs if feasible where just > supplying the frame number would be fine or a workaround. Thank you for > your assistance. > > -- > Cheers > Peter > -- Cheers Peter From a.mecklenfeld at tu-braunschweig.de Thu Feb 20 16:09:33 2020 From: a.mecklenfeld at tu-braunschweig.de (Andreas Mecklenfeld) Date: Thu, 20 Feb 2020 15:09:33 -0000 Subject: [gmx-users] PMF in inhomogeneous fluid phase Message-ID: <86dad905-85a8-eccb-4a3a-fc9f13f4ea09@tu-braunschweig.de> Dear Gromacs-users, I have a question that may not be directly Gromacs-related. I want to calculate the potential of mean force (PMF) for a solute that is pulled away from a crystal surface. The issue is that the fluid phase is inhomogeneous, as it consists of water and cluster-forming ions. From my understanding, this would make the PMF calculation not only dependent on the pull-coordinate (z-axis of the simulation box), but the PMF would be also influenced by the position of the clusters which might change their position randomly in different umbrella windows. One could restrain the positions of the ions to freeze the local composition. However, this would be an enormous interference into the system and I'm not really comfortable in doing so. Any suggestions would be highly appreciated. Bests, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universit?t Braunschweig Institut f?r Thermodynamik Hans-Sommer-Stra?e 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 https://www.tu-braunschweig.de/ift https://www.tu-braunschweig.de/ift/agmolth From jalemkul at vt.edu Thu Feb 20 16:37:58 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:37:58 -0000 Subject: [gmx-users] CGENFF validation / optimization In-Reply-To: References: Message-ID: <16c417e2-aa8c-7188-739f-b36dddbba8c2@vt.edu> On 2/18/20 2:28 PM, Adarsh V. K. wrote: > Dear all, > > While suing CGENFF server for " *.str " file generation, Few of the > penalties were found to be higher than 50. How to do > validation/optimization.? Is there any recommended softwares / servers > available for I suggest you read the 2010 JCC paper on CGenFF, which is itself a case study/tutorial on what to do. Other subsequent papers explain what the penalties mean and how to interpret them. -Justin > * " extensive validation / optimization." or any standard procedure > available to do validation / optimization ?The *.str file also contains the > following message.* > ------------------------------------------------------------------------------------------------------------ > ! "penalty" is the highest penalty score of the associated parameters. > ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 > ! and 50 mean some basic validation is recommended; penalties higher than > ! 50 indicate poor analogy and mandate extensive validation/optimization. > ------------------------------------------------------------------------------------------------------------- -- ================================================== 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 Feb 20 16:38:26 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:38:26 -0000 Subject: [gmx-users] Problem in energy minimization and domain decomposition In-Reply-To: References: Message-ID: <60db6ce0-bb6f-48aa-95d1-30498e86f21e@vt.edu> On 2/18/20 3:57 PM, Sadaf Rani wrote: > Dear Gromacs users > > I am getting the following message while running an energy minimization:- > > There is no domain decomposition for 32 ranks that is compatible with the > given box and a minimum cell size of 1.85723 nm > I am not using any distance restraint, and selecting box size by the > following command : > gmx editconf -f rescloselig.gro -o rescloseligbox.gro -bt cubic -d 1.2 > > Can you please suggest me how should I fix it. Use fewer processors. Your system is too small to be decomposed the way you have requested. -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 Feb 20 16:39:55 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:39:55 -0000 Subject: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) In-Reply-To: References: Message-ID: On 2/19/20 6:29 AM, Sadaf Rani wrote: > Thank you, Alessandra, for your reply. > I have tried TER in the PDB file but it doesn't work. It requires an N and > C terminal for amino acid residue. I have prepared residue in avogadros and > used these coordinates. > ATOM 1 N PHE A 1 0.000 0.000 0.000 1.00 0.00 > N1+ > ATOM 2 CA PHE A 1 1.462 0.000 0.000 1.00 0.00 > C > ATOM 3 C PHE A 1 1.902 0.000 1.473 1.00 0.00 > C > ATOM 4 O PHE A 1 1.105 0.000 2.411 1.00 0.00 > O > ATOM 5 CB PHE A 1 2.020 1.225 -0.743 1.00 0.00 > C > ATOM 6 CG PHE A 1 3.442 1.037 -1.219 1.00 0.00 > C > ATOM 7 CD2 PHE A 1 4.512 1.642 -0.547 1.00 0.00 > C > ATOM 8 CE2 PHE A 1 5.823 1.440 -0.982 1.00 0.00 > C > ATOM 9 CZ PHE A 1 6.074 0.642 -2.097 1.00 0.00 > C > ATOM 10 CE1 PHE A 1 5.015 0.044 -2.777 1.00 0.00 > C > ATOM 11 CD1 PHE A 1 3.705 0.238 -2.340 1.00 0.00 > C > ATOM 12 H PHE A 1 -0.467 0.280 0.859 1.00 0.00 > H > ATOM 13 HA PHE A 1 1.790 -0.939 -0.463 1.00 0.00 > H > ATOM 14 HB1 PHE A 1 1.956 2.118 -0.106 1.00 0.00 > H > ATOM 15 HB2 PHE A 1 1.405 1.454 -1.623 1.00 0.00 > H > ATOM 16 HD2 PHE A 1 4.334 2.273 0.322 1.00 0.00 > H > ATOM 17 HE2 PHE A 1 6.649 1.912 -0.456 1.00 0.00 > H > ATOM 18 HZ PHE A 1 7.094 0.492 -2.441 1.00 0.00 > H > ATOM 19 HE1 PHE A 1 5.208 -0.570 -3.654 1.00 0.00 > H > ATOM 20 HD1 PHE A 1 2.885 -0.231 -2.885 1.00 0.00 > H > ATOM 21 HN PHE A 1 -0.339 0.853 -0.435 1.00 0.00 > H > ATOM 22 2HN PHE A 1 -0.339 -0.853 -0.435 1.00 0.00 > H > ATOM 23 OXT PHE A 1 3.231 -0.000 1.717 1.00 0.00 > O1- > > However, it claims that in the chosen force field there is no residue type > for 'PHE' as a standalone > (starting & ending) residue > I am using AMBER99SB-ILDN force field for protein. > I have looked into the force field both CPHE and NPHE are different as > below:- > > > [ CPHE ] > [ atoms ] > N N -0.38210 1 > H H 0.26810 2 > CA CT -0.18250 3 > HA H1 0.10980 4 > CB CT -0.09590 5 > HB1 HC 0.04430 6 > HB2 HC 0.04430 7 > CG CA 0.05520 8 > CD1 CA -0.13000 9 > HD1 HA 0.14080 10 > CE1 CA -0.18470 11 > HE1 HA 0.14610 12 > CZ CA -0.09440 13 > HZ HA 0.12800 14 > CE2 CA -0.18470 15 > HE2 HA 0.14610 16 > CD2 CA -0.13000 17 > HD2 HA 0.14080 18 > C C 0.76600 19 > OC1 O2 -0.80260 20 > OC2 O2 -0.80260 21 > [ bonds ] > N H > N CA > CA HA > CA CB > CA C > CB HB1 > CB HB2 > CB CG > CG CD1 > CG CD2 > CD1 HD1 > CD1 CE1 > CE1 HE1 > CE1 CZ > CZ HZ > CZ CE2 > CE2 HE2 > CE2 CD2 > CD2 HD2 > C OC1 > C OC2 > -C N > [ impropers ] > -C CA N H > CA OC1 C OC2 > CG CE2 CD2 HD2 > CZ CD2 CE2 HE2 > CE1 CE2 CZ HZ > CD1 CZ CE1 HE1 > CG CE1 CD1 HD1 > CD1 CD2 CG CB > > [ NPHE ] > [ atoms ] > N N3 0.17370 1 > H1 H 0.19210 2 > H2 H 0.19210 3 > H3 H 0.19210 4 > CA CT 0.07330 5 > HA HP 0.10410 6 > CB CT 0.03300 7 > HB1 HC 0.01040 8 > HB2 HC 0.01040 9 > CG CA 0.00310 10 > CD1 CA -0.13920 11 > HD1 HA 0.13740 12 > CE1 CA -0.16020 13 > HE1 HA 0.14330 14 > CZ CA -0.12080 15 > HZ HA 0.13290 16 > CE2 CA -0.16030 17 > HE2 HA 0.14330 18 > CD2 CA -0.13910 19 > HD2 HA 0.13740 20 > C C 0.61230 21 > O O -0.57130 22 > [ bonds ] > N H1 > N H2 > N H3 > N CA > CA HA > CA CB > CA C > CB HB1 > CB HB2 > CB CG > CG CD1 > CG CD2 > CD1 HD1 > CD1 CE1 > CE1 HE1 > CE1 CZ > CZ HZ > CZ CE2 > CE2 HE2 > CE2 CD2 > CD2 HD2 > C O > C +N > [ impropers ] > CA +N C O > CG CE2 CD2 HD2 > CZ CD2 CE2 HE2 > CE1 CE2 CZ HZ > CD1 CZ CE1 HE1 > CG CE1 CD1 HD1 > CD1 CD2 CG CB > > How should I build it. If you're trying to simulate a zwitterionic Phe residue, the AMBER force field (at least, as implemented in GROMACS) does not support such a species. If you want to cap it with acetyl and amide caps, you will need to build those entities yourself and specify them as separate residues (ACE and NME). -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 Feb 20 16:40:58 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:40:58 -0000 Subject: [gmx-users] Converting Charmm to gmx format using cgenff In-Reply-To: <81ee07b7-b601-d63b-88dd-15ed0339a924@fz-juelich.de> References: <81ee07b7-b601-d63b-88dd-15ed0339a924@fz-juelich.de> Message-ID: <28f760dc-c1d8-ef64-7e88-b6674eee6980@vt.edu> On 2/19/20 10:45 AM, Maryam wrote: > Dear gmx users, > > I am trying to generate topology for small ligands using cgenff . I will > like to confirm if the Charmm to gmx script available on the Mackerell > website is compatible with all versions of charmm forcefield or can only > be used with Charm36 forcefield. P.S. I have tried it with charm22* and > did not get any error, I will just like to double check.? Looking > forward to your reply. > The conversion script is for CGenFF stream files produced by the online CGenFF server. It is not associated with any CHARMM force field 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 jalemkul at vt.edu Thu Feb 20 16:42:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:42:05 -0000 Subject: [gmx-users] gmx trjconv -force option doesn't seem to work. In-Reply-To: <5e4e1c133fda_@_imoxion.com> References: <5e4e1c133fda_@_imoxion.com> Message-ID: On 2/20/20 12:34 AM, ??? wrote: > > > Hello! > > I have a question about gmx trjconv -force option because it seems to work at all. > > > I'm using GROMACS-5.1.5 version and I want to extract forces using gmx trjconv command. > > > So I tried. > > > gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -novel -force yes -pbc mol -o test.gro > > > > > > However, the force was not obtained in test.gro. > > > > > > How do I get the force corresponding to specific coordinates. > > Did you save forces in the .trr file? What does gmx check tell you? Also please note that version 5.1.5 is outdated so if there is some kind of bug it is not going to be fixed in that version and you should try using a more modern/supported 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 jalemkul at vt.edu Thu Feb 20 16:43:08 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 20 Feb 2020 15:43:08 -0000 Subject: [gmx-users] Output trajectory frames as separate coordinate files In-Reply-To: References: Message-ID: On 2/20/20 8:30 AM, Peter Mawanga wrote: > My apologies, this can be achieved easily with the command below: > > gmx trjconv -s -f -n > -split interval (in picoseconds)> -o . It's even easier. You can just use gmx trjconv -sep (with -b/-e as needed to define a time interval). -Justin > > > On Thu, Feb 20, 2020 at 2:15 PM Peter Mawanga > wrote: > >> Hello everyone >> >> Is it possible to output different frames of a .trr trajectory as single >> .gro files without supplying an index (.ndx) file each time? >> >> In VMD this can be achieved with: >> >> set mol [molinfo top] >> set sel [atomselect $mol all] >> set n [molinfo $mol get numframes] >> for {set i 0} {$i < $n} {incr i} { >> $sel frame $i >> $sel update >> $sel writepdb $i.pdb >> } >> $sel delete >> >> I am searching for a similar command in Gromacs if feasible where just >> supplying the frame number would be fine or a workaround. Thank you for >> your assistance. >> >> -- >> Cheers >> Peter >> > -- ================================================== 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 aa.hind at hotmail.com Thu Feb 20 17:37:00 2020 From: aa.hind at hotmail.com (hind ahmed) Date: Thu, 20 Feb 2020 16:37:00 -0000 Subject: [gmx-users] couple-moltype in FREE ENERGY calculation Message-ID: Dear All, I want to calculate the free energy of two different types of molecules in the same system. Is there a way to do this in gromacs? couple-moltype = CHOL DPPC Did not find any molecules of type 'CHOL DPPC' for coupling, Regards, Hind From dburns at iastate.edu Thu Feb 20 22:10:33 2020 From: dburns at iastate.edu (Daniel Burns) Date: Thu, 20 Feb 2020 21:10:33 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: Hi again, It seems including our openmp module was responsible for the issue the whole time. When I submit the job only loading pmix and gromacs, replica exchange proceeds. Thank you, Dan On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham wrote: > Hi, > > That could be caused by configuration of the parallel file system or MPI on > your cluster. If only one file descriptor is available per node to an MPI > job, then your symptoms are explained. Some kinds of compute jobs follow > such a model, so maybe someone optimized something for that. > > Mark > > On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: > > > HI Szilard, > > > > I've deleted all my output but all the writing to the log and console > stops > > around the step noting the domain decomposition (or other preliminary > > task). It is the same with or without Plumed - the TREMD with Gromacs > only > > was the first thing to present this issue. > > > > I've discovered that if each replica is assigned its own node, the > > simulations proceed. If I try to run several replicas on each node > > (divided evenly), the simulations stall out before any trajectories get > > written. > > > > I have tried many different -np and -ntomp options as well as several > slurm > > job submission scripts with node/ thread configurations but multiple > > simulations per node will not work. I need to be able to run several > > replicas on the same node to get enough data since it's hard to get more > > than 8 nodes (and as a result, replicas). > > > > Thanks for your reply. > > > > -Dan > > > > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns > wrote: > > > > > Hi, > > > > > > I continue to have trouble getting an REMD job to run. It never makes > it > > > to the point that it generates trajectory files but it never gives any > > > error either. > > > > > > I have switched from a large TREMD with 72 replicas to the Plumed > > > Hamiltonian method with only 6 replicas. Everything is now on one node > > and > > > each replica has 6 cores. I've turned off the dynamic load balancing > on > > > this attempt per the recommendation from the Plumed site. > > > > > > Any ideas on how to troubleshoot? > > > > > > Thank you, > > > > > > Dan > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 Thu Feb 20 22:34:41 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 20 Feb 2020 21:34:41 -0000 Subject: [gmx-users] restraints failure problem Message-ID: Dear Gromacs users I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 71 29 10 0.403 0.403 10.0 0.0 0.403 0.403 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 29 71 69 71 1 104.92 0.0 1 104.92 41.840 1 71 29 31 29 1 147.02 0.0 1 147.02 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 69 71 29 31 1 146.72 0.0 0.0 146.72 0.0 41.840 72 71 29 31 1 17.55 0.0 0.0 17.55 0.0 41.840 72 71 29 25 1 173.10 0.0 0.0 173.10 0.0 41.840 However, after energy minimization, I observed that my restraints are not working and I find the following change:- bonds changed from 0.403 *0.413* angles:- 104.92 changed to *109.24* 147.02 changed to *147.65* dihedrals:- 146.72 changed to *133.39* 17.55 changed to *12.94* 173.10 changed to *-166.16* How should I work with these so that they may not change much? Dihedrals seem to be changing more than bonds and angles. I have to apply these in the free energy calculation which already crashed because of restraint failure. I would really be thankful for your kind suggestions, please. Thanks. Sadaf From sadafrani6 at gmail.com Thu Feb 20 22:49:27 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 20 Feb 2020 21:49:27 -0000 Subject: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul) Message-ID: Dear Justin, thank you for your reply. I have also tried adding ACE and NME as below but it didn't work. 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 Could you please suggest how should I do that? Thanks Sadaf From jalemkul at vt.edu Fri Feb 21 01:53:03 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 21 Feb 2020 00:53:03 -0000 Subject: [gmx-users] How to cap a single residue in gromacs (Alessandra Villa) (Justin Lemkul) In-Reply-To: References: Message-ID: On 2/20/20 4:49 PM, Sadaf Rani wrote: > Dear Justin, thank you for your reply. I have also tried adding ACE and > NME as below but it didn't work. Please provide your full command and entire screen output, including any applicable errors. Saying something "didn't work" is impossible to diagnose. Note also that your coordinates are completely nonfunctional because all of the ACE and NME atoms are at (0,0,0) so all the atoms overlap. It will be hopeless to try to proceed with such coordinates. You need to actually construct the atoms, not just enter dummy values. -Justin > 1ACE HC 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE CT 2 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 3 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE HC 4 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE C 5 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 1ACE O 6 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 2PHE N 7 5.066 4.671 6.042 0.2692 -0.2632 0.1330 > 2PHE H 8 5.027 4.600 5.982 -1.5227 1.0889 -0.3963 > 2PHE CA 9 5.013 4.811 6.023 0.0535 0.3709 0.0960 > 2PHE HA 10 5.058 4.868 6.105 -1.0081 1.0531 0.2242 > 2PHE CB 11 5.052 4.871 5.883 -0.0860 0.7332 0.2870 > 2PHE HB1 12 4.990 4.822 5.809 1.1212 -0.4628 0.0312 > 2PHE HB2 13 5.153 4.841 5.853 0.2157 2.3973 -0.5141 > 2PHE CG 14 5.062 5.017 5.867 0.0161 0.4565 0.5724 > 2PHE CD1 15 4.951 5.101 5.874 -0.1757 -0.2234 -0.3056 > 2PHE HD1 16 4.855 5.054 5.884 -0.9265 1.6156 2.3658 > 2PHE CE1 17 4.958 5.242 5.856 -0.3304 0.7195 0.1599 > 2PHE HE1 18 4.866 5.298 5.857 0.2928 1.7852 -0.4831 > 2PHE CZ 19 5.085 5.297 5.832 -0.3945 -1.0394 -0.7463 > 2PHE HZ 20 5.101 5.404 5.842 -0.5983 -1.2279 3.1660 > 2PHE CE2 21 5.200 5.216 5.830 -0.1669 -0.6131 1.1550 > 2PHE HE2 22 5.293 5.264 5.804 -1.0122 1.2508 1.4080 > 2PHE CD2 23 5.186 5.075 5.852 0.3885 0.2183 -0.6920 > 2PHE HD2 24 5.276 5.015 5.847 -0.0823 -0.3875 -3.1559 > 2PHE C 25 4.859 4.799 6.042 0.1650 -0.6772 0.7098 > 2PHE O 26 4.794 4.721 5.968 0.0339 0.0386 -0.1578 > 3NME N 27 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H 28 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME CT 29 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 30 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 31 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 3NME H1 32 0.000 0.000 0.000 0.0000 0.0000 0.0000 > 4G6P P 33 5.063 5.809 5.979 0.5468 0.1315 -0.0198 > 4G6P O1P 34 5.208 5.823 5.982 0.3151 -0.5087 0.1960 > 4G6P O2P 35 5.020 5.704 6.075 0.0937 -0.0791 -0.0538 > 4G6P O3P 36 5.028 5.939 6.039 -0.2953 0.3030 -0.2016 > 4G6P C1 37 4.985 5.671 5.430 0.5407 0.1917 0.2635 > 4G6P O1 38 5.118 5.662 5.388 -0.4011 0.4548 -0.8044 > 4G6P C2 39 4.889 5.558 5.383 0.3352 0.1447 0.3610 > 4G6P O2 40 4.876 5.546 5.239 -0.2019 -0.6192 -1.0434 > 4G6P C3 41 4.753 5.566 5.458 0.0668 0.4155 -0.3386 > 4G6P O3 42 4.674 5.438 5.425 -0.8214 0.3092 -0.1367 > 4G6P C4 43 4.783 5.561 5.611 0.3702 -0.3821 -0.5929 > 4G6P O4 44 4.661 5.608 5.676 -0.1025 0.6063 -0.0795 > 4G6P C5 45 4.890 5.667 5.654 -0.3851 0.4555 -0.1137 > 4G6P O5 46 5.006 5.658 5.573 -0.0288 0.1296 -0.6207 > 4G6P C6 47 4.935 5.670 5.809 -0.1636 0.0426 0.3771 > 4G6P O6 48 5.001 5.791 5.841 0.2972 -0.6933 -0.1489 > 4G6P H1 49 4.939 5.768 5.412 2.0772 1.3511 2.0534 > 4G6P H2 50 4.932 5.464 5.418 0.0848 -0.0506 0.1425 > 4G6P H3 51 4.706 5.660 5.427 0.9723 0.2387 -2.4228 > 4G6P H4 52 4.804 5.459 5.646 -0.3467 -0.2084 0.3693 > 4G6P H5 53 4.845 5.766 5.640 -0.6619 0.2119 -1.0742 > 4G6P H61 54 5.002 5.587 5.833 2.3826 1.5930 -0.8342 > 4G6P H62 55 4.851 5.665 5.878 1.0230 1.5442 2.0329 > 4G6P HO1 56 5.160 5.619 5.465 0. 23 -0.1270 -1.6233 > 4G6P HO2 57 4.816 5.469 5.232 -0.0502 -0.7762 -0.6581 > 4G6P HO3 58 4.671 5.441 5.328 0.3044 0.1862 -0.1954 > 4G6P HO4 59 4.649 5.553 5.755 -1.5501 2.1018 0.8000 > > Could you please suggest how should I do that? > > Thanks > > Sadaf -- ================================================== 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 Feb 21 01:54:02 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 21 Feb 2020 00:54:02 -0000 Subject: [gmx-users] couple-moltype in FREE ENERGY calculation In-Reply-To: References: Message-ID: <1829e10e-6386-d04a-48e6-74df4503203d@vt.edu> On 2/20/20 11:36 AM, hind ahmed wrote: > Dear All, > I want to calculate the free energy of two different types of molecules in the same system. Is there a way to do this in gromacs? > couple-moltype = CHOL DPPC > Did not find any molecules of type 'CHOL DPPC' for coupling, You can only decouple one [moleculetype] at a time. If you have a DPPC:CHOL bilayer, you shouldn't be attempting this because all you're going to do is cause the entire bilayer to disapper. Even if it's part of a larger mixture, you'll probably have a very hard time getting the simulations to converge. -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 Fri Feb 21 06:59:49 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Fri, 21 Feb 2020 05:59:49 -0000 Subject: [gmx-users] gmx trjconv -force option doesn't seem to work. In-Reply-To: References: <5e4e1c133fda_@_imoxion.com> Message-ID: Hi, Gro format doesn't support fields for forces. Either write out.g96 file, or use gmx traj (better) Mark On Thu., 20 Feb. 2020, 16:43 Justin Lemkul, wrote: > > > On 2/20/20 12:34 AM, ??? wrote: > > > > > > Hello! > > > > I have a question about gmx trjconv -force option because it seems to > work at all. > > > > > > I'm using GROMACS-5.1.5 version and I want to extract forces using > gmx trjconv command. > > > > > > So I tried. > > > > > > gmx trjconv -f alad.trr -s alad.tpr -n alad.ndx -novel -force yes > -pbc mol -o test.gro > > > > > > > > > > > > However, the force was not obtained in test.gro. > > > > > > > > > > > > How do I get the force corresponding to specific coordinates. > > > > > > Did you save forces in the .trr file? What does gmx check tell you? Also > please note that version 5.1.5 is outdated so if there is some kind of > bug it is not going to be fixed in that version and you should try using > a more modern/supported 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 > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Feb 21 09:08:23 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Fri, 21 Feb 2020 08:08:23 -0000 Subject: [gmx-users] Regarding to pme on gpu In-Reply-To: References: Message-ID: Hi. On Tue, Feb 18, 2020 at 5:11 PM Jimmy Chen wrote: > > Hi, > > When set -pme gpu in mdrun, only one rank can be set for pme, -npme 1. What > is the reason about only one rank for pme if use gpu to offload. Is it the > limitation or somehow? This is a limitation of the implementation, currently PME decomposition is not supported with PME offload. Hence, PME work needs to be assigned to a single GPU, be it the same as the one that does the PP computation or a separate one (assigned to the PME rank). > I am interesting in any performance improvement is still doable and any > improved plan for gpu kernel of pme and pp. there is no too much different > in pme and pp between 2019.3 and 2020. Can you please clarify what you mean? The 2020 release has made some improvements to both PP (bonded kernels) and PME performance, but these can indeed be minor. Cheers, -- Szil?rd > > Thanks, > Jimmy > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 henry.p.a.wittler at gmail.com Fri Feb 21 10:21:57 2020 From: henry.p.a.wittler at gmail.com (Henry Wittler) Date: Fri, 21 Feb 2020 09:21:57 -0000 Subject: [gmx-users] Thesis developed software; which Open-source License? Message-ID: Greetings comrades. This question may be somewhat redundant, so dont expect reply to every aspect, may ask at RG also. However if anyone have more or less insight, please reply. My thesis has calculation software that are built upon partly innovative and partly basic calculation/plotting/graphing software based upon "VMD/tcl? coding, GROMACS (GMX) and Python/MatplotlibScipy/Numpy (etc). The solvated protein data (chap. 6 of thesis) are obtained from GMX simulations, moreover the analysis data by VMD/tcl etc. I have uploaded so far just part of the code (for chap. 4.1) I intend to upload code from whole thesis to github link https://wittler-github.github.io/A_MD_Analysis_of_Insulin/ The following thesis link(downloadable) contains the calculated data along with the graphs. http://hdl.handle.net/1959.9/568798 ( https://www.researchgate.net/project/A-Molecular-Dynamics-Analysis-of-Insulin) I mainly want to share the novel GMX simulated data and tools I?ve developed from the above-mentioned softwares, that are described in my thesis. I do not expect to contribute to GMX directly from this repository, possibly via other created repository if so. Currently I have applied the BSD-3 clause version, which I understand to be the most relevant and simple to use. Choice is not set-in stone it appears, however if changing I understand one need to notify everyone that has taken part of, or are using the code. The BSD-3 do appears to be one of the most popular for open-source code and compatible between different softwares. I thought of using LGPL2 since GMX uses that, however BSD-3 does appear more simple to understand. The only innovative scripts including GMX are just linux bash/automatic scripts that make the simulation of replicas straightforward. Can I share these script under the BSD-3 license, even though technically they are modified scripts using standard gmx commands (not altering the original gmx software v.5.0.4)? Can I share some of the GMX code (parameter files etc) and some of the original GMX simulated solvated protein data (in addition to data calculated/graphed by matplotlib etc), at my github repository with no issues between BSD-3 license and LGPL2? The other python, and VMD/tcl softwares I do not see any issue with. Are there any clash with these above-mentioned softwares to be aware of? Any other insights anyone else has here about open-source licensing when distributing code? *Kind regards,* *Dr. Henry P.A. Wittler* *Department of Chemistry and Physics, LIMS, La Trobe University, MelbourneWorking in Ludvika, Sweden* *Skype: henry.wittler* Researchgate & Linkedin linkedin.com/in/henry-per-andreas-wittler-b03256191 From 15110700076 at fudan.edu.cn Fri Feb 21 11:41:55 2020 From: 15110700076 at fudan.edu.cn (Qing Liu) Date: Fri, 21 Feb 2020 10:41:55 -0000 Subject: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? Message-ID: <7222d988.fcee.170673aca8d.Coremail.15110700076@fudan.edu.cn> Dear Gromacs users, I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: Step 2029: The total potential energy is nan, which is not finite. The LJ and electrostatic contributions to the energy are 746119 and -5.71229e+06, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal. How should I do to solve the problem? -- Best wishes, ------------------------------------------------------------ Qing Liu Fudan Univ. Mobile: +86?13358129621 E-mail: 15110700076 at fudan.edu.cn From faizanabulqais at gmail.com Fri Feb 21 12:14:43 2020 From: faizanabulqais at gmail.com (Faizan Abul Qais) Date: Fri, 21 Feb 2020 11:14:43 -0000 Subject: [gmx-users] Regarding gpu acceleration Message-ID: Dear sir, I am trying to use gpu for gromacs. It gives error as "cuda is depracted". I am using Ubuntu 18.04.4 Cudua toolkit 10.2 Gromacs 2018.1 gcc version 7.4 Nvidia driver version 435 Nvidia GTX GeForce 1050 Ti Does these Versions support gpu acceleration? Plz help. From jalemkul at vt.edu Fri Feb 21 15:21:46 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 21 Feb 2020 14:21:46 -0000 Subject: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? In-Reply-To: <7222d988.fcee.170673aca8d.Coremail.15110700076@fudan.edu.cn> References: <7222d988.fcee.170673aca8d.Coremail.15110700076@fudan.edu.cn> Message-ID: On 2/21/20 5:11 AM, Qing Liu wrote: > Dear Gromacs users, > I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: > > > > > > Step 2029: The total potential energy is nan, which is not finite. The LJ and > electrostatic contributions to the energy are 746119 and -5.71229e+06, > respectively. A non-finite potential energy can be caused by overlapping > interactions in bonded interactions or very large or Nan coordinate values. > Usually this is caused by a badly- or non-equilibrated initial configuration, > incorrect interactions or parameters in the topology. > > > I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal. How should I do to solve the problem? > Your initial configuration is unreasonable as you have a massive LJ repulsion. How did you construct the coordinates of the system? Likely energy minimization will have reported unreasonable forces, as well. -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 dburns at iastate.edu Fri Feb 21 16:48:25 2020 From: dburns at iastate.edu (Daniel Burns) Date: Fri, 21 Feb 2020 15:48:25 -0000 Subject: [gmx-users] REMD stall out In-Reply-To: References: Message-ID: This was not actually the solution. Wanted to follow up in case someone else is experiencing this problem. We are reinstalling the openmp version. On Thu, Feb 20, 2020 at 3:10 PM Daniel Burns wrote: > Hi again, > > It seems including our openmp module was responsible for the issue the > whole time. When I submit the job only loading pmix and gromacs, replica > exchange proceeds. > > Thank you, > > Dan > > On Mon, Feb 17, 2020 at 9:09 AM Mark Abraham > wrote: > >> Hi, >> >> That could be caused by configuration of the parallel file system or MPI >> on >> your cluster. If only one file descriptor is available per node to an MPI >> job, then your symptoms are explained. Some kinds of compute jobs follow >> such a model, so maybe someone optimized something for that. >> >> Mark >> >> On Mon, 17 Feb 2020 at 15:56, Daniel Burns wrote: >> >> > HI Szilard, >> > >> > I've deleted all my output but all the writing to the log and console >> stops >> > around the step noting the domain decomposition (or other preliminary >> > task). It is the same with or without Plumed - the TREMD with Gromacs >> only >> > was the first thing to present this issue. >> > >> > I've discovered that if each replica is assigned its own node, the >> > simulations proceed. If I try to run several replicas on each node >> > (divided evenly), the simulations stall out before any trajectories get >> > written. >> > >> > I have tried many different -np and -ntomp options as well as several >> slurm >> > job submission scripts with node/ thread configurations but multiple >> > simulations per node will not work. I need to be able to run several >> > replicas on the same node to get enough data since it's hard to get more >> > than 8 nodes (and as a result, replicas). >> > >> > Thanks for your reply. >> > >> > -Dan >> > >> > On Tue, Feb 11, 2020 at 12:56 PM Daniel Burns >> wrote: >> > >> > > Hi, >> > > >> > > I continue to have trouble getting an REMD job to run. It never >> makes it >> > > to the point that it generates trajectory files but it never gives any >> > > error either. >> > > >> > > I have switched from a large TREMD with 72 replicas to the Plumed >> > > Hamiltonian method with only 6 replicas. Everything is now on one >> node >> > and >> > > each replica has 6 cores. I've turned off the dynamic load balancing >> on >> > > this attempt per the recommendation from the Plumed site. >> > > >> > > Any ideas on how to troubleshoot? >> > > >> > > Thank you, >> > > >> > > Dan >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe 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 15110700076 at fudan.edu.cn Fri Feb 21 19:01:43 2020 From: 15110700076 at fudan.edu.cn (Qing Liu) Date: Fri, 21 Feb 2020 18:01:43 -0000 Subject: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? In-Reply-To: References: Message-ID: <6388d1d4.de7.17068e9400c.Coremail.15110700076@fudan.edu.cn> Dear Justin Lemkul, Thanks for your reply. I just downloaded the Cryo-EM structure of the dimer from RCSB, added missing residues using Modeller and built systems by the following commands: gmx pdb2gmx -f dimer.pdb -o dimer.gro -p dimer.top -water tip3p -ff amber99sb-ildn -ignh gmx editconf -f dimer.gro -o vac-min-pbc.gro -bt cubic -d 1.5 -c gmx solvate -cp vac-min-pbc.gro -cs spc216.gro -p dimer.top -o vac-min-pbc-solv.gro gmx grompp -v -f sol-min.mdp -c vac-min-pbc-solv.gro -p dimer.top -o vac-min-pbc-solv.tpr gmx genion -s vac-min-pbc-solv.tpr -o vac-min-pbc-solv-salt.gro -conc 0.15 -neutral -pname NA -nname CL -p dimer.top gmx grompp -f sol-min.mdp -c vac-min-pbc-solv-salt.gro -p dimer.top -o vac-min-pbc-solv-salt-min.tpr gmx mdrun -v -deffnm vac-min-pbc-solv-salt-min gmx grompp -f pr-md.mdp -c vac-min-pbc-solv-salt-min.gro -p dimer.top -o pr-md.tpr -r vac-min-pbc-solv-salt-min.gro gmx mdrun -nb gpu -v -deffnm pr-md The contents of sol-min.mdp file are: ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) sc-coul = yes The log file of energy minimization shows: Steepest Descents converged to machine precision in 2108 steps, but did not reach the requested Fmax < 1. Potential Energy = -2.0181694e+07 Maximum force = 3.4778253e+02 on atom 114839 Norm of force = 3.9966155e+01 The contents of pr-md.mdp are: title = PR MD define =-DPOSRES ;run control integrator =md tinit =0 dt =0.002 nsteps =500000 comm_mode =Linear nstcomm =10 comm_grps =System ;output control nstxout =0 nstvout =0 nstlog =50000 nstcalcenergy =1 nstenergy =50000 nstxtcout =50000 xtc_grps =System energygrps =System ;neighbor searching nstlist =10 ns_type =grid pbc =xyz rlist =1.4 ;electrostatics coulombtype =PME rcoulomb =1.4 ;vdw vdwtype =Cut-off rvdw =1.4 dispCorr =EnerPres ;Ewald fourierspacing =0.1 pme_order =4 ewald_rtol =1e-5 ;temperature coupling tcoupl =v-rescale tc_grps =System tau_t =0.1 ref_t =200 ;velocity generation gen-vel =no ;bonds constraints =all-bonds constraint_algorithm =SHAKE shake-tol =0.0001 morse =no continuation =yes sc-coul =yes The pr-md.log shows: Fatal error: Step 2460: The total potential energy is nan, which is not finite. The LJ and electrostatic contributions to the energy are 3.25168e+06 and -1.99067e+07, respectively. A non-finite potential energy can be caused by overlapping interactions in bonded interactions or very large or Nan coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. -- Best wishes, ------------------------------------------------------------ Qing Liu Fudan Univ. Mobile: +86?13358129621 E-mail: 15110700076 at fudan.edu.cn >Message: 5 >Date: Fri, 21 Feb 2020 09:21:34 -0500 >From: Justin Lemkul >To: gmx-users at gromacs.org >Subject: Re: [gmx-users] How to avoid the infinite potential energy in > simulations of dimers? >Message-ID: >Content-Type: text/plain; charset=gbk; format=flowed > > > >On 2/21/20 5:11 AM, Qing Liu wrote: >> Dear Gromacs users, >> I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: >> >> >> >> >> >> Step 2029: The total potential energy is nan, which is not finite. The LJ and >> electrostatic contributions to the energy are 746119 and -5.71229e+06, >> respectively. A non-finite potential energy can be caused by overlapping >> interactions in bonded interactions or very large or Nan coordinate values. >> Usually this is caused by a badly- or non-equilibrated initial configuration, >> incorrect interactions or parameters in the topology. >> >> >> I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal. How should I do to solve the problem? >> > >Your initial configuration is unreasonable as you have a massive LJ >repulsion. How did you construct the coordinates of the system? Likely >energy minimization will have reported unreasonable forces, as well. > >-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 Fri Feb 21 21:41:08 2020 From: 272699575 at qq.com (=?gb18030?B?WkhBTkcgQ2hlbmc=?=) Date: Fri, 21 Feb 2020 20:41:08 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx Message-ID: I want to run more than 300 MD, each with a different PDB (more precisely, variants derived from a same wild type). I need to manually assign the protonation states using the "-inter" option every time, which is impossible for more than 300 times.  gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge interactive  The protonation states come from the pdb2pqr website. Is there an alternative way to obtain the .gro file by providing the necessary inputs (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding .gro files? I know the "echo" could not work for the charge assignment. It would be ultimately possible if I can understand the fundamental codes behind "pdb2gmx", then write a batch code to process multiple PDB files at once. But is there a simpler route? From mark.j.abraham at gmail.com Sat Feb 22 09:45:47 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 22 Feb 2020 08:45:47 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx In-Reply-To: References: Message-ID: Hi, Echo works just fine - you just need a way to script what input it injects to the stdin of pdb2gmx. That's logic you need for any solution so is probably easiest. The expect tool may be another option. Mark On Fri., 21 Feb. 2020, 21:41 ZHANG Cheng, <272699575 at qq.com> wrote: > I want to run more than 300 MD, each with a different PDB (more precisely, > variants derived from a same wild type). I need to manually assign the > protonation states using the "-inter" option every time, which is > impossible for more than 300 times.  > > > gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce  > -inter  -ignh -merge interactive  > > > The protonation states come from the pdb2pqr website. Is there an > alternative way to obtain the .gro file by providing the necessary inputs > (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding > .gro files? > > > I know the "echo" could not work for the charge assignment. > > > It would be ultimately possible if I can understand the fundamental codes > behind "pdb2gmx", then write a batch code to process multiple PDB files at > once. But is there a simpler route? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Sat Feb 22 14:06:52 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Sat, 22 Feb 2020 13:06:52 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx In-Reply-To: References: Message-ID: Thank you Mark! Sorry could you please explain the details of "stdin" of "pdb2gmx"? Is there a link for it? I think "echo" only works for choosing the force field, but not work for the charge assignment.  e.g. when I use: echo 15 0 0 0 0 | gmx pdb2gmx  -f protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge interactive I got error message: Which GLUTAMINE type do you want for residue 3 0. Not protonated (charge 0) (GLN) 1. Protonated (charge +1) (QLN) Type a number: ------------------------------------------------------- Program:     gmx pdb2gmx, version 2020-beta2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130) Fatal error: Answer me for res GLUTAMINE 3! ------------------ Original ------------------ From: "ZHANG Cheng"<272699575 at qq.com>; Date: Sat, Feb 22, 2020 04:39 AM To: "gromacs.org_gmx-users" References: Message-ID: Thank you Justin, just sharing the sample script here: -------------------- #!/bin/bash for i in {1..n} do j=$((i+1)) gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr gmx mdrun -deffnm nvt${j} gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr gmx mdrun -deffnm md${j} done ---------------------- Question: Now that I have n .edr files, is there a script I can write to extract say potential energy from these n files? Thank you for your time and knowledge, Neena ________________________________ From: Neena Susan Eappen Sent: Saturday, February 15, 2020 4:44 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] Script for looping n simulations Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. Many thanks, Neena From miro.astore at gmail.com Sat Feb 22 17:05:26 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sat, 22 Feb 2020 16:05:26 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: I have something like this on my github. https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi File is memb0.pbs let me know if you have any questions. On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, < neena.susaneappen at mail.utoronto.ca> wrote: > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation > (equilibration and production) n times, with each cycle starting with > structure from the end of previous cycle. > > Many thanks, > Neena > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 miro.astore at gmail.com Sat Feb 22 17:05:26 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sat, 22 Feb 2020 16:05:26 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: I have something like this on my github. https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi File is memb0.pbs let me know if you have any questions. On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, < neena.susaneappen at mail.utoronto.ca> wrote: > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation > (equilibration and production) n times, with each cycle starting with > structure from the end of previous cycle. > > Many thanks, > Neena > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 neena.susaneappen at mail.utoronto.ca Sat Feb 22 17:28:46 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Sat, 22 Feb 2020 16:28:46 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: , Message-ID: Thank you Miro, but I don't think I found what I wanted in your script. Let me be more clear: I ran n simulations in a loop, I have corresponding n energy files (.edr). I want to extract potential energy from each file. How would I go about that with a script? Many thanks, Neena ________________________________ From: Neena Susan Eappen Sent: Saturday, February 22, 2020 2:41 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] Script for looping n simulations Thank you Justin, just sharing the sample script here: -------------------- #!/bin/bash for i in {1..n} do j=$((i+1)) gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr gmx mdrun -deffnm nvt${j} gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr gmx mdrun -deffnm md${j} done ---------------------- Question: Now that I have n .edr files, is there a script I can write to extract say potential energy from these n files? Thank you for your time and knowledge, Neena ________________________________ From: Neena Susan Eappen Sent: Saturday, February 15, 2020 4:44 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] Script for looping n simulations Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. Many thanks, Neena From jalemkul at vt.edu Sat Feb 22 19:47:58 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 22 Feb 2020 18:47:58 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: On 2/22/20 9:41 AM, Neena Susan Eappen wrote: > Thank you Justin, just sharing the sample script here: > -------------------- > #!/bin/bash > for i in {1..n} > do j=$((i+1)) > gmx grompp -f nvt.mdp -c em${i}.gro -r em${i}.gro -p topol.top -o nvt${j}.tpr > gmx mdrun -deffnm nvt${j} > gmx grompp -f md.mdp -c nvt${j}.gro -t nvt${j}.cpt -p topol.top -o md${j}.tpr > gmx mdrun -deffnm md${j} > done > ---------------------- > Question: Now that I have n .edr files, is there a script I can write to extract say potential energy from these n files? Apply the exact same logic. Loop over calls to gmx energy. See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts -Justin > Thank you for your time and knowledge, > Neena > > > ________________________________ > From: Neena Susan Eappen > Sent: Saturday, February 15, 2020 4:44 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] Script for looping n simulations > > Hello gromacs users, > > I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. > > Many thanks, > 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 jalemkul at vt.edu Sat Feb 22 19:49:12 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 22 Feb 2020 18:49:12 -0000 Subject: [gmx-users] How to avoid the infinite potential energy in simulations of dimers? In-Reply-To: <6388d1d4.de7.17068e9400c.Coremail.15110700076@fudan.edu.cn> References: <6388d1d4.de7.17068e9400c.Coremail.15110700076@fudan.edu.cn> Message-ID: <7b8d3947-20d2-8172-7018-52496e9c2a83@vt.edu> On 2/21/20 1:01 PM, Qing Liu wrote: > Dear Justin Lemkul, > > Thanks for your reply. I just downloaded the Cryo-EM structure of the dimer from RCSB, added missing residues using Modeller and built systems by the following commands: > > > > gmx pdb2gmx -f dimer.pdb -o dimer.gro -p dimer.top -water tip3p -ff amber99sb-ildn -ignh > gmx editconf -f dimer.gro -o vac-min-pbc.gro -bt cubic -d 1.5 -c > gmx solvate -cp vac-min-pbc.gro -cs spc216.gro -p dimer.top -o vac-min-pbc-solv.gro > gmx grompp -v -f sol-min.mdp -c vac-min-pbc-solv.gro -p dimer.top -o vac-min-pbc-solv.tpr > gmx genion -s vac-min-pbc-solv.tpr -o vac-min-pbc-solv-salt.gro -conc 0.15 -neutral -pname NA -nname CL -p dimer.top > gmx grompp -f sol-min.mdp -c vac-min-pbc-solv-salt.gro -p dimer.top -o vac-min-pbc-solv-salt-min.tpr > gmx mdrun -v -deffnm vac-min-pbc-solv-salt-min > gmx grompp -f pr-md.mdp -c vac-min-pbc-solv-salt-min.gro -p dimer.top -o pr-md.tpr -r vac-min-pbc-solv-salt-min.gro > gmx mdrun -nb gpu -v -deffnm pr-md > > > The contents of sol-min.mdp file are: > > > ; Define can be used to control processes > define = -DFLEXIBLE > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol > nsteps = 5000 ; Maximum number of (minimization) steps to perform > nstenergy = 1 ; Write energies to disk every nstenergy steps > energygrps = System ; Which energy group(s) to write to disk > ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions > ns_type = grid ; Method to determine neighbor list (simple, grid) > coulombtype = cut-off ; Treatment of long range electrostatic interactions > rcoulomb = 1.0 ; long range electrostatic cut-off > rvdw = 1.0 ; long range Van der Waals cut-off > constraints = none ; Bond types to replace by constraints > pbc = xyz ; Periodic Boundary Conditions (yes/no) > sc-coul = yes > > > > The log file of energy minimization shows: > Steepest Descents converged to machine precision in 2108 steps, > but did not reach the requested Fmax < 1. > Potential Energy = -2.0181694e+07 > Maximum force = 3.4778253e+02 on atom 114839 > Norm of force = 3.9966155e+01 > > > The contents of pr-md.mdp are: > title = PR MD > define =-DPOSRES > ;run control > integrator =md > tinit =0 > dt =0.002 > nsteps =500000 > comm_mode =Linear > nstcomm =10 > comm_grps =System > ;output control > nstxout =0 > nstvout =0 > nstlog =50000 > nstcalcenergy =1 > nstenergy =50000 > nstxtcout =50000 > xtc_grps =System > energygrps =System > ;neighbor searching > nstlist =10 > ns_type =grid > pbc =xyz > rlist =1.4 > ;electrostatics > coulombtype =PME > rcoulomb =1.4 > ;vdw > vdwtype =Cut-off > rvdw =1.4 > dispCorr =EnerPres > ;Ewald > fourierspacing =0.1 > pme_order =4 > ewald_rtol =1e-5 > ;temperature coupling > tcoupl =v-rescale > tc_grps =System > tau_t =0.1 > ref_t =200 > ;velocity generation > gen-vel =no > ;bonds > constraints =all-bonds > constraint_algorithm =SHAKE > shake-tol =0.0001 > morse =no > continuation =yes > sc-coul =yes > > > > The pr-md.log shows: > > Fatal error: > Step 2460: The total potential energy is nan, which is not finite. The LJ and > electrostatic contributions to the energy are 3.25168e+06 and -1.99067e+07, > respectively. A non-finite potential energy can be caused by overlapping > interactions in bonded interactions or very large or Nan coordinate values. > Usually this is caused by a badly- or non-equilibrated initial configuration, > incorrect interactions or parameters in the topology. > > You're changing cutoffs, treatment of constraints, etc. at various points in your protocol. Don't do that. Be consistent. You probably have a water molecule that got stretched too far via -DFLEXIBLE and now it can't be constrained properly. -Justin > > > > > > -- > > > Best wishes, > > ------------------------------------------------------------ > > Qing Liu > > Fudan Univ. > > Mobile: +86?13358129621 > > E-mail: 15110700076 at fudan.edu.cn > > > > > > >> Message: 5 >> Date: Fri, 21 Feb 2020 09:21:34 -0500 >> From: Justin Lemkul >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] How to avoid the infinite potential energy in >> simulations of dimers? >> Message-ID: >> Content-Type: text/plain; charset=gbk; format=flowed >> >> >> >> On 2/21/20 5:11 AM, Qing Liu wrote: >>> Dear Gromacs users, >>> I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages, they will crash with the following: >>> >>> >>> >>> >>> >>> Step 2029: The total potential energy is nan, which is not finite. The LJ and >>> electrostatic contributions to the energy are 746119 and -5.71229e+06, >>> respectively. A non-finite potential energy can be caused by overlapping >>> interactions in bonded interactions or very large or Nan coordinate values. >>> Usually this is caused by a badly- or non-equilibrated initial configuration, >>> incorrect interactions or parameters in the topology. >>> >>> >>> I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal. How should I do to solve the problem? >>> >> Your initial configuration is unreasonable as you have a massive LJ >> repulsion. How did you construct the coordinates of the system? Likely >> energy minimization will have reported unreasonable forces, as well. >> >> -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 bonjour899 at 126.com Sun Feb 23 04:33:14 2020 From: bonjour899 at 126.com (bonjour899) Date: Sun, 23 Feb 2020 03:33:14 -0000 Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory Message-ID: <5324bb38.76fa.170701adc1e.Coremail.bonjour899@126.com> I also tried to restricting to different GPU using -gpu_id, but still with the same error. I've also posting my question on https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/ Following is the output of nvidia-smi: +-----------------------------------------------------------------------------+ | NVIDIA-SMI 440.33.01 Driver Version: 440.33.01 CUDA Version: 10.2 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... On | 00000000:04:00.0 Off | 0 | | N/A 35C P0 34W / 250W | 16008MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 1 Tesla P100-PCIE... On | 00000000:06:00.0 Off | 0 | | N/A 35C P0 28W / 250W | 10MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 2 Tesla P100-PCIE... On | 00000000:07:00.0 Off | 0 | | N/A 35C P0 33W / 250W | 16063MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 3 Tesla P100-PCIE... On | 00000000:08:00.0 Off | 0 | | N/A 36C P0 29W / 250W | 10MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 4 Quadro P4000 On | 00000000:0B:00.0 Off | N/A | | 46% 27C P8 8W / 105W | 12MiB / 8119MiB | 0% Default | +-------------------------------+----------------------+----------------------+ ? +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | 0 20497 C /usr/bin/python3 5861MiB | | 0 24503 C /usr/bin/python3 10137MiB | | 2 23162 C /home/appuser/Miniconda3/bin/python 16049MiB | +-----------------------------------------------------------------------------+ -------- Forwarding messages -------- From: "bonjour899" Date: 2020-02-20 10:30:36 To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: cudaFuncGetAttributes failed: out of memory Hello, I have encountered a weird problem. I've been using GROMACS with GPU on a server and always performance good. However when I just reran a job today and suddenly got this error: Command line: gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3? Back Off! I just backed up pull.log to ./#pull.log.1# ------------------------------------------------------- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) ? Fatal error: cudaFuncGetAttributes failed: out of memory ? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems the GPU is 0 occupied and I can run other apps with GPU, but I cannot run GROMACS mdrun anymore, even if doing energy minimization. From bonjour899 at 126.com Sun Feb 23 07:49:15 2020 From: bonjour899 at 126.com (bonjour899) Date: Sun, 23 Feb 2020 06:49:15 -0000 Subject: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory Message-ID: <40cf1027.940f.17070ce7162.Coremail.bonjour899@126.com> I think I've temporarily solved this problem. Only when I use CUDA_VISIABLE_DEVICE to block the memory-almost-fully-occupied GPUs, I can run GROMACS smoothly (using -gpu_id only is useless). I think there may be some bug in GROMACS's GPU usage model in a multi-GPU environment (It seems like as long as one of the GPUs is fully occupied, GROMACS cannot submit to any GPUs and return an error with "cudaFuncGetAttributes failed: out of memory"). Best regards, W -------- Forwarding messages -------- From: "bonjour899" Date: 2020-02-23 11:32:53 To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory I also tried to restricting to different GPU using -gpu_id, but still with the same error. I've also posting my question on https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/ Following is the output of nvidia-smi: +-----------------------------------------------------------------------------+ | NVIDIA-SMI 440.33.01 Driver Version: 440.33.01 CUDA Version: 10.2 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... On | 00000000:04:00.0 Off | 0 | | N/A 35C P0 34W / 250W | 16008MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 1 Tesla P100-PCIE... On | 00000000:06:00.0 Off | 0 | | N/A 35C P0 28W / 250W | 10MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 2 Tesla P100-PCIE... On | 00000000:07:00.0 Off | 0 | | N/A 35C P0 33W / 250W | 16063MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 3 Tesla P100-PCIE... On | 00000000:08:00.0 Off | 0 | | N/A 36C P0 29W / 250W | 10MiB / 16280MiB | 0% Default | +-------------------------------+----------------------+----------------------+ | 4 Quadro P4000 On | 00000000:0B:00.0 Off | N/A | | 46% 27C P8 8W / 105W | 12MiB / 8119MiB | 0% Default | +-------------------------------+----------------------+----------------------+ ? +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | 0 20497 C /usr/bin/python3 5861MiB | | 0 24503 C /usr/bin/python3 10137MiB | | 2 23162 C /home/appuser/Miniconda3/bin/python 16049MiB | +-----------------------------------------------------------------------------+ -------- Forwarding messages -------- From: "bonjour899" Date: 2020-02-20 10:30:36 To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: cudaFuncGetAttributes failed: out of memory Hello, I have encountered a weird problem. I've been using GROMACS with GPU on a server and always performance good. However when I just reran a job today and suddenly got this error: Command line: gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3? Back Off! I just backed up pull.log to ./#pull.log.1# ------------------------------------------------------- Program: gmx mdrun, version 2019.4 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) ? Fatal error: cudaFuncGetAttributes failed: out of memory ? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems the GPU is 0 occupied and I can run other apps with GPU, but I cannot run GROMACS mdrun anymore, even if doing energy minimization. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 Sun Feb 23 11:46:39 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sun, 23 Feb 2020 10:46:39 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx In-Reply-To: References: Message-ID: Hi, On Sat, 22 Feb 2020 at 14:07, ZHANG Cheng <272699575 at qq.com> wrote: > Thank you Mark! Sorry could you please explain the details of "stdin" of > "pdb2gmx"? Is there a link for it? > The stdin stream is a fundamental concept in how unix terminals work. The echo tool fills that stream for pdb2gmx to consume. This is a pattern followed by thousands of tools. > I think "echo" only works for choosing the force field, but not work for > the charge assignment.  > > > e.g. when I use: > > > echo 15 0 0 0 0 | gmx pdb2gmx  -f protein.pdb -o > protein_processed.gro -water spce  -inter  -ignh -merge > interactive > > > I got error message: > > > Which GLUTAMINE type do you want for residue 3 > 0. Not protonated (charge 0) (GLN) > 1. Protonated (charge +1) (QLN) > Type a number: > ------------------------------------------------------- > Program:     gmx pdb2gmx, version 2020-beta2 > Please install a proper version of GROMACS, not a pre-release one, which we asked you not to use for scientific work. > Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130) > Fatal error: > That's probably because you haven't given enough numbers to echo to satisfy the needs of pdb2gmx, but I can't tell on the information you've given. Mark > Answer me for res GLUTAMINE 3! > > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Sat, Feb 22, 2020 04:39 AM > To: "gromacs.org_gmx-users" >; > Cc: "ZHANG Cheng"<272699575 at qq.com>; > Subject: Automatically assign the protonation states for pdb2gmx > > > > I want to run more than 300 MD, each with a different PDB (more precisely, > variants derived from a same wild type). I need to manually assign the > protonation states using the "-inter" option every time, which is > impossible for more than 300 times. > > > gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce  > -inter  -ignh -merge interactive > > > The protonation states come from the pdb2pqr website. Is there an > alternative way to obtain the .gro file by providing the necessary inputs > (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding > .gro files? > > > I know the "echo" could not work for the charge assignment. > > > It would be ultimately possible if I can understand the fundamental codes > behind "pdb2gmx", then write a batch code to process multiple PDB files at > once. But is there a simpler route? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Sun Feb 23 11:46:39 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sun, 23 Feb 2020 10:46:39 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx In-Reply-To: References: Message-ID: Hi, On Sat, 22 Feb 2020 at 14:07, ZHANG Cheng <272699575 at qq.com> wrote: > Thank you Mark! Sorry could you please explain the details of "stdin" of > "pdb2gmx"? Is there a link for it? > The stdin stream is a fundamental concept in how unix terminals work. The echo tool fills that stream for pdb2gmx to consume. This is a pattern followed by thousands of tools. > I think "echo" only works for choosing the force field, but not work for > the charge assignment.  > > > e.g. when I use: > > > echo 15 0 0 0 0 | gmx pdb2gmx  -f protein.pdb -o > protein_processed.gro -water spce  -inter  -ignh -merge > interactive > > > I got error message: > > > Which GLUTAMINE type do you want for residue 3 > 0. Not protonated (charge 0) (GLN) > 1. Protonated (charge +1) (QLN) > Type a number: > ------------------------------------------------------- > Program:     gmx pdb2gmx, version 2020-beta2 > Please install a proper version of GROMACS, not a pre-release one, which we asked you not to use for scientific work. > Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130) > Fatal error: > That's probably because you haven't given enough numbers to echo to satisfy the needs of pdb2gmx, but I can't tell on the information you've given. Mark > Answer me for res GLUTAMINE 3! > > > > > > ------------------ Original ------------------ > From: "ZHANG Cheng"<272699575 at qq.com>; > Date: Sat, Feb 22, 2020 04:39 AM > To: "gromacs.org_gmx-users" >; > Cc: "ZHANG Cheng"<272699575 at qq.com>; > Subject: Automatically assign the protonation states for pdb2gmx > > > > I want to run more than 300 MD, each with a different PDB (more precisely, > variants derived from a same wild type). I need to manually assign the > protonation states using the "-inter" option every time, which is > impossible for more than 300 times. > > > gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce  > -inter  -ignh -merge interactive > > > The protonation states come from the pdb2pqr website. Is there an > alternative way to obtain the .gro file by providing the necessary inputs > (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding > .gro files? > > > I know the "echo" could not work for the charge assignment. > > > It would be ultimately possible if I can understand the fundamental codes > behind "pdb2gmx", then write a batch code to process multiple PDB files at > once. But is there a simpler route? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 rajawat.manindersingh at gmail.com Sun Feb 23 13:32:21 2020 From: rajawat.manindersingh at gmail.com (manindersingh rajawat) Date: Sun, 23 Feb 2020 12:32:21 -0000 Subject: [gmx-users] error occurred during simulation of HRAS protein (PDB ID: 3K8Y) in the presence of GTP, Calcium acetate, and crystal waters Message-ID: Dear all, I am trying to simulate *HRAS protein (PDB ID: 3K8Y)* in the presence of water in* GROMACS5.1.3* using *charmm36_nov2018 forcefield*. The protein has bound GTP analog GNP in the active site and calcium acetate in the allosteric site. I have changed the GNP to GTP. Separately saved PDB files of GTP, and protein (containing protein, calcium and acetate ions and crystal waters). Calcium and acetate ions of allosteric site and crystal waters were retained. Others ions were deleted. Calcium ion residue and atom was renamed as CAL ( original CA) and acetate residue as ACET (original ACT). Generated the topology parameters for GTP by swissparam. During simulation setup error occurred in the very first topology generation step. *command used:* gmx pdb2gmx -f receptor_water_calciumacetate.pdb -o processed.pdb -water spc -ignh *Fatal error:* *Atom C in residue ACET 0 was not found in rtp entry ACET with 7 atoms* *while sorting atoms.* Please suggest what to do next and how to rectify the above error. Or another way to setup this simulation. I have checked the merged.rtp file in charmm36 forcefield folder, it contains the following description for ACET: [ ACET ] [ atoms ] C1 CG331 -0.370 0 C2 CG2O3 0.620 1 H1 HGA3 0.090 2 H2 HGA3 0.090 3 H3 HGA3 0.090 4 O1 OG2D2 -0.760 5 O2 OG2D2 -0.760 6 [ bonds ] C1 H1 C1 H2 C1 H3 C1 C2 C2 O1 C2 O2 [ impropers ] C2 O2 O1 C1 Coordinates of calcium and acetate ion in the receptor_water_calciumacetate.pdb ATOM 1322 NE2 HIS A 166 -28.827 57.264 -83.683 1.00 33.20 N ATOM 1323 OXT HIS A 166 -34.901 59.235 -83.148 1.00 41.11 O *HETATM 1359 CAL CAL A 169 -24.508 52.328 -83.059 1.00 26.85 CA* *HETATM 1361 C ACET A 719 -24.066 52.359 -79.976 1.00 29.56 C * *HETATM 1362 O ACET A 719 -25.026 52.986 -80.477 1.00 29.41 O * *HETATM 1363 OXT ACET A 719 -23.241 51.869 -80.781 1.00 29.13 O * *HETATM 1364 CH3 ACET A 719 -23.910 52.206 -78.493 1.00 29.01 C* HETATM 1365 O HOH A 171 -0.065 68.481 -70.366 1.00 31.55 O HETATM 1366 O HOH A 172 -9.411 68.271 -67.530 1.00 15.88 O HETATM 1367 O HOH A 173 -13.003 66.200 -68.672 1.00 15.10 O Thanks, Maninder -- Maninder Singh Research Fellow, LSN-104, Computational Biology and Bioinformatics Unit, Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur road, Lucknow India-226031 M: +919129206276 Email: rajawat.manindersingh at gmail.com From 272699575 at qq.com Sun Feb 23 14:13:33 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Sun, 23 Feb 2020 13:13:33 -0000 Subject: [gmx-users] Automatically assign the protonation states for pdb2gmx In-Reply-To: References: Message-ID: Thank you Mark! I have tried version 2019.3 as well.  Again, the manual input works all fine https://github.com/lanselibai/gromacs-20200223/blob/master/manually_type but the command using "echo" still had the same problem https://github.com/lanselibai/gromacs-20200223/blob/master/echo I also uploaded my protein.pdb at (it would be great if you can test it?) https://github.com/lanselibai/gromacs-20200223/blob/master/protein.pdb but I think it is not the pdb issue, also not the Gromacs version problem. I took a look at the meaning of stdin, stdout, and stderr. So do you mean "echo" is used in the "stdin"? Basically, do you mean it should be possible to use "echo"? I am sure I have supplied enough numbers to the "echo". echo 15 0 0 0 0 |gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive Here,  ) "15" is to choose the OPLS forcefield; ) The second and third number "0" is to assign the charges; ) The last two "0" is to select the terminus type. ------------------ Original ------------------ From: "Mark Abraham" References: Message-ID: Thank you Mark! I have tried version 2019.3 as well.  Again, the manual input works all fine https://github.com/lanselibai/gromacs-20200223/blob/master/manually_type but the command using "echo" still had the same problem https://github.com/lanselibai/gromacs-20200223/blob/master/echo I also uploaded my protein.pdb at (it would be great if you can test it?) https://github.com/lanselibai/gromacs-20200223/blob/master/protein.pdb but I think it is not the pdb issue, also not the Gromacs version problem. I took a look at the meaning of stdin, stdout, and stderr. So do you mean "echo" is used in the "stdin"? Basically, do you mean it should be possible to use "echo"? I am sure I have supplied enough numbers to the "echo". echo 15 0 0 0 0 |gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive Here,  ) "15" is to choose the OPLS forcefield; ) The second and third number "0" is to assign the charges; ) The last two "0" is to select the terminus type. ------------------ Original ------------------ From: "Mark Abraham" References: Message-ID: The error message is informing you of what the issue is, pdb2gmx is expecting the atom names within the coordinate file to match exactly what is specified in the residue database (rtp) http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#atom-x-in-residue-yyy-not-found-in-rtp-entry Your rtp entry shows that it expects the atoms to be named "C1 C2 H1 H2 ..." and then your coordinate file shows they are actually named "C O OXT ..." 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 Sun, 23 Feb 2020 at 23:32, manindersingh rajawat < rajawat.manindersingh at gmail.com> wrote: > Dear all, > I am trying to simulate *HRAS protein (PDB ID: 3K8Y)* in the presence of > water in* GROMACS5.1.3* using *charmm36_nov2018 forcefield*. The protein > has bound GTP analog GNP in the active site and calcium acetate in the > allosteric site. I have changed the GNP to GTP. Separately saved PDB files > of GTP, and protein (containing protein, calcium and acetate ions and > crystal waters). Calcium and acetate ions of allosteric site and crystal > waters were retained. Others ions were deleted. Calcium ion residue and > atom was renamed as CAL ( original CA) and acetate residue as ACET > (original ACT). Generated the topology parameters for GTP by swissparam. > During simulation setup error occurred in the very first topology > generation step. > *command used:* > gmx pdb2gmx -f receptor_water_calciumacetate.pdb -o processed.pdb -water > spc -ignh > > *Fatal error:* > *Atom C in residue ACET 0 was not found in rtp entry ACET with 7 atoms* > *while sorting atoms.* > Please suggest what to do next and how to rectify the above error. Or > another way to setup this simulation. > I have checked the merged.rtp file in charmm36 forcefield folder, it > contains the following description for ACET: > [ ACET ] > [ atoms ] > C1 CG331 -0.370 0 > C2 CG2O3 0.620 1 > H1 HGA3 0.090 2 > H2 HGA3 0.090 3 > H3 HGA3 0.090 4 > O1 OG2D2 -0.760 5 > O2 OG2D2 -0.760 6 > [ bonds ] > C1 H1 > C1 H2 > C1 H3 > C1 C2 > C2 O1 > C2 O2 > [ impropers ] > C2 O2 O1 C1 > Coordinates of calcium and acetate ion in the > receptor_water_calciumacetate.pdb > ATOM 1322 NE2 HIS A 166 -28.827 57.264 -83.683 1.00 33.20 N > ATOM 1323 OXT HIS A 166 -34.901 59.235 -83.148 1.00 41.11 O > *HETATM 1359 CAL CAL A 169 -24.508 52.328 -83.059 1.00 26.85 CA* > *HETATM 1361 C ACET A 719 -24.066 52.359 -79.976 1.00 29.56 C * > *HETATM 1362 O ACET A 719 -25.026 52.986 -80.477 1.00 29.41 O * > *HETATM 1363 OXT ACET A 719 -23.241 51.869 -80.781 1.00 29.13 O * > *HETATM 1364 CH3 ACET A 719 -23.910 52.206 -78.493 1.00 29.01 C* > HETATM 1365 O HOH A 171 -0.065 68.481 -70.366 1.00 31.55 O > HETATM 1366 O HOH A 172 -9.411 68.271 -67.530 1.00 15.88 O > HETATM 1367 O HOH A 173 -13.003 66.200 -68.672 1.00 15.10 O > > Thanks, > Maninder > > > -- > Maninder Singh > Research Fellow, > LSN-104, Computational Biology and Bioinformatics Unit, > Molecular and Structural Biology Division, > CSIR-Central Drug Research Institute, > Sector-10, Janakipuram Extension, > Sitapur road, > Lucknow > India-226031 > M: +919129206276 > Email: rajawat.manindersingh at gmail.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 carlo.martinotti at postgrad.curtin.edu.au Mon Feb 24 06:42:43 2020 From: carlo.martinotti at postgrad.curtin.edu.au (Carlo Martinotti) Date: Mon, 24 Feb 2020 05:42:43 -0000 Subject: [gmx-users] Are parameters for NME group available for GROMOS 54a7? Message-ID: I'm looking to set up a simulation of a capped di-alanine in vacuum using GROMOS54a7, but I can't find the parameters for the NME group. It seems strange to me that there are no standard parameters for the capping group, anybody knows if they are available somewhere? Cheers, Carlo Martinotti From pragati2325 at gmail.com Mon Feb 24 07:58:58 2020 From: pragati2325 at gmail.com (Pragati Sharma) Date: Mon, 24 Feb 2020 06:58:58 -0000 Subject: [gmx-users] Which output of gmx energy represents stress Message-ID: Dear all, I am calculating stress-strain using uniaxial deformation with deform option. Which output of gmx energy represents stress *Is it Press-XX or VIR-XX,* or some other value.(supposing the deformation is in x direction) Thanks in advance Pragati From pragati2325 at gmail.com Mon Feb 24 08:12:49 2020 From: pragati2325 at gmail.com (Pragati Sharma) Date: Mon, 24 Feb 2020 07:12:49 -0000 Subject: [gmx-users] Fwd: Which output of gmx energy represents stress In-Reply-To: References: Message-ID: Dear all, I am calculating stress-strain using uniaxial deformation with deform option. Which output of gmx energy represents stress *Is it Press-XX or VIR-XX,* or some other value.(supposing the deformation is in x direction) Thanks in advance, Pragati From pall.szilard at gmail.com Mon Feb 24 17:44:08 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 24 Feb 2020 16:44:08 -0000 Subject: [gmx-users] GPU considerations for GROMACS In-Reply-To: References: Message-ID: Hi, Whether investing in one of the fastest or two medium-high end GPU depends on your workload: system size, type of run, single or multiple simulations, etc. If you have multiple simulations you can run independently or coupled only weakly in ensemble runs (e.g. using -multidir), multiple mid-tier GPUs will be a better investment. On the other hand, if single simulation performance is what you want to maximize and you have a relatively small simulation system (e.g. 50k atoms), you will be better off with a single fast GPU. Regarding your CPU choice, I suggest you consider alternatives: e.g. a Ryzen 3800X will cost a lot less and will be faster. Xeon generally does not have much benefit for the use-case in question. Cheers, -- Szil?rd On Tue, Feb 18, 2020 at 3:21 PM hairul.ikmal at gmail.com < hairul.ikmal at gmail.com> wrote: > Hello, > > Previously, I have helped building a workstation for my fellow > researcher who heavily uses GROMACS for his MD simulations, with the > following base specs: > > -CPU: 8 cores (Xeon E2278G) > -RAM: 32GB > -GPU: 1x RTX2080Ti > > > With this setup, he managed to shrink down each simulation runtime to, > say approximately 12 hours, compared to previous system (purely CPU > only, no GPU support), which took days to complete. > > > 1) Based on the current progress, we plan to build another system > (which will also run GROMACS most of the time) using the existing > workstation as reference. But currently we are unsure which setup > (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, > when running the same set of GROMACS simulation : > > > Option 1: > Retain same CPU, RAM and GPU specs (1x RTX2080Ti) > > > Option 2: > Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead > of 1x RTX2080Ti > > > 2) Besides building another system, we are considering to upgrade the > existing system, too. For example, assuming the system has the > expansion capability (enough PCI-e 16x slots, power supply), will > adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) > into existing setup will significantly cut down current runtime? If > yes, by how much time reduction can we expect generally with this > upgrade? > > > Appreciate if someone can share their thoughts and experience. > Thank you! > > > -Hairul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Feb 24 17:44:09 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 24 Feb 2020 16:44:09 -0000 Subject: [gmx-users] GPU considerations for GROMACS In-Reply-To: References: Message-ID: Hi, Whether investing in one of the fastest or two medium-high end GPU depends on your workload: system size, type of run, single or multiple simulations, etc. If you have multiple simulations you can run independently or coupled only weakly in ensemble runs (e.g. using -multidir), multiple mid-tier GPUs will be a better investment. On the other hand, if single simulation performance is what you want to maximize and you have a relatively small simulation system (e.g. 50k atoms), you will be better off with a single fast GPU. Regarding your CPU choice, I suggest you consider alternatives: e.g. a Ryzen 3800X will cost a lot less and will be faster. Xeon generally does not have much benefit for the use-case in question. Cheers, -- Szil?rd On Tue, Feb 18, 2020 at 3:21 PM hairul.ikmal at gmail.com < hairul.ikmal at gmail.com> wrote: > Hello, > > Previously, I have helped building a workstation for my fellow > researcher who heavily uses GROMACS for his MD simulations, with the > following base specs: > > -CPU: 8 cores (Xeon E2278G) > -RAM: 32GB > -GPU: 1x RTX2080Ti > > > With this setup, he managed to shrink down each simulation runtime to, > say approximately 12 hours, compared to previous system (purely CPU > only, no GPU support), which took days to complete. > > > 1) Based on the current progress, we plan to build another system > (which will also run GROMACS most of the time) using the existing > workstation as reference. But currently we are unsure which setup > (Option 1 vs Option 2) will GENERALLY give shortest/fastest runtime, > when running the same set of GROMACS simulation : > > > Option 1: > Retain same CPU, RAM and GPU specs (1x RTX2080Ti) > > > Option 2: > Retain same CPU and RAM specs, but GPU wise, use 2x RTX 2070S instead > of 1x RTX2080Ti > > > 2) Besides building another system, we are considering to upgrade the > existing system, too. For example, assuming the system has the > expansion capability (enough PCI-e 16x slots, power supply), will > adding another card (making it 2x RTX2080Ti instead of 1x RTX2080Ti) > into existing setup will significantly cut down current runtime? If > yes, by how much time reduction can we expect generally with this > upgrade? > > > Appreciate if someone can share their thoughts and experience. > Thank you! > > > -Hairul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Tue Feb 25 00:36:21 2020 From: dburns at iastate.edu (Daniel Burns) Date: Mon, 24 Feb 2020 23:36:21 -0000 Subject: [gmx-users] replica exchange 1% Message-ID: Hi, I'm using the Plumed plugin to perform a "Hamiltonian" replica exchange. I have histograms of the total energies of each system that share a huge overlap - on the order of 80%. Only a small subset of the residues have perturbed energy functions. Replica exchange attempts only happen every 2000 steps. Pressure coupling is every 5 steps. Despite the above, I am only experiencing successful exchanges 1% of the time. Any suggestions on what might be the reason for such low exchange probabilities? Thank you! Dan From sadafrani6 at gmail.com Tue Feb 25 00:55:45 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 24 Feb 2020 23:55:45 -0000 Subject: [gmx-users] How to calculate the dihedral angle as a function of time? Message-ID: Dear Gromacs users I want to calculate the dihedral angle over the simulation time. I tried following commands:- gmx mk_angndx -s topol.tpr -type dihedral which generates an index file for dihedral angles then running:- gmx angle -f md_prod.trr -n angle.ndx -type dihedral gives following group options, How can I identify these groups show which part of the system. I want to calculate the dihedral angle as a function of time in the simulation. Group 0 ( Phi=0.0_3_0.65) has 228 elements Group 1 ( Phi=0.0_1_0.84) has 8 elements Group 2 ( Phi=0.0_2_0.84) has 8 elements Group 3 ( Phi=0.0_3_1.67) has 16 elements Group 4 ( Phi=0.0_3_0.67) has 52 elements Group 5 ( Phi=0.0_1_1.05) has 96 elements Group 6 ( Phi=0.0_3_0.70) has 4 elements Group 7 (Phi=180.0_2_10.46) has 32 elements Group 8 ( Phi=0.0_1_8.37) has 16 elements Group 9 ( Phi=0.0_2_8.37) has 8 elements Group 10 ( Phi=0.0_2_1.13) has 8 elements Group 11 ( Phi=0.0_3_1.76) has 8 elements Group 12 (Phi=180.0_1_1.88) has 4 elements Group 13 (Phi=180.0_2_6.61) has 4 elements Group 14 (Phi=180.0_3_2.30) has 4 elements Group 15 ( Phi=0.0_1_3.35) has 4 elements Group 16 (Phi=180.0_3_0.33) has 4 elements Group 17 (Phi=180.0_2_15.17) has 96 elements Group 18 ( Phi=0.0_3_0.75) has 8 elements Group 19 (Phi=180.0_2_1.05) has 20 elements Group 20 (Phi=180.0_1_0.84) has 20 elements Group 21 ( Phi=0.0_3_0.63) has 32 elements Group 22 ( Phi=0.0_2_3.35) has 12 elements Group 23 ( Phi=0.0_3_0.67) has 28 elements Group 24 ( Phi=0.0_3_0.70) has 20 elements Group 25 ( Phi=0.0_3_0.60) has 24 elements Group 26 ( Phi=0.0_2_4.92) has 24 elements Group 27 ( Phi=0.0_3_0.65) has 96 elements Group 28 ( Phi=0.0_3_1.60) has 24 elements Group 29 ( Phi=0.0_3_1.60) has 12 elements Group 30 (Phi=180.0_2_0.42) has 12 elements Group 31 ( Phi=0.0_3_0.75) has 12 elements I tried gmx chi also by the following command:- gmx chi -s md.gro -f md.xtc -all 1 -o dihedral.xvg The out put file indicate following information xaxis label "Residue" yaxis label "S2" What is S2 on y-axis. How should I interpret it? Could anyone please help me with this? I would really appreciate your kind suggestions. Thanks. Sadaf From sadafrani6 at gmail.com Tue Feb 25 01:04:08 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Tue, 25 Feb 2020 00:04:08 -0000 Subject: [gmx-users] Fwd: restraints failure problem In-Reply-To: References: Message-ID: Dear Gromacs users I am posting this problem third time in hope to get some suggestions regarding my problem. I am doing a test calculation in MD simulation between ligand and a protein residue for bond angle and dihedral restraints. I have set them in my topology file as below:- ; distance restraints [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB 71 29 10 0.403 0.403 10.0 0.0 0.403 0.403 10.0 4184.000 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 29 71 69 71 1 104.92 0.0 1 104.92 41.840 1 71 29 31 29 1 147.02 0.0 1 147.02 41.840 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 69 71 29 31 1 146.72 0.0 0.0 146.72 0.0 41.840 72 71 29 31 1 17.55 0.0 0.0 17.55 0.0 41.840 72 71 29 25 1 173.10 0.0 0.0 173.10 0.0 41.840 However, after energy minimization, I observed that my restraints are not working and I find the following change:- bonds changed from 0.403 *0.401* angles:- 104.92 changed to *107.98* 147.02 changed to *152.76* dihedrals:- 146.72 changed to *141.72* 17.55 changed to 2*2.13* 173.10 changed to *174.23* The fluctuation in restraints goes on increasing till the production run which shows that my restraints are not working. How should I work with these so that they may not change much? Do I need to increase force for restraints if yes then how much increase? any idea? I have tried these simulations with position restraints. Is the method of putting restraints correct or should I try some other? I have to apply these in the free energy calculation which already crashed because of restraint failure. I would really be thankful for your kind suggestions, please. Thanks. Sadaf From prinebula23 at gmail.com Tue Feb 25 06:40:05 2020 From: prinebula23 at gmail.com (Priyanka Singh) Date: Tue, 25 Feb 2020 05:40:05 -0000 Subject: [gmx-users] spliting of long trajectories to generate many small trajectories Message-ID: Hi all Can a long md trajectory be split into into small trajectories of equal length to apply markov state modelling on it using gromacs? Thank you all in advance. From 177cy500.bratin at nitk.edu.in Tue Feb 25 19:03:14 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Tue, 25 Feb 2020 18:03:14 -0000 Subject: [gmx-users] spliting of long trajectories to generate many small trajectories In-Reply-To: References: Message-ID: Hi You can use gmx trjconv command to cut your long trajectory in to small and equal pieces by passing -b -e flag For more info see gmx trjconv -h On Tue 25 Feb, 2020, 11:10 AM Priyanka Singh, wrote: > Hi all > Can a long md trajectory be split into into small trajectories of equal > length to apply markov state modelling on it using gromacs? > Thank you all in advance. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Tue Feb 25 21:12:40 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Tue, 25 Feb 2020 20:12:40 -0000 Subject: [gmx-users] How to calculate the dihedral angle as a function of time? In-Reply-To: References: Message-ID: To work out which dihedrals those index groups refer to, you will need to look at the index numbers in each index group, then match them with those in the coordinate file. Do you have a specific dihedral(s) that you want to follow, or is all all dihedrals of the same type? If specific dihedrals, then generate an index group for each specific dihedral of four atoms and then process using gmx angle -ov 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, 25 Feb 2020 at 10:55, Sadaf Rani wrote: > Dear Gromacs users > > I want to calculate the dihedral angle over the simulation time. I tried > following commands:- > gmx mk_angndx -s topol.tpr -type dihedral > > which generates an index file for dihedral angles then running:- > > gmx angle -f md_prod.trr -n angle.ndx -type dihedral > gives following group options, How can I identify these groups show which > part of the system. I want to calculate the dihedral angle as a function of > time in the simulation. > > Group 0 ( Phi=0.0_3_0.65) has 228 elements > Group 1 ( Phi=0.0_1_0.84) has 8 elements > Group 2 ( Phi=0.0_2_0.84) has 8 elements > Group 3 ( Phi=0.0_3_1.67) has 16 elements > Group 4 ( Phi=0.0_3_0.67) has 52 elements > Group 5 ( Phi=0.0_1_1.05) has 96 elements > Group 6 ( Phi=0.0_3_0.70) has 4 elements > Group 7 (Phi=180.0_2_10.46) has 32 elements > Group 8 ( Phi=0.0_1_8.37) has 16 elements > Group 9 ( Phi=0.0_2_8.37) has 8 elements > Group 10 ( Phi=0.0_2_1.13) has 8 elements > Group 11 ( Phi=0.0_3_1.76) has 8 elements > Group 12 (Phi=180.0_1_1.88) has 4 elements > Group 13 (Phi=180.0_2_6.61) has 4 elements > Group 14 (Phi=180.0_3_2.30) has 4 elements > Group 15 ( Phi=0.0_1_3.35) has 4 elements > Group 16 (Phi=180.0_3_0.33) has 4 elements > Group 17 (Phi=180.0_2_15.17) has 96 elements > Group 18 ( Phi=0.0_3_0.75) has 8 elements > Group 19 (Phi=180.0_2_1.05) has 20 elements > Group 20 (Phi=180.0_1_0.84) has 20 elements > Group 21 ( Phi=0.0_3_0.63) has 32 elements > Group 22 ( Phi=0.0_2_3.35) has 12 elements > Group 23 ( Phi=0.0_3_0.67) has 28 elements > Group 24 ( Phi=0.0_3_0.70) has 20 elements > Group 25 ( Phi=0.0_3_0.60) has 24 elements > Group 26 ( Phi=0.0_2_4.92) has 24 elements > Group 27 ( Phi=0.0_3_0.65) has 96 elements > Group 28 ( Phi=0.0_3_1.60) has 24 elements > Group 29 ( Phi=0.0_3_1.60) has 12 elements > Group 30 (Phi=180.0_2_0.42) has 12 elements > Group 31 ( Phi=0.0_3_0.75) has 12 elements > > I tried gmx chi also by the following command:- > > gmx chi -s md.gro -f md.xtc -all 1 -o dihedral.xvg > The out put file indicate following information > xaxis label "Residue" > yaxis label "S2" > What is S2 on y-axis. > How should I interpret it? Could anyone please help me with this? I would > really appreciate your kind suggestions. > > 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 m.b.abdelaal at gmail.com Tue Feb 25 22:13:12 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 25 Feb 2020 21:13:12 -0000 Subject: [gmx-users] Energy minimization Message-ID: Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I should restrain the graphene sheet along the z axis. I did that using force =1000. and the problem was solved and nothing moved. After that I tried to insert 25 molecule of (C60) inside a box which contains the graphene sheet. I did that and did the energy minimization but part of the graphene sheet moved again from its place although the maximum force was less than 1000 which is the force I used to restrain the graphene sheet. However I didn't have any error during the energy minimization. Does this means that the problem is just in visualization or I might have a problem in my energy minimization ? It is also worth mentioning that the C60 molecules are not spherical as it should be. I read about that and I found people mentioning that this shape deformation in only a visualization problem and can be solved by using gmx trjconv. is it possible that this problem has happened to my whole system including the graphene sheet or it shouldn't affect my graphene sheet as long as I have restrained it ? more info: I used periodic_molecules = yes while trying to minimize my whole system. (I also tried without it but no impact) I wrote: gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p C60_GRM_box.top -o min1.tpr -maxwarn 2 followed by gmx mdrun -v -deffnm min1 and I got the below result: writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 3293 steps Potential Energy = 6.3598562e+05 Maximum force = 9.9486487e+02 on atom 12087 Norm of force = 6.5454323e+01 Can anybody help me please. Thanks Mohamed From dallas.warren at monash.edu Tue Feb 25 23:46:05 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Tue, 25 Feb 2020 22:46:05 -0000 Subject: [gmx-users] Energy minimization In-Reply-To: References: Message-ID: This all sounds like http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc Remember, the box is just a visualisation of what the system looks like, and you can move that box anywhere. What is in the center of the box is entirely up to you and the post processing you do. What comes out of the mdrun engine is arbitrary. 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 Wed, 26 Feb 2020 at 08:13, Mohamed Abdelaal wrote: > Hello all, > > I created a graphene sheet and performed energy minimization, after energy > minimization I found that parts of the graphene sheet was moved from the > box bottom to the box topside at the same place (as if it was translated > upwards). I looked online for the problem and I understood that I should > restrain the graphene sheet along the z axis. I did that using force =1000. > and the problem was solved and nothing moved. > > After that I tried to insert 25 molecule of (C60) inside a box which > contains the graphene sheet. I did that and did the energy minimization but > part of the graphene sheet moved again from its place although the maximum > force was less than 1000 which is the force I used to restrain the graphene > sheet. However I didn't have any error during the energy minimization. Does > this means that the problem is just in visualization or I might have a > problem in my energy minimization ? > > It is also worth mentioning that the C60 molecules are not spherical as it > should be. I read about that and I found people mentioning that this shape > deformation in only a visualization problem and can be solved by using gmx > trjconv. is it possible that this problem has happened to my whole system > including the graphene sheet or it shouldn't affect my graphene sheet as > long as I have restrained it ? > > more info: > I used periodic_molecules = yes while trying to minimize my whole system. > (I also tried without it but no impact) > I wrote: > > gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p > C60_GRM_box.top -o min1.tpr -maxwarn 2 > > followed by > gmx mdrun -v -deffnm min1 > > and I got the below result: > writing lowest energy coordinates. > > Steepest Descents converged to Fmax < 1000 in 3293 steps > Potential Energy = 6.3598562e+05 > Maximum force = 9.9486487e+02 on atom 12087 > Norm of force = 6.5454323e+01 > > Can anybody help me please. > > 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 b.mijiddorj at gmail.com Wed Feb 26 05:42:30 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Wed, 26 Feb 2020 04:42:30 -0000 Subject: [gmx-users] Umbrella sampling of peptide-membrane system Message-ID: Dear GMX users, I would like to ask about position restraint during the umbrella sampling. 1. Is it need to make position restraint of lipid bilayer during the umbrella sampling simulation? 2. The position restraint was used for the B chain of amyloid-beta peptides in prof. Justin's tutorial. Can I run the simulations without position restrain of lipid molecules in the case of lipid bilayer? or 3. Can I use the position restraint for only phosphorus atoms of the headgroups of both leaflets? If you have any experience, please let me advise which one is better for this kind of calculation. Best regards, Mijiddorj From prinebula23 at gmail.com Wed Feb 26 07:29:05 2020 From: prinebula23 at gmail.com (Priyanka Singh) Date: Wed, 26 Feb 2020 06:29:05 -0000 Subject: [gmx-users] RNA md simulation In-Reply-To: <9ec947f0-2b7c-8f05-88ec-28638b1b373e@vt.edu> References: <9ec947f0-2b7c-8f05-88ec-28638b1b373e@vt.edu> Message-ID: Thank you. On Fri, Feb 14, 2020 at 7:32 PM Justin Lemkul wrote: > > > On 2/14/20 5:20 AM, Priyanka Singh wrote: > > Hi can anyone help with the problem of terminal end notation for charmm36 > > ff for RNA molecule to generate .gro file usind gromac-2019.3 > > The standard 5'-OH and 3'-OH are 5TER and 3TER. > > -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 johnwhittake at zedat.fu-berlin.de Wed Feb 26 11:17:30 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 26 Feb 2020 10:17:30 -0000 Subject: [gmx-users] Umbrella sampling of peptide-membrane system In-Reply-To: References: Message-ID: <37778.160.45.109.123.1582712245.webmail@webmail.zedat.fu-berlin.de> Hi, Justin's tutorial is not a fully generalized procedure for umbrella sampling; it shows a workflow for one specific example which is not always applicable to other systems. In general, you don't have to use position restraints for anything in umbrella sampling. Justin uses them to keep the fibril in place for specific reasons, as noted in the paper he based the tutorial on. That said, what are you trying to do? Adding restraints to the bilayer is probably a bad idea, seeing as how the motion of the bilayer is an important physical behavior. Are you calculating the PMF for a molecule traversing a lipid bilayer? If so, there are many examples in the literature that detail a procedure that's probably much more relevant to you. Best, John > Dear GMX users, > > I would like to ask about position restraint during the umbrella sampling. > 1. Is it need to make position restraint of lipid bilayer during the > umbrella sampling simulation? > 2. The position restraint was used for the B chain of amyloid-beta > peptides > in prof. Justin's tutorial. Can I run the simulations without position > restrain of lipid molecules in the case of lipid bilayer? > or > 3. Can I use the position restraint for only phosphorus atoms of the > headgroups of both leaflets? > > If you have any experience, please let me advise which one is better for > this kind of calculation. > > Best regards, > > Mijiddorj > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 p.c.kroon at rug.nl Wed Feb 26 12:19:28 2020 From: p.c.kroon at rug.nl (p.c.kroon at rug.nl) Date: Wed, 26 Feb 2020 11:19:28 -0000 Subject: [gmx-users] Thesis developed software; which Open-source License? In-Reply-To: References: Message-ID: <026301d5ec96$98708c60$c951a520$@rug.nl> Hi Henry, Although I'm not a lawyer here's how I understand it. You may want to check it with your department/university/company's legal department. I don't know anything about licensing data, but take a look at creative commons licenses if you want it to be open. See also: https://opensource.org/licenses/ Relicensing (from BSD-3 to something else, for example) can be tedious, depending on how many people contributed to your code. Everyone who has a claim to the IP (your code) has to agree with the change. If you're the only contributor, or if all contributors are nearby, it can be pretty straightforward. It's also possible (I think with the same conditions) to have different licenses for different users. Either way, users of your code do not need to be notified. They can keep using your code under the BSD-3 license under which they obtained it. BSD-3 and MIT are very simple and permissive licenses. Apache2 is also a very permissive license, but there's a bit more legalese involved, reducing ambiguity. This is the license I chose for my FOSS projects after consulting with my uni's legal department. (L)GPL and friends are so-called copy-left licenses. Whenever you use GPL licensed code in your project, your code also *must* be GPL licensed. This becomes a little fuzzy when you're linking against GPL libraries, or importing them in your python code. For this reason LGPL was made, which explicitly allows compiling against LGPL licensed libraries without making you also GPL license your own code. As I see it, as long as you haven't looked at GPL licensed source code you can license your code however you want. I *think* scripts that just call gmx tools do not have to be GPL licensed. I personally consider parameter files to be data (and not code subject to the LGPL license). So using/adapting those should (I think) be ok. I don?t know which "original GMX simulated solvated protein data" you mean, or how that is licensed. As I said I know very little about the licensing of data, and I think that in general it's something to which not enough attention is being paid (at least up until now). Has anyone looked up the license for the RSCB PDB for example? I hope this helps, and that it's not too factually incorrect ? Peter -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Henry Wittler Sent: Friday, February 21, 2020 10:22 AM To: gmx-users at gromacs.org Subject: [gmx-users] Thesis developed software; which Open-source License? Greetings comrades. This question may be somewhat redundant, so dont expect reply to every aspect, may ask at RG also. However if anyone have more or less insight, please reply. My thesis has calculation software that are built upon partly innovative and partly basic calculation/plotting/graphing software based upon "VMD/tcl? coding, GROMACS (GMX) and Python/MatplotlibScipy/Numpy (etc). The solvated protein data (chap. 6 of thesis) are obtained from GMX simulations, moreover the analysis data by VMD/tcl etc. I have uploaded so far just part of the code (for chap. 4.1) I intend to upload code from whole thesis to github link https://wittler-github.github.io/A_MD_Analysis_of_Insulin/ The following thesis link(downloadable) contains the calculated data along with the graphs. http://hdl.handle.net/1959.9/568798 ( https://www.researchgate.net/project/A-Molecular-Dynamics-Analysis-of-Insulin) I mainly want to share the novel GMX simulated data and tools I?ve developed from the above-mentioned softwares, that are described in my thesis. I do not expect to contribute to GMX directly from this repository, possibly via other created repository if so. Currently I have applied the BSD-3 clause version, which I understand to be the most relevant and simple to use. Choice is not set-in stone it appears, however if changing I understand one need to notify everyone that has taken part of, or are using the code. The BSD-3 do appears to be one of the most popular for open-source code and compatible between different softwares. I thought of using LGPL2 since GMX uses that, however BSD-3 does appear more simple to understand. The only innovative scripts including GMX are just linux bash/automatic scripts that make the simulation of replicas straightforward. Can I share these script under the BSD-3 license, even though technically they are modified scripts using standard gmx commands (not altering the original gmx software v.5.0.4)? Can I share some of the GMX code (parameter files etc) and some of the original GMX simulated solvated protein data (in addition to data calculated/graphed by matplotlib etc), at my github repository with no issues between BSD-3 license and LGPL2? The other python, and VMD/tcl softwares I do not see any issue with. Are there any clash with these above-mentioned softwares to be aware of? Any other insights anyone else has here about open-source licensing when distributing code? *Kind regards,* *Dr. Henry P.A. Wittler* *Department of Chemistry and Physics, LIMS, La Trobe University, MelbourneWorking in Ludvika, Sweden* *Skype: henry.wittler* Researchgate & Linkedin linkedin.com/in/henry-per-andreas-wittler-b03256191 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 katrien.clerx at student.kuleuven.be Wed Feb 26 12:32:01 2020 From: katrien.clerx at student.kuleuven.be (Katrien Clerx) Date: Wed, 26 Feb 2020 11:32:01 -0000 Subject: [gmx-users] Normal mode analysis Message-ID: <1582716716981.87@student.kuleuven.be> ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien From smithmd at ornl.gov Wed Feb 26 13:38:46 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Wed, 26 Feb 2020 12:38:46 -0000 Subject: [gmx-users] Normal mode analysis In-Reply-To: <1582716716981.87@student.kuleuven.be> References: <1582716716981.87@student.kuleuven.be> Message-ID: Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien From subhomoy.bk at gmail.com Wed Feb 26 13:44:27 2020 From: subhomoy.bk at gmail.com (Subhomoi Borkotoky) Date: Wed, 26 Feb 2020 12:44:27 -0000 Subject: [gmx-users] Listing residues in gromacs In-Reply-To: <286b11ad-d7bc-ac3a-434a-9d61ca409282@kth.se> References: <286b11ad-d7bc-ac3a-434a-9d61ca409282@kth.se> Message-ID: Hi Christian, Thank you for your reply. The command worked well. I got the indices of the residues. I want to calculate the occupancies of the residues near my reference ion within say 0.5 nm. It will help me a lot if you could suggest something for it. I have tried gmx distance and gmx mindist with the index file from gmx select, but not successful. Thanks & Regards, -------------------------- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India. Alternate E-mail : subhomoi at yahoo.com On Tue, Feb 18, 2020 at 6:58 PM Christian Blau wrote: > Hi Subhomoi, > > > Yes, > > gmx select > > can do that (see > http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) > > > > For what you want to do, it's beneficial to have a look at the selection > syntax here > > http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html > < > http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html?highlight=selection > > > > > Best, > > Christian > > On 2020-02-18 13:14, Subhomoi Borkotoky wrote: > > Hi, > > > > Is there any option in gromacs to list residues/atoms around a reference > > group? I have checked trjorder , but it only gives number of molecules. > > > > Thanks & Regards, > > -------------------------- > > *Subhomoi Borkotoky, Ph. D.* > > Kusuma School of Biological Sciences, > > Indian Institute of Technology Delhi, > > New Delhi-110016, > > India. > > > > Alternate E-mail : subhomoi at yahoo.com > > > > https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokAAAAJ > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 katrien.clerx at student.kuleuven.be Wed Feb 26 13:52:11 2020 From: katrien.clerx at student.kuleuven.be (Katrien Clerx) Date: Wed, 26 Feb 2020 12:52:11 -0000 Subject: [gmx-users] Normal mode analysis In-Reply-To: References: <1582716716981.87@student.kuleuven.be>, Message-ID: <9504915a224c4dee931dd05faf6b48e2@ICTS-S-EXMBX3.luna.kuleuven.be> Yes I used double precision for everything. -Katrien From: Smith, Micholas D. Sent: woensdag 26 februari 2020 13:39 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 Wed Feb 26 14:08:43 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Wed, 26 Feb 2020 13:08:43 -0000 Subject: [gmx-users] Normal mode analysis In-Reply-To: <9504915a224c4dee931dd05faf6b48e2@ICTS-S-EXMBX3.luna.kuleuven.be> References: <1582716716981.87@student.kuleuven.be>, , <9504915a224c4dee931dd05faf6b48e2@ICTS-S-EXMBX3.luna.kuleuven.be> Message-ID: Hmmm.... How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 7:52 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis Yes I used double precision for everything. -Katrien From: Smith, Micholas D. Sent: woensdag 26 februari 2020 13:39 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 katrien.clerx at student.kuleuven.be Wed Feb 26 14:30:01 2020 From: katrien.clerx at student.kuleuven.be (Katrien Clerx) Date: Wed, 26 Feb 2020 13:30:01 -0000 Subject: [gmx-users] Normal mode analysis In-Reply-To: References: <1582716716981.87@student.kuleuven.be>, , <9504915a224c4dee931dd05faf6b48e2@ICTS-S-EXMBX3.luna.kuleuven.be>, Message-ID: <48e5efbfbdfe46529755aa0ebab81eec@ICTS-S-EXMBX3.luna.kuleuven.be> My structure does not contain any ions. Here are the commands that I used: gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water tip3p -ignh gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5 gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr gmx_d mdrun -deffnm cg -v gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr -maxwarn 1 gmx_d mdrun -deffnm bfgs -v gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr The used mdp files: cg.mdp : ; Parameters describing what to do, when to stop and what to save integrator = cg ; Algorithm (cg= Conjugate Gradient minimization) emtol = 0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps = 500000 ; Maximum number of (minimization) steps to perform nstcgsteep = 1000 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 1.0 ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) bfgs.mdp: ;mdp for l-bfgs energy minimization define = -DFLEXIBLE constraints = none integrator = l-bfgs ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field coulomb-modifier = potential-shift ; Treatment of long range electrostatic interactions rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 fourierspacing = 0.12 pme_order = 4 epsilon_surface = 0 ewald_rtol = 1e-9 pbc = xyz ; Periodic Boundary Conditions (yes/no) ; ; Energy minimizing stuff ; emtol = 0.0 emstep = 0.0001 nstcgsteep = 1000 nbfgscorr = 100000 nsteps = 500000 nm.mdp: ; Parameters describing what to do, when to stop and what to save define = -DFLEXIBLE integrator = nm ; Algorithm (normal mode) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions coulomb-modifier = potential-shift rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = Cut-off vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) nsteps = 10000000 From: Smith, Micholas D. Sent: woensdag 26 februari 2020 14:10 To: Katrien Clerx; gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Hmmm.... How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 7:52 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis Yes I used double precision for everything. -Katrien From: Smith, Micholas D. Sent: woensdag 26 februari 2020 13:39 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 smithmd at ornl.gov Wed Feb 26 14:40:28 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Wed, 26 Feb 2020 13:40:28 -0000 Subject: [gmx-users] Normal mode analysis In-Reply-To: <48e5efbfbdfe46529755aa0ebab81eec@ICTS-S-EXMBX3.luna.kuleuven.be> References: <1582716716981.87@student.kuleuven.be>, , <9504915a224c4dee931dd05faf6b48e2@ICTS-S-EXMBX3.luna.kuleuven.be>, , <48e5efbfbdfe46529755aa0ebab81eec@ICTS-S-EXMBX3.luna.kuleuven.be> Message-ID: Where did you obtain your PDB? Is this a known crystal structure or other experimentally derived structure or is it a homology model? Sometimes the initial structures have minor artifacts that make energy minimization difficult. Perhaps a short-restrained MD simulation (10ps perhaps) with 10kJ/mol position restraints could remove these artifacts and then you can re-minimize and run your normal mode calculation. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: Katrien Clerx Sent: Wednesday, February 26, 2020 8:29 AM To: Smith, Micholas D. ; gmx-users at gromacs.org Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis My structure does not contain any ions. Here are the commands that I used: gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water tip3p -ignh gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5 gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr gmx_d mdrun -deffnm cg -v gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr -maxwarn 1 gmx_d mdrun -deffnm bfgs -v gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr The used mdp files: cg.mdp : ; Parameters describing what to do, when to stop and what to save integrator = cg ; Algorithm (cg= Conjugate Gradient minimization) emtol = 0 ; Stop minimization when the maximum force < 10.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps = 500000 ; Maximum number of (minimization) steps to perform nstcgsteep = 1000 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 1.0 ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) bfgs.mdp: ;mdp for l-bfgs energy minimization define = -DFLEXIBLE constraints = none integrator = l-bfgs ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field coulomb-modifier = potential-shift ; Treatment of long range electrostatic interactions rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 fourierspacing = 0.12 pme_order = 4 epsilon_surface = 0 ewald_rtol = 1e-9 pbc = xyz ; Periodic Boundary Conditions (yes/no) ; ; Energy minimizing stuff ; emtol = 0.0 emstep = 0.0001 nstcgsteep = 1000 nbfgscorr = 100000 nsteps = 500000 nm.mdp: ; Parameters describing what to do, when to stop and what to save define = -DFLEXIBLE integrator = nm ; Algorithm (normal mode) ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = verlet nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions coulomb-modifier = potential-shift rcoulomb-switch = 1.0 rcoulomb = 1.2 ; Short-range electrostatic cut-off vdwtype = Cut-off vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2; Short-range Van der Waals cut-off fourierspacing = 0.12 pme_order = 4 ewald_rtol =1e-09 epsilon_surface = 0 pbc = xyz ; Periodic Boundary Conditions (yes/no) nsteps = 10000000 From: Smith, Micholas D. Sent: woensdag 26 februari 2020 14:10 To: Katrien Clerx; gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Hmmm.... How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 7:52 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis Yes I used double precision for everything. -Katrien From: Smith, Micholas D. Sent: woensdag 26 februari 2020 13:39 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Katrien Clerx Sent: Wednesday, February 26, 2020 6:31 AM To: gmx-users at gromacs.org Subject: [EXTERNAL] [gmx-users] Normal mode analysis ?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing wrong and how can I fix it? Kind regards, Katrien -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe 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 andreas.baer at fau.de Wed Feb 26 15:54:26 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Wed, 26 Feb 2020 14:54:26 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 Message-ID: Hello, from a set of benchmark tests with large systems using Gromacs versions 2019.5 and 2020, I obtained some unexpected results: With the same set of parameters and the 2020 version, I obtain a performance that is about 2/3 of the 2019.5 version. Interestingly, according to nvidia-smi, the GPU usage is about 20% higher for the 2020 version. Also from the log files it seems, that the 2020 version does the computations more efficiently, but spends so much more time waiting, that the overall performance drops. Some background info on the benchmarks: - System contains about 2.1 million atoms. - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + SMT; 4x NVIDIA Tesla V100 ? (similar results with less significant performance drop (~15%) on a different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find the optimal set. However the performance drop seems to be persistent for all such options. Two representative log files are attached. Does anyone have an idea, where this drop comes from, and how to choose the parameters for the 2020 version to circumvent this? Regards, Andreas From paul.bauer.q at gmail.com Wed Feb 26 16:07:05 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Wed, 26 Feb 2020 15:07:05 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: Message-ID: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> Hello, you can't add attachments to the list, please upload the files somewhere to share them. This might be quite important to us, because the performance regression is not expected by us. Cheers Paul On 26/02/2020 15:54, Andreas Baer wrote: > Hello, > > from a set of benchmark tests with large systems using Gromacs > versions 2019.5 and 2020, I obtained some unexpected results: > With the same set of parameters and the 2020 version, I obtain a > performance that is about 2/3 of the 2019.5 version. Interestingly, > according to nvidia-smi, the GPU usage is about 20% higher for the > 2020 version. > Also from the log files it seems, that the 2020 version does the > computations more efficiently, but spends so much more time waiting, > that the overall performance drops. > > Some background info on the benchmarks: > - System contains about 2.1 million atoms. > - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + > SMT; 4x NVIDIA Tesla V100 > ? (similar results with less significant performance drop (~15%) on a > different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy > Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > the optimal set. However the performance drop seems to be persistent > for all such options. > > Two representative log files are attached. > Does anyone have an idea, where this drop comes from, and how to > choose the parameters for the 2020 version to circumvent this? > > Regards, > Andreas > -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From andreas.baer at fau.de Wed Feb 26 16:11:33 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Wed, 26 Feb 2020 15:11:33 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> Message-ID: Hello, here is a link to the logfiles. https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 If necessary, I can also provide some more log or tpr/gro/... files. Cheers, Andreas On 26.02.20 16:09, Paul bauer wrote: > Hello, > > you can't add attachments to the list, please upload the files > somewhere to share them. > This might be quite important to us, because the performance > regression is not expected by us. > > Cheers > > Paul > > On 26/02/2020 15:54, Andreas Baer wrote: >> Hello, >> >> from a set of benchmark tests with large systems using Gromacs >> versions 2019.5 and 2020, I obtained some unexpected results: >> With the same set of parameters and the 2020 version, I obtain a >> performance that is about 2/3 of the 2019.5 version. Interestingly, >> according to nvidia-smi, the GPU usage is about 20% higher for the >> 2020 version. >> Also from the log files it seems, that the 2020 version does the >> computations more efficiently, but spends so much more time waiting, >> that the overall performance drops. >> >> Some background info on the benchmarks: >> - System contains about 2.1 million atoms. >> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + >> SMT; 4x NVIDIA Tesla V100 >> ? (similar results with less significant performance drop (~15%) on a >> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy >> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) >> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find >> the optimal set. However the performance drop seems to be persistent >> for all such options. >> >> Two representative log files are attached. >> Does anyone have an idea, where this drop comes from, and how to >> choose the parameters for the 2020 version to circumvent this? >> >> Regards, >> Andreas >> > From pall.szilard at gmail.com Wed Feb 26 16:29:09 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Wed, 26 Feb 2020 15:29:09 -0000 Subject: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory In-Reply-To: <40cf1027.940f.17070ce7162.Coremail.bonjour899@126.com> References: <40cf1027.940f.17070ce7162.Coremail.bonjour899@126.com> Message-ID: Hi, Indeed, there is an issue with the GPU detection code's consistency checks that trip and abort the run if any of the detected GPUs behaves in unexpected ways (e.g. runs out of memory during checks). This should be fixed in an upcoming release, but until then as you have observed, you can always restrict the set of GPUs exposed to GROMACS using the CUDA_VISIBLE_DEVICES environment variable. Cheers, -- Szil?rd On Sun, Feb 23, 2020 at 7:51 AM bonjour899 wrote: > I think I've temporarily solved this problem. Only when I use > CUDA_VISIABLE_DEVICE to block the memory-almost-fully-occupied GPUs, I can > run GROMACS smoothly (using -gpu_id only is useless). I think there may be > some bug in GROMACS's GPU usage model in a multi-GPU environment (It seems > like as long as one of the GPUs is fully occupied, GROMACS cannot submit to > any GPUs and return an error with "cudaFuncGetAttributes failed: out of > memory"). > > > > Best regards, > W > > > > > -------- Forwarding messages -------- > From: "bonjour899" > Date: 2020-02-23 11:32:53 > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory > I also tried to restricting to different GPU using -gpu_id, but still with > the same error. I've also posting my question on > https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/ > Following is the output of nvidia-smi: > > > +-----------------------------------------------------------------------------+ > > | NVIDIA-SMI 440.33.01 Driver Version: 440.33.01 CUDA Version: 10.2 | > > > |-------------------------------+----------------------+----------------------+ > > | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | > > > |===============================+======================+======================| > > | 0 Tesla P100-PCIE... On | 00000000:04:00.0 Off | 0 | > > | N/A 35C P0 34W / 250W | 16008MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 1 Tesla P100-PCIE... On | 00000000:06:00.0 Off | 0 | > > | N/A 35C P0 28W / 250W | 10MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 2 Tesla P100-PCIE... On | 00000000:07:00.0 Off | 0 | > > | N/A 35C P0 33W / 250W | 16063MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 3 Tesla P100-PCIE... On | 00000000:08:00.0 Off | 0 | > > | N/A 36C P0 29W / 250W | 10MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 4 Quadro P4000 On | 00000000:0B:00.0 Off | N/A | > > | 46% 27C P8 8W / 105W | 12MiB / 8119MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > > > > +-----------------------------------------------------------------------------+ > > | Processes: GPU Memory | > > | GPU PID Type Process name Usage | > > > |=============================================================================| > > | 0 20497 C /usr/bin/python3 5861MiB | > > | 0 24503 C /usr/bin/python3 10137MiB | > > | 2 23162 C /home/appuser/Miniconda3/bin/python 16049MiB | > > > +-----------------------------------------------------------------------------+ > > > > > > > > -------- Forwarding messages -------- > From: "bonjour899" > Date: 2020-02-20 10:30:36 > To: "gromacs.org_gmx-users at maillist.sys.kth.se" < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: cudaFuncGetAttributes failed: out of memory > > Hello, > > > I have encountered a weird problem. I've been using GROMACS with GPU on a > server and always performance good. However when I just reran a job today > and suddenly got this error: > > > > Command line: > > gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3 > > Back Off! I just backed up pull.log to ./#pull.log.1# > > ------------------------------------------------------- > > Program: gmx mdrun, version 2019.4 > > Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) > > > > Fatal error: > > cudaFuncGetAttributes failed: out of memory > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > > > > It seems the GPU is 0 occupied and I can run other apps with GPU, but I > cannot run GROMACS mdrun anymore, even if doing energy minimization. > > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Feb 26 16:29:10 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Wed, 26 Feb 2020 15:29:10 -0000 Subject: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory In-Reply-To: <40cf1027.940f.17070ce7162.Coremail.bonjour899@126.com> References: <40cf1027.940f.17070ce7162.Coremail.bonjour899@126.com> Message-ID: Hi, Indeed, there is an issue with the GPU detection code's consistency checks that trip and abort the run if any of the detected GPUs behaves in unexpected ways (e.g. runs out of memory during checks). This should be fixed in an upcoming release, but until then as you have observed, you can always restrict the set of GPUs exposed to GROMACS using the CUDA_VISIBLE_DEVICES environment variable. Cheers, -- Szil?rd On Sun, Feb 23, 2020 at 7:51 AM bonjour899 wrote: > I think I've temporarily solved this problem. Only when I use > CUDA_VISIABLE_DEVICE to block the memory-almost-fully-occupied GPUs, I can > run GROMACS smoothly (using -gpu_id only is useless). I think there may be > some bug in GROMACS's GPU usage model in a multi-GPU environment (It seems > like as long as one of the GPUs is fully occupied, GROMACS cannot submit to > any GPUs and return an error with "cudaFuncGetAttributes failed: out of > memory"). > > > > Best regards, > W > > > > > -------- Forwarding messages -------- > From: "bonjour899" > Date: 2020-02-23 11:32:53 > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] cudaFuncGetAttributes failed: out of memory > I also tried to restricting to different GPU using -gpu_id, but still with > the same error. I've also posting my question on > https://devtalk.nvidia.com/default/topic/1072038/cuda-programming-and-performance/cudafuncgetattributes-failed-out-of-memory/ > Following is the output of nvidia-smi: > > > +-----------------------------------------------------------------------------+ > > | NVIDIA-SMI 440.33.01 Driver Version: 440.33.01 CUDA Version: 10.2 | > > > |-------------------------------+----------------------+----------------------+ > > | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | > > > |===============================+======================+======================| > > | 0 Tesla P100-PCIE... On | 00000000:04:00.0 Off | 0 | > > | N/A 35C P0 34W / 250W | 16008MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 1 Tesla P100-PCIE... On | 00000000:06:00.0 Off | 0 | > > | N/A 35C P0 28W / 250W | 10MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 2 Tesla P100-PCIE... On | 00000000:07:00.0 Off | 0 | > > | N/A 35C P0 33W / 250W | 16063MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 3 Tesla P100-PCIE... On | 00000000:08:00.0 Off | 0 | > > | N/A 36C P0 29W / 250W | 10MiB / 16280MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > | 4 Quadro P4000 On | 00000000:0B:00.0 Off | N/A | > > | 46% 27C P8 8W / 105W | 12MiB / 8119MiB | 0% Default | > > > +-------------------------------+----------------------+----------------------+ > > > > > +-----------------------------------------------------------------------------+ > > | Processes: GPU Memory | > > | GPU PID Type Process name Usage | > > > |=============================================================================| > > | 0 20497 C /usr/bin/python3 5861MiB | > > | 0 24503 C /usr/bin/python3 10137MiB | > > | 2 23162 C /home/appuser/Miniconda3/bin/python 16049MiB | > > > +-----------------------------------------------------------------------------+ > > > > > > > > -------- Forwarding messages -------- > From: "bonjour899" > Date: 2020-02-20 10:30:36 > To: "gromacs.org_gmx-users at maillist.sys.kth.se" < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: cudaFuncGetAttributes failed: out of memory > > Hello, > > > I have encountered a weird problem. I've been using GROMACS with GPU on a > server and always performance good. However when I just reran a job today > and suddenly got this error: > > > > Command line: > > gmx mdrun -deffnm pull -ntmpi 1 -nb gpu -pme gpu -gpu_id 3 > > Back Off! I just backed up pull.log to ./#pull.log.1# > > ------------------------------------------------------- > > Program: gmx mdrun, version 2019.4 > > Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) > > > > Fatal error: > > cudaFuncGetAttributes failed: out of memory > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > > > > It seems the GPU is 0 occupied and I can run other apps with GPU, but I > cannot run GROMACS mdrun anymore, even if doing energy minimization. > > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 Feb 26 16:50:48 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Wed, 26 Feb 2020 15:50:48 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> Message-ID: Hi, Can you please check the performance when running on a single GPU 2019 vs 2020 with your inputs? Also note that you are using some peculiar settings that will have an adverse effect on performance (like manually set rlist disallowing the dual pair-list setup, and nstcalcenergy=1). Cheers, -- Szil?rd On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer wrote: > Hello, > > here is a link to the logfiles. > > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > > If necessary, I can also provide some more log or tpr/gro/... files. > > Cheers, > Andreas > > > On 26.02.20 16:09, Paul bauer wrote: > > Hello, > > > > you can't add attachments to the list, please upload the files > > somewhere to share them. > > This might be quite important to us, because the performance > > regression is not expected by us. > > > > Cheers > > > > Paul > > > > On 26/02/2020 15:54, Andreas Baer wrote: > >> Hello, > >> > >> from a set of benchmark tests with large systems using Gromacs > >> versions 2019.5 and 2020, I obtained some unexpected results: > >> With the same set of parameters and the 2020 version, I obtain a > >> performance that is about 2/3 of the 2019.5 version. Interestingly, > >> according to nvidia-smi, the GPU usage is about 20% higher for the > >> 2020 version. > >> Also from the log files it seems, that the 2020 version does the > >> computations more efficiently, but spends so much more time waiting, > >> that the overall performance drops. > >> > >> Some background info on the benchmarks: > >> - System contains about 2.1 million atoms. > >> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + > >> SMT; 4x NVIDIA Tesla V100 > >> (similar results with less significant performance drop (~15%) on a > >> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy > >> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > >> the optimal set. However the performance drop seems to be persistent > >> for all such options. > >> > >> Two representative log files are attached. > >> Does anyone have an idea, where this drop comes from, and how to > >> choose the parameters for the 2020 version to circumvent this? > >> > >> Regards, > >> Andreas > >> > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 nt2614888 at gmail.com Wed Feb 26 19:26:38 2020 From: nt2614888 at gmail.com (Neha Tiwari) Date: Wed, 26 Feb 2020 18:26:38 -0000 Subject: [gmx-users] Fwd: error during ions.tpr genereation. In-Reply-To: References: Message-ID: Dear all, I want to know if there is any error in the .itp file of ligand attached here, the ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. As I am unable to generate any extension files in GROMACS using this. Please help. Neha. From jalemkul at vt.edu Wed Feb 26 19:28:14 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 26 Feb 2020 18:28:14 -0000 Subject: [gmx-users] Fwd: error during ions.tpr genereation. In-Reply-To: References: Message-ID: On 2/26/20 1:26 PM, Neha Tiwari wrote: > Dear all, > I want to know if there is any error in the .itp file of ligand attached The mailing list does not accept attachments. > here, the ligand molecule was refined and optimized using G03 calculation > and .itp was generated using the ATB server. > As I am unable to generate any extension files in GROMACS using this. > If you are getting a specific error, please quote it directly (copy and paste from your terminal) and provide it to us. In the absence of an actual error, there's nothing anyone can do to help you. -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 james at ryley.com Thu Feb 27 00:17:56 2020 From: james at ryley.com (James) Date: Wed, 26 Feb 2020 23:17:56 -0000 Subject: [gmx-users] Can GROMACS compute heat flux? Message-ID: Hi, I am interested in testing thermal conductivity at the nano-scale. LAMMPS has a command to control thermal flux: https://lammps.sandia.gov/doc/fix_heat.html But, I cannot find an equivalent command in GROMACS. I know that thermostats can be set in GROMACS, but they do not seem to have a notion of how much energy is added or removed. Is this possible to do in GROMACS? Sincerely, James Ryley From b.mijiddorj at gmail.com Thu Feb 27 01:59:15 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Thu, 27 Feb 2020 00:59:15 -0000 Subject: [gmx-users] Umbrella sampling of peptide-membrane system In-Reply-To: References: Message-ID: Dear John, Thank you very much for your advice. Best regards, Mijiddorj Hi, > > Justin's tutorial is not a fully generalized procedure for umbrella > sampling; it shows a workflow for one specific example which is not always > applicable to other systems. > > In general, you don't have to use position restraints for anything in > umbrella sampling. Justin uses them to keep the fibril in place for > specific reasons, as noted in the paper he based the tutorial on. > > That said, what are you trying to do? Adding restraints to the bilayer is > probably a bad idea, seeing as how the motion of the bilayer is an > important physical behavior. > > Are you calculating the PMF for a molecule traversing a lipid bilayer? If > so, there are many examples in the literature that detail a procedure > that's probably much more relevant to you. > > Best, > > John > > > > > Dear GMX users, > > > > I would like to ask about position restraint during the umbrella > sampling. > > 1. Is it need to make position restraint of lipid bilayer during the > > umbrella sampling simulation? > > 2. The position restraint was used for the B chain of amyloid-beta > > peptides > > in prof. Justin's tutorial. Can I run the simulations without position > > restrain of lipid molecules in the case of lipid bilayer? > > or > > 3. Can I use the position restraint for only phosphorus atoms of the > > headgroups of both leaflets? > > > > If you have any experience, please let me advise which one is better for > > this kind of calculation. > > > > Best regards, > > > > Mijiddorj > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 clarkmaituanh91memory03 at gmail.com Thu Feb 27 02:10:34 2020 From: clarkmaituanh91memory03 at gmail.com (Anh Mai) Date: Thu, 27 Feb 2020 01:10:34 -0000 Subject: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy" In-Reply-To: References: Message-ID: Hi all, Could someone please help me? I have a question about the *temperature outputs *from the two packages "gmx traj" and "gmx energy." I used the two packages to export the Temperature of a "Protein" group. Here is what I did. 1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot Temperature_traj.xvg gmx analyze -f Temperature_traj.xvg *Found: Temperature_traj = 250.475 K* 2. gmx energy -f energy.edr Select "14 Temperature". *Found: Temperature_energy = 300.137 K* Our *parameters.mdp* file has: "... constraints = h-bonds constraint_algorithm = Lincs tc-grps = System ; sd integrator (!) tau_t = 2.0 ; sd integrator (!) ref_t = 300 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ..." I don't know why the two temperatures are that much different from each other, such as by 50 degrees. Looking forward to an explanation. Thanks a lot. Sincerely yours, Anh Mai From jalemkul at vt.edu Thu Feb 27 02:12:06 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 27 Feb 2020 01:12:06 -0000 Subject: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy" In-Reply-To: References: Message-ID: <872a4d91-e72a-ea45-7e6c-e175a3a35ca2@vt.edu> On 2/26/20 8:10 PM, Anh Mai wrote: > Hi all, > Could someone please help me? > > I have a question about the *temperature outputs *from the two > packages "gmx traj" > and "gmx energy." > > I used the two packages to export the Temperature of a "Protein" group. > Here is what I did. > > 1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr -ot > Temperature_traj.xvg > gmx analyze -f Temperature_traj.xvg > *Found: Temperature_traj = 250.475 K* > 2. gmx energy -f energy.edr > Select "14 Temperature". > *Found: Temperature_energy = 300.137 K* > > Our *parameters.mdp* file has: > "... > constraints = h-bonds > constraint_algorithm = Lincs > > tc-grps = System ; sd integrator (!) > tau_t = 2.0 ; sd integrator (!) > ref_t = 300 > > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > ..." > > I don't know why the two temperatures are that much different from each > other, such as by 50 degrees. > Looking forward to an explanation. gmx traj knows nothing about constraints so the number of degrees of freedom for the calculation are 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 navneetcdl at gmail.com Thu Feb 27 06:06:14 2020 From: navneetcdl at gmail.com (Navneet Kumar) Date: Thu, 27 Feb 2020 05:06:14 -0000 Subject: [gmx-users] regressiontests/complex (Failed) Message-ID: -How to solve this problem while installing GROMACS-2018.8 on Dell Tesla C2050. -Previously I installed GROMACS-2018.4 had same problem (one test regressiontests/complex failed) still installed. How does this effect simulation? What kind of error we get if we use gromacs even after failing this test and do some kind of simulations. 35/39 Test #35: regressiontests/complex ..........***Failed 49.02 sec :-) GROMACS - gmx mdrun, 2018.8 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018.8 Executable: /home/navneet/Downloads/gromacs-2018.8/build/bin/gmx Data prefix: /home/navneet/Downloads/gromacs-2018.8 (source tree) Working dir: /home/navneet/Downloads/regressiontests-2018.8 Command line: gmx mdrun -h Thanx for Using GROMACS - Have a Nice Day Abnormal return value for ' gmx mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Re-running nbnxn-vdw-potential-switch using CPU-based PME Re-running nbnxn_pme using CPU-based PME Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Re-running octahedron using CPU-based PME Re-running orientation-restraints using CPU-based PME Re-running pull_geometry_angle using CPU-based PME Re-running pull_geometry_angle-axis using CPU-based PME Re-running pull_geometry_dihedral using CPU-based PME Re-running swap_x using CPU-based PME FAILED. Check checkforce.out (2 errors) file(s) in swap_y for swap_y Re-running swap_y using CPU-based PME FAILED. Check checkforce.out (1 errors) file(s) in swap_z for swap_z Re-running swap_z using CPU-based PME FAILED. Check checkforce.out (1 errors) file(s) in tip4p_continue for tip4p_continue 3 out of 61 complex tests FAILED Start 36: regressiontests/kernel 36/39 Test #36: regressiontests/kernel ........... Passed 81.99 sec Start 37: regressiontests/freeenergy 37/39 Test #37: regressiontests/freeenergy ....... Passed 11.30 sec Start 38: regressiontests/pdb2gmx 38/39 Test #38: regressiontests/pdb2gmx .......... Passed 16.82 sec Start 39: regressiontests/rotation 39/39 Test #39: regressiontests/rotation ......... Passed 5.86 sec 97% tests passed, 1 tests failed out of 39 Label Time Summary: GTest = 15.68 sec (33 tests) IntegrationTest = 8.81 sec (3 tests) MpiTest = 0.18 sec (3 tests) UnitTest = 6.87 sec (30 tests) Total Test time (real) = 187.17 sec The following tests FAILED: 35 - regressiontests/complex (Failed) Errors while running CTest CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target 'CMakeFiles/run-ctest-nophys' failed make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 CMakeFiles/Makefile2:1160: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all' failed make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:546: recipe for target 'check' failed make: *** [check] Error 2 _____________________________ Regards Navneet Kumar From rajeswari.biotech at gmail.com Thu Feb 27 08:00:47 2020 From: rajeswari.biotech at gmail.com (Rajeswari A.) Date: Thu, 27 Feb 2020 07:00:47 -0000 Subject: [gmx-users] Proximal RDF of water around protein? Message-ID: Hi all, Is it possible to calculate proximal RDF of water around protein using gromacs? If not what other programs can I use? Please suggest me. Thanks, Rajeswari From madhu.dhurua94 at gmail.com Thu Feb 27 08:22:16 2020 From: madhu.dhurua94 at gmail.com (shakuntala dhurua) Date: Thu, 27 Feb 2020 07:22:16 -0000 Subject: [gmx-users] regarding calculation on shear viscosity Message-ID: ---------- Forwarded message --------- From: Madhurima Jana Date: Thu, Feb 27, 2020 at 12:10 PM Subject: Re: problem regarding calculation on shear_viscosity To: shakuntala dhurua Dear All, I have calculated shear viscosity (from 5 ns production trajectory) of bulk > water (900 water molecules) by using the following command. > > gmx tcaf -n index.ndx -s water_packmol_30a_pro5.tpr -f > water_packmol_30a_pro5.trr -oc water_packmol_30a_pro5_wat_tcaf.xvg , > > In the output file named visc_k.xvg , I found that while the eta values > for different k are in the range of 0.3 to 0.5 cp, sudden increase in eta > value of 12 cp occurs in one case. I am unable to trace the reason behind > it. Hence I request your help to know if I am doing anything wrong. The > visc_k.xvg file is attached for your reference. > Thanks in advance, Shakuntala From nt2614888 at gmail.com Thu Feb 27 08:50:26 2020 From: nt2614888 at gmail.com (Neha Tiwari) Date: Thu, 27 Feb 2020 07:50:26 -0000 Subject: [gmx-users] Error in ions.tpr generation Message-ID: Dear gmx experts, The ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. Still, I am getting the following error, dirctly copied from the terminal. And I am unable to generate any extension files in GROMACS using this .itp. $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr :-) GROMACS - gmx grompp, 2018.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ya/Desktop/Neha/fecA/gromos Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' NOTE 1 [file ions.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 49113858 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type '4JCP' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file topol.top, line 45350]: System has non-zero total charge: -14.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet ERROR 1 [file topol.top, line 45350]: atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 2 [file topol.top, line 45350]: atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 3 [file topol.top, line 45350]: atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 4 [file topol.top, line 45350]: atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 5 [file topol.top, line 45350]: atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 6 [file topol.top, line 45350]: atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 7 [file topol.top, line 45350]: atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 8 [file topol.top, line 45350]: atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 9 [file topol.top, line 45350]: atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 10 [file topol.top, line 45350]: atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 11 [file topol.top, line 45350]: atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 12 [file topol.top, line 45350]: atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 13 [file topol.top, line 45350]: atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 14 [file topol.top, line 45350]: atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 15 [file topol.top, line 45350]: atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) There were 2 notes ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137) Fatal error: There were 15 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Please help. From micpel at kth.se Thu Feb 27 10:37:26 2020 From: micpel at kth.se (Michele Pellegrino) Date: Thu, 27 Feb 2020 09:37:26 -0000 Subject: [gmx-users] Restart energy minimization with step .pdb files Message-ID: <1582796244403.22670@kth.se> Hi, I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern: step#%_n*.pdb being # and * integers and % a character ('a', 'b' or 'c'). I read the documentation, but I can't understand what those files represent. Could anyone give me some hint? Cheers, Michele p.s. I am running GROMACS 2019.5 From vuqv.phys at gmail.com Thu Feb 27 11:20:19 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Thu, 27 Feb 2020 10:20:19 -0000 Subject: [gmx-users] Restart energy minimization with step .pdb files In-Reply-To: <1582796244403.22670@kth.se> References: <1582796244403.22670@kth.se> Message-ID: It usually happens when you have two or more atoms overlap. step_XXX.pdb is the lowest energy state that steepest descend can give you with your input file. In my opinion, you should look into the log file of energy minimization step, find out which atom is exerted the maximum force, visualize your initial input and check is there any atom overlaps with that atom. Best, On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino wrote: > Hi, > > > I am trying to restart steepest descent using the .pdb files generated by > mdrun. The name of these files has the following pattern: > > step#%_n*.pdb > > being # and * integers and % a character ('a', 'b' or 'c'). > > I read the documentation, but I can't understand what those files > represent. > > Could anyone give me some hint? > > > Cheers, > > Michele > > > p.s. I am running GROMACS 2019.5 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 micpel at kth.se Thu Feb 27 11:28:23 2020 From: micpel at kth.se (Michele Pellegrino) Date: Thu, 27 Feb 2020 10:28:23 -0000 Subject: [gmx-users] Restart energy minimization with step .pdb files In-Reply-To: References: <1582796244403.22670@kth.se>, Message-ID: <1582799301686.4605@kth.se> I am sorry, but I don't fully understand your answer: do you mean step_XXX.pdb files are generated when atoms are overlapping? In any case I still do not get the meaning of the labels; what 'a', 'b' and 'c' stand for? Thank you for your quick response. Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Quyen V. Vu Sent: 27 February 2020 11:22 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Restart energy minimization with step .pdb files It usually happens when you have two or more atoms overlap. step_XXX.pdb is the lowest energy state that steepest descend can give you with your input file. In my opinion, you should look into the log file of energy minimization step, find out which atom is exerted the maximum force, visualize your initial input and check is there any atom overlaps with that atom. Best, On Thu, Feb 27, 2020 at 10:37 AM Michele Pellegrino wrote: > Hi, > > > I am trying to restart steepest descent using the .pdb files generated by > mdrun. The name of these files has the following pattern: > > step#%_n*.pdb > > being # and * integers and % a character ('a', 'b' or 'c'). > > I read the documentation, but I can't understand what those files > represent. > > Could anyone give me some hint? > > > Cheers, > > Michele > > > p.s. I am running GROMACS 2019.5 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 andreas.baer at fau.de Thu Feb 27 11:31:25 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Thu, 27 Feb 2020 10:31:25 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> Message-ID: <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> Hi, with the link below, additional log files for runs with 1 GPU should be accessible now. Thank you for the comment with the rlist, I did not know, that this will affect the performance negatively. I know, about the nstcalcenergy, but I need it for several of my simulations. Cheers, Andreas On 26.02.20 16:50, Szil?rd P?ll wrote: > Hi, > > Can you please check the performance when running on a single GPU 2019 vs > 2020 with your inputs? > > Also note that you are using some peculiar settings that will have an > adverse effect on performance (like manually set rlist disallowing the dual > pair-list setup, and nstcalcenergy=1). > > Cheers, > > -- > Szil?rd > > > On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer wrote: > >> Hello, >> >> here is a link to the logfiles. >> >> https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 >> >> If necessary, I can also provide some more log or tpr/gro/... files. >> >> Cheers, >> Andreas >> >> >> On 26.02.20 16:09, Paul bauer wrote: >>> Hello, >>> >>> you can't add attachments to the list, please upload the files >>> somewhere to share them. >>> This might be quite important to us, because the performance >>> regression is not expected by us. >>> >>> Cheers >>> >>> Paul >>> >>> On 26/02/2020 15:54, Andreas Baer wrote: >>>> Hello, >>>> >>>> from a set of benchmark tests with large systems using Gromacs >>>> versions 2019.5 and 2020, I obtained some unexpected results: >>>> With the same set of parameters and the 2020 version, I obtain a >>>> performance that is about 2/3 of the 2019.5 version. Interestingly, >>>> according to nvidia-smi, the GPU usage is about 20% higher for the >>>> 2020 version. >>>> Also from the log files it seems, that the 2020 version does the >>>> computations more efficiently, but spends so much more time waiting, >>>> that the overall performance drops. >>>> >>>> Some background info on the benchmarks: >>>> - System contains about 2.1 million atoms. >>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + >>>> SMT; 4x NVIDIA Tesla V100 >>>> (similar results with less significant performance drop (~15%) on a >>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy >>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) >>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find >>>> the optimal set. However the performance drop seems to be persistent >>>> for all such options. >>>> >>>> Two representative log files are attached. >>>> Does anyone have an idea, where this drop comes from, and how to >>>> choose the parameters for the 2020 version to circumvent this? >>>> >>>> Regards, >>>> Andreas >>>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 Thu Feb 27 12:34:40 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Thu, 27 Feb 2020 11:34:40 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> Message-ID: Hi On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer wrote: > Hi, > > with the link below, additional log files for runs with 1 GPU should be > accessible now. > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun -ntmpi 1. It would also help if you could share some input files in case if further testing is needed. > Thank you for the comment with the rlist, I did not know, that this will > affect the performance negatively. It does in multiple ways. First, you are using a rather long list buffer which will make the nonbonded pair-interaction calculation more computational expensive than it could be if you just used a tolerance and let the buffer be calculated. Secondly, as setting a manual rlist disables the automated verlet buffer calculation, it prevents mdrun from using a dual pairl-list setup (see http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning) which has additional performance benefits. Cheers, -- Szil?rd > I know, about the nstcalcenergy, but > I need it for several of my simulations. Cheers, > Andreas > > On 26.02.20 16:50, Szil?rd P?ll wrote: > > Hi, > > > > Can you please check the performance when running on a single GPU 2019 vs > > 2020 with your inputs? > > > > Also note that you are using some peculiar settings that will have an > > adverse effect on performance (like manually set rlist disallowing the > dual > > pair-list setup, and nstcalcenergy=1). > > > > Cheers, > > > > -- > > Szil?rd > > > > > > On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > wrote: > > > >> Hello, > >> > >> here is a link to the logfiles. > >> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >> > >> If necessary, I can also provide some more log or tpr/gro/... files. > >> > >> Cheers, > >> Andreas > >> > >> > >> On 26.02.20 16:09, Paul bauer wrote: > >>> Hello, > >>> > >>> you can't add attachments to the list, please upload the files > >>> somewhere to share them. > >>> This might be quite important to us, because the performance > >>> regression is not expected by us. > >>> > >>> Cheers > >>> > >>> Paul > >>> > >>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>> Hello, > >>>> > >>>> from a set of benchmark tests with large systems using Gromacs > >>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>> With the same set of parameters and the 2020 version, I obtain a > >>>> performance that is about 2/3 of the 2019.5 version. Interestingly, > >>>> according to nvidia-smi, the GPU usage is about 20% higher for the > >>>> 2020 version. > >>>> Also from the log files it seems, that the 2020 version does the > >>>> computations more efficiently, but spends so much more time waiting, > >>>> that the overall performance drops. > >>>> > >>>> Some background info on the benchmarks: > >>>> - System contains about 2.1 million atoms. > >>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + > >>>> SMT; 4x NVIDIA Tesla V100 > >>>> (similar results with less significant performance drop (~15%) on a > >>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy > >>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > >>>> the optimal set. However the performance drop seems to be persistent > >>>> for all such options. > >>>> > >>>> Two representative log files are attached. > >>>> Does anyone have an idea, where this drop comes from, and how to > >>>> choose the parameters for the 2020 version to circumvent this? > >>>> > >>>> Regards, > >>>> Andreas > >>>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe 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 Thu Feb 27 12:34:41 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Thu, 27 Feb 2020 11:34:41 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> Message-ID: Hi On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer wrote: > Hi, > > with the link below, additional log files for runs with 1 GPU should be > accessible now. > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun -ntmpi 1. It would also help if you could share some input files in case if further testing is needed. > Thank you for the comment with the rlist, I did not know, that this will > affect the performance negatively. It does in multiple ways. First, you are using a rather long list buffer which will make the nonbonded pair-interaction calculation more computational expensive than it could be if you just used a tolerance and let the buffer be calculated. Secondly, as setting a manual rlist disables the automated verlet buffer calculation, it prevents mdrun from using a dual pairl-list setup (see http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning) which has additional performance benefits. Cheers, -- Szil?rd > I know, about the nstcalcenergy, but > I need it for several of my simulations. Cheers, > Andreas > > On 26.02.20 16:50, Szil?rd P?ll wrote: > > Hi, > > > > Can you please check the performance when running on a single GPU 2019 vs > > 2020 with your inputs? > > > > Also note that you are using some peculiar settings that will have an > > adverse effect on performance (like manually set rlist disallowing the > dual > > pair-list setup, and nstcalcenergy=1). > > > > Cheers, > > > > -- > > Szil?rd > > > > > > On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > wrote: > > > >> Hello, > >> > >> here is a link to the logfiles. > >> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >> > >> If necessary, I can also provide some more log or tpr/gro/... files. > >> > >> Cheers, > >> Andreas > >> > >> > >> On 26.02.20 16:09, Paul bauer wrote: > >>> Hello, > >>> > >>> you can't add attachments to the list, please upload the files > >>> somewhere to share them. > >>> This might be quite important to us, because the performance > >>> regression is not expected by us. > >>> > >>> Cheers > >>> > >>> Paul > >>> > >>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>> Hello, > >>>> > >>>> from a set of benchmark tests with large systems using Gromacs > >>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>> With the same set of parameters and the 2020 version, I obtain a > >>>> performance that is about 2/3 of the 2019.5 version. Interestingly, > >>>> according to nvidia-smi, the GPU usage is about 20% higher for the > >>>> 2020 version. > >>>> Also from the log files it seems, that the 2020 version does the > >>>> computations more efficiently, but spends so much more time waiting, > >>>> that the overall performance drops. > >>>> > >>>> Some background info on the benchmarks: > >>>> - System contains about 2.1 million atoms. > >>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + > >>>> SMT; 4x NVIDIA Tesla V100 > >>>> (similar results with less significant performance drop (~15%) on a > >>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy > >>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > >>>> the optimal set. However the performance drop seems to be persistent > >>>> for all such options. > >>>> > >>>> Two representative log files are attached. > >>>> Does anyone have an idea, where this drop comes from, and how to > >>>> choose the parameters for the 2020 version to circumvent this? > >>>> > >>>> Regards, > >>>> Andreas > >>>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe 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 andreas.baer at fau.de Thu Feb 27 13:07:38 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Thu, 27 Feb 2020 12:07:38 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> Message-ID: <150df543-9084-3adb-50c3-4276818dbf61@fau.de> Hi, On 27.02.20 12:34, Szil?rd P?ll wrote: > Hi > > On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer wrote: > >> Hi, >> >> with the link below, additional log files for runs with 1 GPU should be >> accessible now. >> > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun -ntmpi 1. > > It would also help if you could share some input files in case if further > testing is needed. Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4 -bonded gpu -update gpu` as parameters. However, it is run on the same machine with smt disabled. With the following link, I provide all the tests on this machine, I did by now, along with a summary of the performance for the several input parameters (both in `logfiles`), as well as input files (`C60xh.7z`) and the scripts to run these. I hope, this helps. If there is anything else, I can do to help, please let me know! > > >> Thank you for the comment with the rlist, I did not know, that this will >> affect the performance negatively. > > It does in multiple ways. First, you are using a rather long list buffer > which will make the nonbonded pair-interaction calculation more > computational expensive than it could be if you just used a tolerance and > let the buffer be calculated. Secondly, as setting a manual rlist disables > the automated verlet buffer calculation, it prevents mdrun from using a > dual pairl-list setup (see > http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning) > which has additional performance benefits. Ok, thank you for the explanation! > > Cheers, > -- > Szil?rd Cheers, Andreas > > > >> I know, about the nstcalcenergy, but >> I need it for several of my simulations. > Cheers, >> Andreas >> >> On 26.02.20 16:50, Szil?rd P?ll wrote: >>> Hi, >>> >>> Can you please check the performance when running on a single GPU 2019 vs >>> 2020 with your inputs? >>> >>> Also note that you are using some peculiar settings that will have an >>> adverse effect on performance (like manually set rlist disallowing the >> dual >>> pair-list setup, and nstcalcenergy=1). >>> >>> Cheers, >>> >>> -- >>> Szil?rd >>> >>> >>> On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer >> wrote: >>>> Hello, >>>> >>>> here is a link to the logfiles. >>>> >>>> >> https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 >>>> If necessary, I can also provide some more log or tpr/gro/... files. >>>> >>>> Cheers, >>>> Andreas >>>> >>>> >>>> On 26.02.20 16:09, Paul bauer wrote: >>>>> Hello, >>>>> >>>>> you can't add attachments to the list, please upload the files >>>>> somewhere to share them. >>>>> This might be quite important to us, because the performance >>>>> regression is not expected by us. >>>>> >>>>> Cheers >>>>> >>>>> Paul >>>>> >>>>> On 26/02/2020 15:54, Andreas Baer wrote: >>>>>> Hello, >>>>>> >>>>>> from a set of benchmark tests with large systems using Gromacs >>>>>> versions 2019.5 and 2020, I obtained some unexpected results: >>>>>> With the same set of parameters and the 2020 version, I obtain a >>>>>> performance that is about 2/3 of the 2019.5 version. Interestingly, >>>>>> according to nvidia-smi, the GPU usage is about 20% higher for the >>>>>> 2020 version. >>>>>> Also from the log files it seems, that the 2020 version does the >>>>>> computations more efficiently, but spends so much more time waiting, >>>>>> that the overall performance drops. >>>>>> >>>>>> Some background info on the benchmarks: >>>>>> - System contains about 2.1 million atoms. >>>>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores + >>>>>> SMT; 4x NVIDIA Tesla V100 >>>>>> (similar results with less significant performance drop (~15%) on a >>>>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 (?Ivy >>>>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) >>>>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find >>>>>> the optimal set. However the performance drop seems to be persistent >>>>>> for all such options. >>>>>> >>>>>> Two representative log files are attached. >>>>>> Does anyone have an idea, where this drop comes from, and how to >>>>>> choose the parameters for the 2020 version to circumvent this? >>>>>> >>>>>> Regards, >>>>>> Andreas >>>>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe 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 Thu Feb 27 13:11:53 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 27 Feb 2020 12:11:53 -0000 Subject: [gmx-users] Restart energy minimization with step .pdb files In-Reply-To: <1582796244403.22670@kth.se> References: <1582796244403.22670@kth.se> Message-ID: On 2/27/20 4:37 AM, Michele Pellegrino wrote: > Hi, > > > I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern: > > step#%_n*.pdb > > being # and * integers and % a character ('a', 'b' or 'c'). > > I read the documentation, but I can't understand what those files represent. > > Could anyone give me some hint? step*.pdb files are the coordinates in each spatial domain in an attempt to help you debug what is going on. I have never been able to employ them in any useful way. All they really indicate is that your mdrun process is going to crash due to instability. -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 Feb 27 13:12:31 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 27 Feb 2020 12:12:31 -0000 Subject: [gmx-users] Error in ions.tpr generation In-Reply-To: References: Message-ID: <15a882a2-e922-6553-38c9-3289a5672d32@vt.edu> On 2/27/20 2:50 AM, Neha Tiwari wrote: > Dear gmx experts, > The ligand molecule was refined and optimized using G03 calculation and > .itp was generated using the ATB server. Still, I am getting the > following error, dirctly copied from the terminal. > And I am unable to generate any extension files in GROMACS using this .itp. > > > > $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > :-) GROMACS - gmx grompp, 2018.1 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra > > Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru > > Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus > > > Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl > > Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola > > Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov > > Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen > > Christian Wennberg Maarten Wolf > > and the project leaders: > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2017, The GROMACS development team at > > Uppsala University, Stockholm University and > > the Royal Institute of Technology, Sweden. > > check out http://www.gromacs.org for more information. > > > > GROMACS is free software; you can redistribute it and/or modify it > > under the terms of the GNU Lesser General Public License > > as published by the Free Software Foundation; either version 2.1 > > of the License, or (at your option) any later version. > > > > GROMACS: gmx grompp, version 2018.1 > > Executable: /usr/bin/gmx > > Data prefix: /usr > > Working dir: /home/ya/Desktop/Neha/fecA/gromos > > Command line: > > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > > > Ignoring obsolete mdp entry 'title' > > > > NOTE 1 [file ions.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 49113858 > > Generated 165 of the 1596 non-bonded parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein' > > Excluding 3 bonded neighbours molecule type '4JCP' > > Excluding 2 bonded neighbours molecule type 'SOL' > > > > NOTE 2 [file topol.top, line 45350]: > > System has non-zero total charge: -14.000000 > > Total charge should normally be an integer. See > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > for discussion on how close it should be to an integer. > > > > > > > > Removing all charge groups because cutoff-scheme=Verlet > > > > ERROR 1 [file topol.top, line 45350]: > > atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) Apparently your topology is incorrectly formatted and does not contain masses of the atoms. You will need to correct its contents. -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 micpel at kth.se Thu Feb 27 13:23:21 2020 From: micpel at kth.se (Michele Pellegrino) Date: Thu, 27 Feb 2020 12:23:21 -0000 Subject: [gmx-users] Restart energy minimization with step .pdb files In-Reply-To: References: <1582796244403.22670@kth.se>, Message-ID: <1582806198538.81635@kth.se> Ok, thank you for the clarification; I thought those files where generated no matter what. By the way, I am not trying to restart because the simulation crashed: it's just that I am running on a cluster and the job exceded the prescibed time limit. The minimimization itself seems to work fine (at least this is what I can see from ener.edr). Cheers, Michele ________________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Justin Lemkul Sent: 27 February 2020 13:11 To: gmx-users at gromacs.org Subject: Re: [gmx-users] Restart energy minimization with step .pdb files On 2/27/20 4:37 AM, Michele Pellegrino wrote: > Hi, > > > I am trying to restart steepest descent using the .pdb files generated by mdrun. The name of these files has the following pattern: > > step#%_n*.pdb > > being # and * integers and % a character ('a', 'b' or 'c'). > > I read the documentation, but I can't understand what those files represent. > > Could anyone give me some hint? step*.pdb files are the coordinates in each spatial domain in an attempt to help you debug what is going on. I have never been able to employ them in any useful way. All they really indicate is that your mdrun process is going to crash due to instability. -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 navneetcdl at gmail.com Thu Feb 27 15:09:33 2020 From: navneetcdl at gmail.com (Navneet Kumar) Date: Thu, 27 Feb 2020 14:09:33 -0000 Subject: [gmx-users] regressiontests/complex (Failed) Message-ID: Hello Everyone! -During installation GROMACS-2018.8 on ubuntu with Tesla C2050 -During step - "sudo make check" -One test (regressiontests/complex) out of 39 tests failed. attached details while installation ____________________________________________________________ 35/39 Test #35: regressiontests/complex ..........***Failed 49.02 sec :-) GROMACS - gmx mdrun, 2018.8 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018.8 Executable: /home/navneet/Downloads/gromacs-2018.8/build/bin/gmx Data prefix: /home/navneet/Downloads/gromacs-2018.8 (source tree) Working dir: /home/navneet/Downloads/regressiontests-2018.8 Command line: gmx mdrun -h Thanx for Using GROMACS - Have a Nice Day Abnormal return value for ' gmx mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Re-running nbnxn-vdw-potential-switch using CPU-based PME Re-running nbnxn_pme using CPU-based PME Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1' was 1 Retrying mdrun with better settings... Re-running octahedron using CPU-based PME Re-running orientation-restraints using CPU-based PME Re-running pull_geometry_angle using CPU-based PME Re-running pull_geometry_angle-axis using CPU-based PME Re-running pull_geometry_dihedral using CPU-based PME Re-running swap_x using CPU-based PME FAILED. Check checkforce.out (2 errors) file(s) in swap_y for swap_y Re-running swap_y using CPU-based PME FAILED. Check checkforce.out (1 errors) file(s) in swap_z for swap_z Re-running swap_z using CPU-based PME FAILED. Check checkforce.out (1 errors) file(s) in tip4p_continue for tip4p_continue 3 out of 61 complex tests FAILED Start 36: regressiontests/kernel 36/39 Test #36: regressiontests/kernel ........... Passed 81.99 sec Start 37: regressiontests/freeenergy 37/39 Test #37: regressiontests/freeenergy ....... Passed 11.30 sec Start 38: regressiontests/pdb2gmx 38/39 Test #38: regressiontests/pdb2gmx .......... Passed 16.82 sec Start 39: regressiontests/rotation 39/39 Test #39: regressiontests/rotation ......... Passed 5.86 sec 97% tests passed, 1 tests failed out of 39 Label Time Summary: GTest = 15.68 sec (33 tests) IntegrationTest = 8.81 sec (3 tests) MpiTest = 0.18 sec (3 tests) UnitTest = 6.87 sec (30 tests) Total Test time (real) = 187.17 sec The following tests FAILED: 35 - regressiontests/complex (Failed) Errors while running CTest CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target 'CMakeFiles/run-ctest-nophys' failed make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 CMakeFiles/Makefile2:1160: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all' failed make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:546: recipe for target 'check' failed make: *** [check] Error 2 _____________________________________________________________________ How to solve this error. Earlier this error also arises while installing GROMACS-2018.4 on the same system. How to solve this problem. What artefacts/error one can expect even if we install the gromacs after this particular test fails. Regards Navneet From pall.szilard at gmail.com Thu Feb 27 18:00:12 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Thu, 27 Feb 2020 17:00:12 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <150df543-9084-3adb-50c3-4276818dbf61@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> Message-ID: On Thu, Feb 27, 2020 at 1:08 PM Andreas Baer wrote: > Hi, > > On 27.02.20 12:34, Szil?rd P?ll wrote: > > Hi > > > > On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer > wrote: > > > >> Hi, > >> > >> with the link below, additional log files for runs with 1 GPU should be > >> accessible now. > >> > > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun -ntmpi 1. > > > > It would also help if you could share some input files in case if further > > testing is needed. > Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4 > -bonded gpu -update gpu` as parameters. However, it is run on the same > machine with smt disabled. > With the following link, I provide all the tests on this machine, I did > by now, along with a summary of the performance for the several input > parameters (both in `logfiles`), as well as input files (`C60xh.7z`) and > the scripts to run these. > Links seems to be missing. -- Szil?rd > I hope, this helps. If there is anything else, I can do to help, please > let me know! > > > > > >> Thank you for the comment with the rlist, I did not know, that this will > >> affect the performance negatively. > > > > It does in multiple ways. First, you are using a rather long list buffer > > which will make the nonbonded pair-interaction calculation more > > computational expensive than it could be if you just used a tolerance and > > let the buffer be calculated. Secondly, as setting a manual rlist > disables > > the automated verlet buffer calculation, it prevents mdrun from using a > > dual pairl-list setup (see > > > http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning > ) > > which has additional performance benefits. > Ok, thank you for the explanation! > > > > Cheers, > > -- > > Szil?rd > Cheers, > Andreas > > > > > > > >> I know, about the nstcalcenergy, but > >> I need it for several of my simulations. > > Cheers, > >> Andreas > >> > >> On 26.02.20 16:50, Szil?rd P?ll wrote: > >>> Hi, > >>> > >>> Can you please check the performance when running on a single GPU 2019 > vs > >>> 2020 with your inputs? > >>> > >>> Also note that you are using some peculiar settings that will have an > >>> adverse effect on performance (like manually set rlist disallowing the > >> dual > >>> pair-list setup, and nstcalcenergy=1). > >>> > >>> Cheers, > >>> > >>> -- > >>> Szil?rd > >>> > >>> > >>> On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > >> wrote: > >>>> Hello, > >>>> > >>>> here is a link to the logfiles. > >>>> > >>>> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >>>> If necessary, I can also provide some more log or tpr/gro/... files. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> On 26.02.20 16:09, Paul bauer wrote: > >>>>> Hello, > >>>>> > >>>>> you can't add attachments to the list, please upload the files > >>>>> somewhere to share them. > >>>>> This might be quite important to us, because the performance > >>>>> regression is not expected by us. > >>>>> > >>>>> Cheers > >>>>> > >>>>> Paul > >>>>> > >>>>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>>>> Hello, > >>>>>> > >>>>>> from a set of benchmark tests with large systems using Gromacs > >>>>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>>>> With the same set of parameters and the 2020 version, I obtain a > >>>>>> performance that is about 2/3 of the 2019.5 version. Interestingly, > >>>>>> according to nvidia-smi, the GPU usage is about 20% higher for the > >>>>>> 2020 version. > >>>>>> Also from the log files it seems, that the 2020 version does the > >>>>>> computations more efficiently, but spends so much more time waiting, > >>>>>> that the overall performance drops. > >>>>>> > >>>>>> Some background info on the benchmarks: > >>>>>> - System contains about 2.1 million atoms. > >>>>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores > + > >>>>>> SMT; 4x NVIDIA Tesla V100 > >>>>>> (similar results with less significant performance drop (~15%) > on a > >>>>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 > (?Ivy > >>>>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > >>>>>> the optimal set. However the performance drop seems to be persistent > >>>>>> for all such options. > >>>>>> > >>>>>> Two representative log files are attached. > >>>>>> Does anyone have an idea, where this drop comes from, and how to > >>>>>> choose the parameters for the 2020 version to circumvent this? > >>>>>> > >>>>>> Regards, > >>>>>> Andreas > >>>>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe 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 Thu Feb 27 18:00:16 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Thu, 27 Feb 2020 17:00:16 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <150df543-9084-3adb-50c3-4276818dbf61@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> Message-ID: On Thu, Feb 27, 2020 at 1:08 PM Andreas Baer wrote: > Hi, > > On 27.02.20 12:34, Szil?rd P?ll wrote: > > Hi > > > > On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer > wrote: > > > >> Hi, > >> > >> with the link below, additional log files for runs with 1 GPU should be > >> accessible now. > >> > > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun -ntmpi 1. > > > > It would also help if you could share some input files in case if further > > testing is needed. > Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4 > -bonded gpu -update gpu` as parameters. However, it is run on the same > machine with smt disabled. > With the following link, I provide all the tests on this machine, I did > by now, along with a summary of the performance for the several input > parameters (both in `logfiles`), as well as input files (`C60xh.7z`) and > the scripts to run these. > Links seems to be missing. -- Szil?rd > I hope, this helps. If there is anything else, I can do to help, please > let me know! > > > > > >> Thank you for the comment with the rlist, I did not know, that this will > >> affect the performance negatively. > > > > It does in multiple ways. First, you are using a rather long list buffer > > which will make the nonbonded pair-interaction calculation more > > computational expensive than it could be if you just used a tolerance and > > let the buffer be calculated. Secondly, as setting a manual rlist > disables > > the automated verlet buffer calculation, it prevents mdrun from using a > > dual pairl-list setup (see > > > http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning > ) > > which has additional performance benefits. > Ok, thank you for the explanation! > > > > Cheers, > > -- > > Szil?rd > Cheers, > Andreas > > > > > > > >> I know, about the nstcalcenergy, but > >> I need it for several of my simulations. > > Cheers, > >> Andreas > >> > >> On 26.02.20 16:50, Szil?rd P?ll wrote: > >>> Hi, > >>> > >>> Can you please check the performance when running on a single GPU 2019 > vs > >>> 2020 with your inputs? > >>> > >>> Also note that you are using some peculiar settings that will have an > >>> adverse effect on performance (like manually set rlist disallowing the > >> dual > >>> pair-list setup, and nstcalcenergy=1). > >>> > >>> Cheers, > >>> > >>> -- > >>> Szil?rd > >>> > >>> > >>> On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > >> wrote: > >>>> Hello, > >>>> > >>>> here is a link to the logfiles. > >>>> > >>>> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >>>> If necessary, I can also provide some more log or tpr/gro/... files. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> On 26.02.20 16:09, Paul bauer wrote: > >>>>> Hello, > >>>>> > >>>>> you can't add attachments to the list, please upload the files > >>>>> somewhere to share them. > >>>>> This might be quite important to us, because the performance > >>>>> regression is not expected by us. > >>>>> > >>>>> Cheers > >>>>> > >>>>> Paul > >>>>> > >>>>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>>>> Hello, > >>>>>> > >>>>>> from a set of benchmark tests with large systems using Gromacs > >>>>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>>>> With the same set of parameters and the 2020 version, I obtain a > >>>>>> performance that is about 2/3 of the 2019.5 version. Interestingly, > >>>>>> according to nvidia-smi, the GPU usage is about 20% higher for the > >>>>>> 2020 version. > >>>>>> Also from the log files it seems, that the 2020 version does the > >>>>>> computations more efficiently, but spends so much more time waiting, > >>>>>> that the overall performance drops. > >>>>>> > >>>>>> Some background info on the benchmarks: > >>>>>> - System contains about 2.1 million atoms. > >>>>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = 16 cores > + > >>>>>> SMT; 4x NVIDIA Tesla V100 > >>>>>> (similar results with less significant performance drop (~15%) > on a > >>>>>> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 > (?Ivy > >>>>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find > >>>>>> the optimal set. However the performance drop seems to be persistent > >>>>>> for all such options. > >>>>>> > >>>>>> Two representative log files are attached. > >>>>>> Does anyone have an idea, where this drop comes from, and how to > >>>>>> choose the parameters for the 2020 version to circumvent this? > >>>>>> > >>>>>> Regards, > >>>>>> Andreas > >>>>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe 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 liu00554 at umn.edu Thu Feb 27 20:42:41 2020 From: liu00554 at umn.edu (Chenyu Liu) Date: Thu, 27 Feb 2020 19:42:41 -0000 Subject: [gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs Message-ID: Hi gromacs users, I was trying to analyze hydrogen bonding interaction of a protein and intended to obtain the detailed list of interactions. Such as amine hydrogen from Lys A residue forms a hydrogen bond with the backbone carbonyl oxygen of some other residue. I tried the gmx hbond command but I cannot find one option for this purpose. I could get results such as hbond donor numbers, distance distribution, but not detailed information about the interactions. I was wondering if there is any command to derive this information from the trajectory. Also, if I wanted to analyze hydrogen bond formed by a specific type of donor/acceptor (such as side chain hydrogen as a donor), what should I do to specify that? I have tried using vmd software (there is a hbond analysis in the extension) to analyze the trajectory, and it worked pretty well for shorter trajectories. My trajectory consists of 5000 frames and when I loaded the trajectory the program terminates at around 4000 frames. So, I think I should divide the trajectories into smaller pieces and analyze each piece. My question is that is there a way I can write a bash script to automate the process so that I can analyze these shorter trajectories without loading them by hand (otherwise there will be 100 shorter trajectories, since I have run several parallel long trajectories). I can write bash script for all operations involving gromacs, but not vmd. I would really appreciate it if you could answer my question, or point out some resources which I could refer to. Thanks in advance! Best regards, Chenyu From liu00554 at umn.edu Thu Feb 27 20:57:30 2020 From: liu00554 at umn.edu (Chenyu Liu) Date: Thu, 27 Feb 2020 19:57:30 -0000 Subject: [gmx-users] Analyzing Hydrogen Bonding Interactions using Gromacs In-Reply-To: References: Message-ID: This is what I mean by detailed information: ........vi hbonds-details.dat Found 360 hbonds. donor acceptor occupancy LYS21-Side-NZ GLU24-Side-OE2 17.31% VAL15-Main-N GLU17-Side-OE1 40.38% LYS16-Main-N GLU17-Side-OE1 11.54% ARG190-Side-NH2 ASP161-Side-OD2 61.54% LYS23-Main-N LEU19-Main-O 19.23% ASP25-Main-N LYS21-Main-O 21.15% SER159-Side-OG TYR156-Main-O 30.77% this .dat file is generated by vmd's hydrogen bond analysis extension. I hope this would clarify the question I have. On Thu, Feb 27, 2020 at 1:42 PM Chenyu Liu wrote: > Hi gromacs users, > > I was trying to analyze hydrogen bonding interaction of a protein and > intended to obtain the detailed list of interactions. Such as amine > hydrogen from Lys A residue forms a hydrogen bond with the backbone > carbonyl oxygen of some other residue. I tried the gmx hbond command but I > cannot find one option for this purpose. I could get results such as hbond > donor numbers, distance distribution, but not detailed information about > the interactions. I was wondering if there is any command to derive this > information from the trajectory. Also, if I wanted to analyze hydrogen bond > formed by a specific type of donor/acceptor (such as side chain hydrogen as > a donor), what should I do to specify that? > > I have tried using vmd software (there is a hbond analysis in the > extension) to analyze the trajectory, and it worked pretty well for shorter > trajectories. My trajectory consists of 5000 frames and when I loaded the > trajectory the program terminates at around 4000 frames. So, I think I > should divide the trajectories into smaller pieces and analyze each piece. > My question is that is there a way I can write a bash script to automate > the process so that I can analyze these shorter trajectories without > loading them by hand (otherwise there will be 100 shorter trajectories, > since I have run several parallel long trajectories). I can write bash > script for all operations involving gromacs, but not vmd. > > I would really appreciate it if you could answer my question, or point out > some resources which I could refer to. Thanks in advance! > > Best regards, > Chenyu > > From oliverdutton at me.com Thu Feb 27 23:36:43 2020 From: oliverdutton at me.com (Oliver Dutton) Date: Thu, 27 Feb 2020 22:36:43 -0000 Subject: [gmx-users] Compiling with OpenCL for Macbook AMD Radeon Pro 560 GPU In-Reply-To: References: <48822E54-F4AC-4ED8-90C5-053DD43CDA8F@me.com> Message-ID: <739DD5A4-5ED1-423B-B204-B6D2D4E9FEA1@me.com> I am sorry. I thought failing 'make check? meant it would fail on install. It works perfectly. Thank you, Oliver > On 18 Feb 2020, at 12:10, Szil?rd P?ll wrote: > > Hi Oliver, > > Does this affect an installation of GROMACS? In previous reports we have > observed that the issue is only present when running "make check" in the > build tree, but not in the case of an installed version. > > Cheers, > -- > Szil?rd > > > On Mon, Feb 17, 2020 at 7:58 PM Oliver Dutton wrote: > >> Hello, >> >> I am trying to do the exact same as Michael in >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html >> < >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-February/124394.html >>> >> but hit the exact same error of it not finding a simple header file. I?ve >> tried building 2019.5 and 2020 Gromacs on a MacBook Pro with AMD Radeon Pro >> 560 GPU. >> >> I?m using the apple inbuilt compiler, same flags and cmake options as >> Michael. Was this ever got working? >> >> Kind regards, >> Oliver >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 florisvaneerden at biken.osaka-u.ac.jp Fri Feb 28 03:06:37 2020 From: florisvaneerden at biken.osaka-u.ac.jp (Floris van Eerden) Date: Fri, 28 Feb 2020 02:06:37 -0000 Subject: [gmx-users] Z shell autocompletion Message-ID: <64E22034-9A27-4214-A423-DBAB99E177AA@biken.osaka-u.ac.jp> Dear Gromacs community, About a year ago I switched from Bash to ZSH as my default shell, although I have been content with the switch, for some reason Gromacs auto completion does not work properly anymore. The problem occurs both on MacOS and CentOS 7, and I have checked multiple versions (2018.1 and 2019.3). The issue has been nicely described and filed as a bug in Redmine. It is of course not a major issue, but I would be glad if anybody knows a solution or workaround for this minor annoyance. Thanks for your help and suggestions, Best, Floris van Eerden From devargyachakraborty.kgp at gmail.com Fri Feb 28 09:23:50 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Fri, 28 Feb 2020 08:23:50 -0000 Subject: [gmx-users] error on graphene sheet simulation Message-ID: while going through your tutorial on graphene sheet i was facing an error. https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ NOTE 2 [file nvt.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to 164492569 Generated 20503 of the 20503 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 17396 of the 20503 1-4 parameter combinations ERROR 1 [file GRA.itp, line 7]: Atomtype CG2R61 not found There were 2 notes ------------------------------------------------------- Program: gmx grompp, version 2019.1 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1333) Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- can you give any suggestion what could have gone wrong... thanks From paul.bauer.q at gmail.com Fri Feb 28 10:44:17 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Fri, 28 Feb 2020 09:44:17 -0000 Subject: [gmx-users] GROMACS 2019.6 patch release available Message-ID: <11e86c2d-3890-1ff2-0f8e-530b81407492@gmail.com> Hi GROMACS users, The official release of GROMACS 2019.6 is available! The sixth patch release fixes several issues found since the previous patch release of GROMACS 2019. We encourage all users of the 2019 series to update to 2019.6. Please see the link to the release notes below for more details. Please note that the 2019 branch is now out of main support, and we will only address critical scientific issues in this branch. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.6.tar.gz Documentation: http://manual.gromacs.org/2019.6/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.6.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From andreas.baer at fau.de Fri Feb 28 11:11:00 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Fri, 28 Feb 2020 10:11:00 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> Message-ID: <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> Hi, sorry for it! https://faubox.rrze.uni-erlangen.de/getlink/fiUpELsXokQr3a7vyeDSKdY3/benchmarks_2019-2020_all Cheers, Andreas On 27.02.20 17:59, Szil?rd P?ll wrote: > On Thu, Feb 27, 2020 at 1:08 PM Andreas Baer > wrote: > > Hi, > > On 27.02.20 12:34, Szil?rd P?ll wrote: > > Hi > > > > On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer > > wrote: > > > >> Hi, > >> > >> with the link below, additional log files for runs with 1 GPU > should be > >> accessible now. > >> > > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun > -ntmpi 1. > > > > It would also help if you could share some input files in case > if further > > testing is needed. > Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4 > -bonded gpu -update gpu` as parameters. However, it is run on the > same > machine with smt disabled. > With the following link, I provide all the tests on this machine, > I did > by now, along with a summary of the performance for the several input > parameters (both in `logfiles`), as well as input files > (`C60xh.7z`) and > the scripts to run these. > > > Links seems to be missing. > -- > Szil?rd > > I hope, this helps. If there is anything else, I can do to help, > please > let me know! > > > > > >> Thank you for the comment with the rlist, I did not know, that > this will > >> affect the performance negatively. > > > > It does in multiple ways. First, you are using a rather long > list buffer > > which will make the nonbonded pair-interaction calculation more > > computational expensive than it could be if you just used a > tolerance and > > let the buffer be calculated. Secondly, as setting a manual > rlist disables > > the automated verlet buffer calculation, it prevents mdrun from > using a > > dual pairl-list setup (see > > > http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning) > > which has additional performance benefits. > Ok, thank you for the explanation! > > > > Cheers, > > -- > > Szil?rd > Cheers, > Andreas > > > > > > > >> I know, about the nstcalcenergy, but > >> I need it for several of my simulations. > > Cheers, > >> Andreas > >> > >> On 26.02.20 16:50, Szil?rd P?ll wrote: > >>> Hi, > >>> > >>> Can you please check the performance when running on a single > GPU 2019 vs > >>> 2020 with your inputs? > >>> > >>> Also note that you are using some peculiar settings that will > have an > >>> adverse effect on performance (like manually set rlist > disallowing the > >> dual > >>> pair-list setup, and nstcalcenergy=1). > >>> > >>> Cheers, > >>> > >>> -- > >>> Szil?rd > >>> > >>> > >>> On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > > > >> wrote: > >>>> Hello, > >>>> > >>>> here is a link to the logfiles. > >>>> > >>>> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >>>> If necessary, I can also provide some more log or tpr/gro/... > files. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> On 26.02.20 16:09, Paul bauer wrote: > >>>>> Hello, > >>>>> > >>>>> you can't add attachments to the list, please upload the files > >>>>> somewhere to share them. > >>>>> This might be quite important to us, because the performance > >>>>> regression is not expected by us. > >>>>> > >>>>> Cheers > >>>>> > >>>>> Paul > >>>>> > >>>>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>>>> Hello, > >>>>>> > >>>>>> from a set of benchmark tests with large systems using Gromacs > >>>>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>>>> With the same set of parameters and the 2020 version, I > obtain a > >>>>>> performance that is about 2/3 of the 2019.5 version. > Interestingly, > >>>>>> according to nvidia-smi, the GPU usage is about 20% higher > for the > >>>>>> 2020 version. > >>>>>> Also from the log files it seems, that the 2020 version > does the > >>>>>> computations more efficiently, but spends so much more time > waiting, > >>>>>> that the overall performance drops. > >>>>>> > >>>>>> Some background info on the benchmarks: > >>>>>> - System contains about 2.1 million atoms. > >>>>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = > 16 cores + > >>>>>> SMT; 4x NVIDIA Tesla V100 > >>>>>>? ? ?(similar results with less significant performance drop > (~15%) on a > >>>>>> different machine: 2 or 4 nodes with each [2x Intel Xeon > 2660v2 (?Ivy > >>>>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are > used to find > >>>>>> the optimal set. However the performance drop seems to be > persistent > >>>>>> for all such options. > >>>>>> > >>>>>> Two representative log files are attached. > >>>>>> Does anyone have an idea, where this drop comes from, and > how to > >>>>>> choose the parameters for the 2020 version to circumvent this? > >>>>>> > >>>>>> Regards, > >>>>>> Andreas > >>>>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe 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 andreas.baer at fau.de Fri Feb 28 11:11:03 2020 From: andreas.baer at fau.de (Andreas Baer) Date: Fri, 28 Feb 2020 10:11:03 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> Message-ID: <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> Hi, sorry for it! https://faubox.rrze.uni-erlangen.de/getlink/fiUpELsXokQr3a7vyeDSKdY3/benchmarks_2019-2020_all Cheers, Andreas On 27.02.20 17:59, Szil?rd P?ll wrote: > On Thu, Feb 27, 2020 at 1:08 PM Andreas Baer > wrote: > > Hi, > > On 27.02.20 12:34, Szil?rd P?ll wrote: > > Hi > > > > On Thu, Feb 27, 2020 at 11:31 AM Andreas Baer > > wrote: > > > >> Hi, > >> > >> with the link below, additional log files for runs with 1 GPU > should be > >> accessible now. > >> > > I meant to ask you to run single-rank GPU runs, i.e. gmx mdrun > -ntmpi 1. > > > > It would also help if you could share some input files in case > if further > > testing is needed. > Ok, there is now also an additional benchmark with `-ntmpi 1 -ntomp 4 > -bonded gpu -update gpu` as parameters. However, it is run on the > same > machine with smt disabled. > With the following link, I provide all the tests on this machine, > I did > by now, along with a summary of the performance for the several input > parameters (both in `logfiles`), as well as input files > (`C60xh.7z`) and > the scripts to run these. > > > Links seems to be missing. > -- > Szil?rd > > I hope, this helps. If there is anything else, I can do to help, > please > let me know! > > > > > >> Thank you for the comment with the rlist, I did not know, that > this will > >> affect the performance negatively. > > > > It does in multiple ways. First, you are using a rather long > list buffer > > which will make the nonbonded pair-interaction calculation more > > computational expensive than it could be if you just used a > tolerance and > > let the buffer be calculated. Secondly, as setting a manual > rlist disables > > the automated verlet buffer calculation, it prevents mdrun from > using a > > dual pairl-list setup (see > > > http://manual.gromacs.org/documentation/2018.1/release-notes/2018/major/features.html#dual-pair-list-buffer-with-dynamic-pruning) > > which has additional performance benefits. > Ok, thank you for the explanation! > > > > Cheers, > > -- > > Szil?rd > Cheers, > Andreas > > > > > > > >> I know, about the nstcalcenergy, but > >> I need it for several of my simulations. > > Cheers, > >> Andreas > >> > >> On 26.02.20 16:50, Szil?rd P?ll wrote: > >>> Hi, > >>> > >>> Can you please check the performance when running on a single > GPU 2019 vs > >>> 2020 with your inputs? > >>> > >>> Also note that you are using some peculiar settings that will > have an > >>> adverse effect on performance (like manually set rlist > disallowing the > >> dual > >>> pair-list setup, and nstcalcenergy=1). > >>> > >>> Cheers, > >>> > >>> -- > >>> Szil?rd > >>> > >>> > >>> On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer > > > >> wrote: > >>>> Hello, > >>>> > >>>> here is a link to the logfiles. > >>>> > >>>> > >> > https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 > >>>> If necessary, I can also provide some more log or tpr/gro/... > files. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> On 26.02.20 16:09, Paul bauer wrote: > >>>>> Hello, > >>>>> > >>>>> you can't add attachments to the list, please upload the files > >>>>> somewhere to share them. > >>>>> This might be quite important to us, because the performance > >>>>> regression is not expected by us. > >>>>> > >>>>> Cheers > >>>>> > >>>>> Paul > >>>>> > >>>>> On 26/02/2020 15:54, Andreas Baer wrote: > >>>>>> Hello, > >>>>>> > >>>>>> from a set of benchmark tests with large systems using Gromacs > >>>>>> versions 2019.5 and 2020, I obtained some unexpected results: > >>>>>> With the same set of parameters and the 2020 version, I > obtain a > >>>>>> performance that is about 2/3 of the 2019.5 version. > Interestingly, > >>>>>> according to nvidia-smi, the GPU usage is about 20% higher > for the > >>>>>> 2020 version. > >>>>>> Also from the log files it seems, that the 2020 version > does the > >>>>>> computations more efficiently, but spends so much more time > waiting, > >>>>>> that the overall performance drops. > >>>>>> > >>>>>> Some background info on the benchmarks: > >>>>>> - System contains about 2.1 million atoms. > >>>>>> - Hardware: 2x Intel Xeon Gold 6134 (?Skylake?) @3.2 GHz = > 16 cores + > >>>>>> SMT; 4x NVIDIA Tesla V100 > >>>>>>? ? ?(similar results with less significant performance drop > (~15%) on a > >>>>>> different machine: 2 or 4 nodes with each [2x Intel Xeon > 2660v2 (?Ivy > >>>>>> Bridge?) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20]) > >>>>>> - Several options for -ntmpi, -ntomp, -bonded, -pme are > used to find > >>>>>> the optimal set. However the performance drop seems to be > persistent > >>>>>> for all such options. > >>>>>> > >>>>>> Two representative log files are attached. > >>>>>> Does anyone have an idea, where this drop comes from, and > how to > >>>>>> choose the parameters for the 2020 version to circumvent this? > >>>>>> > >>>>>> Regards, > >>>>>> Andreas > >>>>>> > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe 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 johnwhittake at zedat.fu-berlin.de Fri Feb 28 11:11:24 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Fri, 28 Feb 2020 10:11:24 -0000 Subject: [gmx-users] error on graphene sheet simulation In-Reply-To: References: Message-ID: <52060.160.45.109.123.1582884681.webmail@webmail.zedat.fu-berlin.de> Hi, That tutorial is not from the GROMACS team, it is provided by a user. Anyway, something is wrong with your topology. The CHARMM forcefield used in that tutorial has the atomtype CG2R61 available, so it should be defined in your topology as long as you include the CHARMM36 forcefield. Can you copy/paste the contents of your topology in a reply? - John > while going through your tutorial on graphene sheet i was facing an error. > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > NOTE 2 [file nvt.mdp]: > The Berendsen thermostat does not generate the correct kinetic energy > distribution. You might want to consider using the V-rescale thermostat. > > Setting the LD random seed to 164492569 > Generated 20503 of the 20503 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 17396 of the 20503 1-4 parameter combinations > > ERROR 1 [file GRA.itp, line 7]: > Atomtype CG2R61 not found > > > There were 2 notes > > ------------------------------------------------------- > Program: gmx grompp, version 2019.1 > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1333) > > Fatal error: > There was 1 error in input file(s) > > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > can you give any suggestion what could have gone wrong... > 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 pragati2325 at gmail.com Fri Feb 28 13:29:43 2020 From: pragati2325 at gmail.com (Pragati Sharma) Date: Fri, 28 Feb 2020 12:29:43 -0000 Subject: [gmx-users] uni axial deformation with semi-isotropic pressure coupling at 1 bar Message-ID: Dear all, While using 'deform' option for elongation in Z direction, I have set the compressibility to zero. Should I set pressure in z direction also zero (ref_p =0 ) or 1 in that direction. I need to extract -Pzz for plotting stress-strain. Thanks From kamil.rakowski at student.uj.edu.pl Fri Feb 28 22:58:17 2020 From: kamil.rakowski at student.uj.edu.pl (Kamil Rakowski) Date: Fri, 28 Feb 2020 21:58:17 -0000 Subject: [gmx-users] How GROMACS can be compiled with subsystem Ubuntu 18.04 on Windows Server 2019 Standard? Message-ID: How GROMACS can be compiled with subsystem Ubuntu 18.04 on Windows Server 2019 Standard. Installed CUDA for win serwer 2019 and Windows drivers for Xeon Phi ( mpss 3.8.3). I have Dell Poweredge R720 with: 1x Intel Xeon Phi 7120p, 2x Intel Xeon E-2695v2 and GPU Geforce RTX 2060 SUPER. I don't know how to compile this configuration with cmake to run GROMACS with full performance. From m.b.abdelaal at gmail.com Fri Feb 28 23:15:22 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Fri, 28 Feb 2020 22:15:22 -0000 Subject: [gmx-users] Collision Message-ID: Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I should restrain the graphene sheet along the z axis. I did that using force =1000. and the problem was solved and nothing moved. After that I tried to insert 25 molecule of (C60) inside a box which contains the graphene sheet. I did that and did the energy minimization but part of the graphene sheet moved again from its place although the maximum force was less than 1000 which is the force I used to restrain the graphene sheet. However I didn't have any error during the energy minimization. Does this means that the problem is just in visualization or I might have a problem in my energy minimization ? It is also worth mentioning that the C60 molecules are not spherical as it should be. I read about that and I found people mentioning that this shape deformation in only a visualization problem and can be solved by using gmx trjconv. is it possible that this problem has happened to my whole system including the graphene sheet or it shouldn't affect my graphene sheet as long as I have restrained it ? more info: I used periodic_molecules = yes while trying to minimize my whole system. (I also tried without it but no impact) I wrote: gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p C60_GRM_box.top -o min1.tpr -maxwarn 2 followed by gmx mdrun -v -deffnm min1 and I got the below result: writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 3293 steps Potential Energy = 6.3598562e+05 Maximum force = 9.9486487e+02 on atom 12087 Norm of force = 6.5454323e+01 Can anybody help me please. Thanks Mohamed