From atila.petrosian at gmail.com Sun Mar 1 09:41:25 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Sun, 01 Mar 2020 08:41:25 -0000 Subject: [gmx-users] grompp error : Atomtype CAro 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 Membrane Protein: KALP15 in DPPC gromacs tutorial method for lipid molecules (based on Justin Lemkul suggestion in my previous post: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html ). --------------------------------------- My topology file is as follows: --------------------------------------- ; Include forcefield parameters #include "gromos53a6_lipid.ff/forcefield.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include DPPC chain topology #include "dppc.itp" ; Include drug topology #include "lig.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif [ system ] ; Name dopc/lig/sol in water [ molecules ] ; Compound #mols DPPC 128 LIG 2 SOL 8257 --------------------------------------- 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 grompp -f em1.mdp -c system.gro -p topol.top -o em1.tpr, I encountered with the following error: --------------------------------------- ERROR 1 [file lig.itp, line 66]: Atomtype CAro not found --------------------------------------- How to resole it? Best, Atila From dallas.warren at monash.edu Sun Mar 1 22:58:58 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Sun, 01 Mar 2020 21:58:58 -0000 Subject: [gmx-users] Collision 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. With VMD, and I suspect the other MD visualisation software such as pymol, you can turn on the periodic images. Have you done that to see where things are actually located? What did you see? Have you actually processed it using trjconv to put it back in the center of the box to see what is actually going on? What command did you use, and how did it then look? 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 Sat, 29 Feb 2020 at 09:15, 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 dallas.warren at monash.edu Sun Mar 1 23:05:50 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Sun, 01 Mar 2020 22:05:50 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found In-Reply-To: References: Message-ID: Did you read what the ATB told you about the topologies it generates, and what forcefield you have to use? There is a warning posted on the page where you download your topology files that applies directly to this error you have encountered: "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield. To use these atom types the internal GROMACS parameter files must be updated. These can be downloaded using the link below. Instructions on where to place (and how to use) the files are provided in the README file included in the archive." ATB uses GROMOS 54a7 ATB, and you have to download and use that forcefield for any molecules you generate using that server. You cannot just mix it with GROMOS 53a6 like you have tried to, since 54a7_atb has additional atom types. Stick with a single forcefield, do not mix then because the vast majority are not compatible in that manner. 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, 1 Mar 2020 at 19:41, 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 Membrane Protein: KALP15 in DPPC > gromacs tutorial method for lipid molecules (based on Justin Lemkul > suggestion in my previous post: > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html > ). > > --------------------------------------- > My topology file is as follows: > --------------------------------------- > ; Include forcefield parameters > #include "gromos53a6_lipid.ff/forcefield.itp" > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include DPPC chain topology > #include "dppc.itp" > > ; Include drug topology > #include "lig.itp" > > ; Include water topology > #include "gromos53a6_lipid.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > [ system ] > ; Name > dopc/lig/sol in water > > [ molecules ] > ; Compound #mols > DPPC 128 > LIG 2 > SOL 8257 > --------------------------------------- > 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 grompp -f em1.mdp -c system.gro -p topol.top -o > em1.tpr, > I encountered with the following error: > --------------------------------------- > ERROR 1 [file lig.itp, line 66]: > Atomtype CAro not found > --------------------------------------- > How to resole it? > > Best, > Atila > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From bogdanov.7 at osu.edu Mon Mar 2 04:34:13 2020 From: bogdanov.7 at osu.edu (Bogdanov, Vladimir) Date: Mon, 02 Mar 2020 03:34:13 -0000 Subject: [gmx-users] PC turned off after starting minimization Message-ID: Hi all, I have installed From bogdanov.7 at osu.edu Mon Mar 2 04:38:15 2020 From: bogdanov.7 at osu.edu (Bogdanov, Vladimir) Date: Mon, 02 Mar 2020 03:38:15 -0000 Subject: [gmx-users] install and mdrun problems Message-ID: Hi all, I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but when I did make check, my PC turned off. I also tried to install Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried to do mdrun, my PC also shut down. I also tried the following combination: nvidia-smi 440.59, CUDA 9.2. Any ideas would be helpful. Thanks, Vlad From dallas.warren at monash.edu Mon Mar 2 07:14:56 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 02 Mar 2020 06:14:56 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Sounds bit like it may be overheating. Are all ventilation fans fully operational? On Mon, 2 Mar. 2020, 2:38 pm Bogdanov, Vladimir, wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From atila.petrosian at gmail.com Mon Mar 2 08:40:40 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Mon, 02 Mar 2020 07:40:40 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found Message-ID: Hi Dallas, thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB server. My system contains lipid molecules and small molecule. For lipid molecules, Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both of gromos54a7_atb.ff and gromos53a6_lipid.ff in topology file. Please guide me. Best, Atila From jalemkul at vt.edu Mon Mar 2 14:45:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 02 Mar 2020 13:45:21 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found In-Reply-To: References: Message-ID: <0c5c6820-20cb-6d8b-127f-d7b024faf524@vt.edu> On 3/2/20 2:40 AM, Atila Petrosian wrote: > Hi Dallas, > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB > server. > > My system contains lipid molecules and small molecule. For lipid molecules, > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both > of gromos54a7_atb.ff I explicitly do not endorse/suggest the force field combination, as noted on the home page of that tutorial: "*Please note*that the purpose of this tutorial is instructional, to build a membrane protein system and also to understand GROMACS force field organization and methods for modification. *This tutorial is not an endorsement or suggestion that you use these specific parameters for your simulation.* The approach taken here works well in the case where one needs to augment a parameter set with other parameters that have been derived in a consistent manner." http://www.mdtutorials.com/gmx/membrane_protein/index.html But in any event, the logic is the same if you need to augment any force field with new parameters (that are compatible with the parent force field). There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008 and it reflected a common protocol at the time. I have acknowledged within the tutorial that the force field and methods used are somewhat outdated but that the logic of extending a force field and using the tutorial as a vehicle to understand GROMACS force field organization remains valuable. -Justin > and gromos53a6_lipid.ff in topology file. > > Please guide me. > > 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 mamapcr at gmail.com Mon Mar 2 14:56:37 2020 From: mamapcr at gmail.com (Kunal Dutta) Date: Mon, 02 Mar 2020 13:56:37 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* From mamapcr at gmail.com Mon Mar 2 14:56:37 2020 From: mamapcr at gmail.com (Kunal Dutta) Date: Mon, 02 Mar 2020 13:56:37 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* From kamrangul at uop.edu.pk Mon Mar 2 16:03:37 2020 From: kamrangul at uop.edu.pk (Kamran Gul, M.Phil. Scholar, Institute of Chemical Sciences, UoP) Date: Mon, 02 Mar 2020 15:03:37 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Try gromacs 2019.2. And then update your cuda and nvidia. On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta, wrote: > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > *--------------Every life is precious------------* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From paul.bauer.q at gmail.com Mon Mar 2 16:07:38 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 02 Mar 2020 15:07:38 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Hello, If you try an updated version, please try an actually recent one, either 2019.6 or the 2020 release. If you could provide us with some error or log messages we might be able to find out what happened there. Cheers Paul On 02/03/2020 16:03, Kamran Gul, M.Phil. Scholar, Institute of Chemical Sciences, UoP wrote: > Try gromacs 2019.2. > And then update your cuda and nvidia. > > On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta, wrote: > >> Hello Sir, >> May I know the detailed configuration of your system. >> Sincerely, >> Kunal >> >> >> >> >> On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir >> wrote: >> >>> Hi all, >>> >>> I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), >> but >>> when I did make check, my PC turned off. I also tried to install >>> Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I >> tried >>> to do mdrun, my PC also shut down. I also tried the following >> combination: >>> nvidia-smi 440.59, CUDA 9.2. >>> >>> Any ideas would be helpful. >>> >>> Thanks, >>> Vlad >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> >> >> -- >> *--------------Every life is precious------------* >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From bogdanov.7 at osu.edu Mon Mar 2 17:21:49 2020 From: bogdanov.7 at osu.edu (Bogdanov, Vladimir) Date: Mon, 02 Mar 2020 16:21:49 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: , Message-ID: Hi Dallas, The temperature of CPU is fine, it is less than 59C. Mdrun started work properly after I changed Bios settings to the default settings. ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Dallas Warren Sent: Monday, March 2, 2020 1:14 AM To: GROMACS users Subject: Re: [gmx-users] install and mdrun problems Sounds bit like it may be overheating. Are all ventilation fans fully operational? On Mon, 2 Mar. 2020, 2:38 pm Bogdanov, Vladimir, wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOjowitk0g$ before > posting! > > * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOiJ4yRjLA$ > > * For (un)subscribe requests visit > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOgPV7JmZQ$ or > send a mail to gmx-users-request at gromacs.org. > -- Gromacs Users mailing list * Please search the archive at https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOjowitk0g$ before posting! * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOiJ4yRjLA$ * For (un)subscribe requests visit https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOgPV7JmZQ$ or send a mail to gmx-users-request at gromacs.org. From bogdanov.7 at osu.edu Mon Mar 2 17:37:13 2020 From: bogdanov.7 at osu.edu (Bogdanov, Vladimir) Date: Mon, 02 Mar 2020 16:37:13 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: , Message-ID: Hi Kunal, Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. It looks like the reason of my PC shut down is lying in the Bios settings, but I don't know the version of BIOS, I can look it later, if you need. ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Kunal Dutta Sent: Monday, March 2, 2020 8:56 AM To: gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] install and mdrun problems Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ before > posting! > > * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ or > send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* -- Gromacs Users mailing list * Please search the archive at https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ before posting! * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ * For (un)subscribe requests visit https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ or send a mail to gmx-users-request at gromacs.org. From bogdanov.7 at osu.edu Mon Mar 2 17:37:13 2020 From: bogdanov.7 at osu.edu (Bogdanov, Vladimir) Date: Mon, 02 Mar 2020 16:37:13 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: , Message-ID: Hi Kunal, Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. It looks like the reason of my PC shut down is lying in the Bios settings, but I don't know the version of BIOS, I can look it later, if you need. ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Kunal Dutta Sent: Monday, March 2, 2020 8:56 AM To: gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] install and mdrun problems Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ before > posting! > > * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ or > send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* -- Gromacs Users mailing list * Please search the archive at https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ before posting! * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ * For (un)subscribe requests visit https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ or send a mail to gmx-users-request at gromacs.org. From no-reply at dropbox.com Mon Mar 2 18:41:41 2020 From: no-reply at dropbox.com (sadaf rani (via Dropbox)) Date: Mon, 02 Mar 2020 17:41:41 -0000 Subject: [gmx-users] =?utf-8?q?sadaf_rani_shared_=22dihedral=5Fangles=22_w?= =?utf-8?q?ith_you?= Message-ID: <010101709c56c090-a1ed7cc6-040d-4995-8ebf-bcf73051118a-000000@us-west-2.amazonses.com> Hi Nikhil, sadaf rani (sadafrani6 at gmail.com) invited you to view the folder " dihedral_angles " on Dropbox. sadaf said: "Dihedral angles graphs" Go to folder[1] Enjoy! The Dropbox team sadaf and others will be able to see when you view files in this folder. Other files shared with you through Dropbox may also show this info. Learn more[2] in our help center. [1]: https://www.dropbox.com/l/scl/AACA-vmaSSldqrMmtwPiRsCZm4gGyXu3HHY [2]: https://www.dropbox.com/l/AAB8qx9y7zEdVmqC5iR2EtvSb49UsMPBKQk From sadafrani6 at gmail.com Mon Mar 2 18:42:26 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 02 Mar 2020 17:42:26 -0000 Subject: [gmx-users] regarding dihedral restraints Message-ID: Dear Gromacs users I am restraining three dihedral angles between atoms of two different residues. when I measure it using the following command:- gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg I am getting one of my dihedrals graphs as mentioned in the link. https://www.dropbox.com/home/dihedral_angles My dihedral angles have a multiplicity of 1 as mentioned below:- [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 72 74 31 33 1 146.72 0.0 0 146.72 0.0 41.840 75 74 31 27 1 173.10 0.0 0 173.10 0.0 41.840 75 74 31 25 1 158.21 0.0 0 158.21 0.0 41.840 However, in gromacs manual, I read this:- *Counting transitions only works for dihedrals with multiplicity 3* Am I doing something wrong? How should I measure dihedral restraint over time? Thanks. Sadaf From sadafrani6 at gmail.com Mon Mar 2 18:44:03 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 02 Mar 2020 17:44:03 -0000 Subject: [gmx-users] Fwd: regarding dihedral restraints In-Reply-To: References: Message-ID: Dear Gromacs users I am restraining three dihedral angles between atoms of two different residues. when I measure it using the following command:- gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg I am getting one of my dihedrals graphs as mentioned in the link. https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0 My dihedral angles have a multiplicity of 1 as mentioned below:- [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 72 74 31 33 1 146.72 0.0 0 146.72 0.0 41.840 75 74 31 27 1 173.10 0.0 0 173.10 0.0 41.840 75 74 31 25 1 158.21 0.0 0 158.21 0.0 41.840 However, in gromacs manual, I read this:- *Counting transitions only works for dihedrals with multiplicity 3* Am I doing something wrong? How should I measure dihedral restraint over time? Thanks. Sadaf From dallas.warren at monash.edu Mon Mar 2 21:37:36 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 02 Mar 2020 20:37:36 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found In-Reply-To: References: Message-ID: You need to use the same forcefield. Since you are using ATB to generate the topology for your small molecule, then it stands to reason that you then should use ATB for the lipid molecule. Search ATB, I'm pretty sure the various lipids will already be there, and suspect they will be some that the developers of the forcefield added themselves, rather than a user submitting. 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, 2 Mar 2020 at 18:40, Atila Petrosian wrote: > Hi Dallas, > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB > server. > > My system contains lipid molecules and small molecule. For lipid molecules, > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both > of gromos54a7_atb.ff > and gromos53a6_lipid.ff in topology file. > > Please guide me. > > Best, > Atila > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From dkozuch at princeton.edu Tue Mar 3 03:54:03 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Tue, 03 Mar 2020 02:54:03 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue Message-ID: Hello, I am experimenting with GROMACS 2020. I have compiled the mpi threaded version and am using the new settings (GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on at the following link: https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. I am running mdrun with the suggested options: "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs and 28 CPUs with "-ntmpi 4 -ntomp 7". I am currently running a membrane system with a transmembrane protein in water solvent. I am using the following settings for COM removal: comm_mode = linear comm_grps = PROT_MEMB SOL_ION Here I choose to couple the the protein and the membrane from the advice in this thread: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108584.html Unfortunately, I still see a large drift in the z-dimension for the entire membrane/protein group. Currently I have nstcalcenergy/nstcomm set to 100, as decreasing them leads to poor performance. (Hopefully it is unnecessary to set them to 1) Does anyone have suggestions for avoiding the COM drift? I know this issue has been discussed before (https://redmine.gromacs.org/issues/2867) but it looks like it was resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. Here are some other potentially relevant mdp options (from CHARMM) in case they help: integrator = md dt = 0.002 nstcalcenergy = 100 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 ; tcoupl = v-rescale tc_grps = PROT_MEMB SOL_ION tau_t = 1.0 1.0 ref_t = 303.15 303.15 ; pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes Best, Dan From tyugashev at niboch.nsc.ru Tue Mar 3 05:55:07 2020 From: tyugashev at niboch.nsc.ru (Timofey Tyugashev) Date: Tue, 03 Mar 2020 04:55:07 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Have you tried running stress test benchmarks for CPU and GPU? Or just looking up any similar issues reported by other users of your MB and CPU models? Sudden shutdowns at high load are generally caused by power or cooling failure. Or both, like CPU or GPU VRMs overheating, since they're commonly both insufficient for the power they are supposed to pull through and insufficiently cooled at the same time. 03.03.2020 03:37, gromacs.org_gmx-users-request at maillist.sys.kth.se ?????: > It looks like the reason of my PC shut down is lying in the Bios settings, but I don't know the version of BIOS, I can look it later, if you need. From oeg at isc-ras.ru Tue Mar 3 07:41:41 2020 From: oeg at isc-ras.ru (=?UTF-8?Q?=D0=95=D0=BA=D0=B0=D1=82=D0=B5=D1=80=D0=B8=D0=BD=D0=B0_?= =?UTF-8?Q?=D0=9E=D0=B4=D0=B8=D0=BD=D1=86=D0=BE=D0=B2=D0=B0?=) Date: Tue, 03 Mar 2020 06:41:41 -0000 Subject: [gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs? Message-ID: Could you help me deal with GC-AdResS approach implemented in Gromacs? Recently I learned about the GC-AdResS approach implemented in Gromacs (https://www.researchgate.net/publication/326361115_Adaptive_resolution_molecular_dynamics_technique_Down_to_the_essential et.al.) I downloaded and installed Gromacs 5.1.5. (I understand that GC-AdResS is implemented in this version). There is a folder (folder attached) for a test run on the site (https://e-cam.readthedocs.io/en/latest/Meso-Multi-Scale-Modelling-Modules/modules/GC-AdResS/Abrupt_AdResS/readme.html). When I tried to launch, I got the following error: Program gmx grompp, VERSION 5.1.5 Source code file: /........./gromacs-5.1.5/src/gromacs/gmxpreprocess/readir.c, line: 2690 Fatal error: 13824 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I had a number of questions: 1) How can I solve this problem? 2) Will the smooth GC-address work by default there? 3) Does it matter that I did not register the existing Source Code (patch file for Abrupt GC-Address) anywhere? -- Sincerely, Ekatherina oeg at isc-ras.ru From atila.petrosian at gmail.com Tue Mar 3 08:53:51 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Tue, 03 Mar 2020 07:53:51 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found Message-ID: Dear Justin and Dallas, Thanks for your answers. I am so confused. I am beginner in MD simulation of lipid + small molecule. '' There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008 and it reflected a common protocol at the time ''. Justin, please suggest me better parameter for lipids, exactly (point out the web site). '' Since you are using ATB to generate the topology for your small molecule, then it stands to reason that you then should use ATB for the lipid molecule. '' Dallas, are you sure ATB can be used for lipids ??? Best, Atila From alessandra.villa.biosim at gmail.com Tue Mar 3 09:00:30 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 03 Mar 2020 08:00:30 -0000 Subject: [gmx-users] regard emails on unsubscription from the gromacs.org_gmx-users mailing list Message-ID: Dear all, Some of you have got a notification (yesterday around 7.30 am) that they have been unsubscribed from the gmx_user mailing list from gromacs.org_gmx-users-bounces at maillist.sys.kth.se. The reason is under investigation. In the meanlime, please re-subscribe to the mailing list via the webpage https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users Best regards Alessandra From eduardomayoyanes at gmail.com Tue Mar 3 10:02:56 2020 From: eduardomayoyanes at gmail.com (Eduardo Mayo) Date: Tue, 03 Mar 2020 09:02:56 -0000 Subject: [gmx-users] Amber14SB In-Reply-To: References: Message-ID: Hi!! I'm sorry if is the amber14sb poster on the gromacs download site good?? I've seen the warning on the page and I don't know what to think. Thanks in advance. On Mon, Mar 2, 2020, 3:38 PM < gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users at maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-request at maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > Today's Topics: > > 1. Re: install and mdrun problems (Bogdanov, Vladimir) > 2. sadaf rani shared "dihedral_angles" with you > (sadaf rani (via Dropbox)) > 3. regarding dihedral restraints (Sadaf Rani) > 4. Fwd: regarding dihedral restraints (Sadaf Rani) > 5. Re: grompp error : Atomtype CAro not found (Dallas Warren) > > > > ---------- Forwarded message ---------- > From: "Bogdanov, Vladimir" > To: Kunal Dutta , "gmx-users at gromacs.org" < > gmx-users at gromacs.org> > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" < > gromacs.org_gmx-users at maillist.sys.kth.se> > Bcc: > Date: Mon, 2 Mar 2020 16:36:59 +0000 > Subject: Re: [gmx-users] install and mdrun problems > Hi Kunal, > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. > > It looks like the reason of my PC shut down is lying in the Bios settings, > but I don't know the version of BIOS, I can look it later, if you need. > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal > Dutta > Sent: Monday, March 2, 2020 8:56 AM > To: gmx-users at gromacs.org > Cc: gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > Subject: Re: [gmx-users] install and mdrun problems > > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > > posting! > > > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > *--------------Every life is precious------------* > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or send a mail to gmx-users-request at gromacs.org. > > > > > ---------- Forwarded message ---------- > From: "sadaf rani (via Dropbox)" > To: gromacs.org_gmx-users at maillist.sys.kth.se > Cc: > Bcc: > Date: Mon, 2 Mar 2020 17:41:36 +0000 > Subject: [gmx-users] sadaf rani shared "dihedral_angles" with you > Hi Nikhil, > > sadaf rani (sadafrani6 at gmail.com) invited you to view the folder " > dihedral_angles " on Dropbox. > > sadaf said: > "Dihedral angles graphs" > > Go to folder[1] > > Enjoy! > The Dropbox team > sadaf and others will be able to see when you view files in this folder. > Other files shared with you through Dropbox may also show this info. Learn > more[2] in our help center. > > [1]: https://www.dropbox.com/l/scl/AACA-vmaSSldqrMmtwPiRsCZm4gGyXu3HHY > [2]: https://www.dropbox.com/l/AAB8qx9y7zEdVmqC5iR2EtvSb49UsMPBKQk > > > > ---------- Forwarded message ---------- > From: Sadaf Rani > To: gromacs.org_gmx-users at maillist.sys.kth.se > Cc: > Bcc: > Date: Mon, 2 Mar 2020 17:42:19 +0000 > Subject: [gmx-users] regarding dihedral restraints > Dear Gromacs users > I am restraining three dihedral angles between atoms of two > different residues. when I measure it using the following command:- > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > trans.xvg > > I am getting one of my dihedrals graphs as mentioned in the link. > https://www.dropbox.com/home/dihedral_angles > My dihedral angles have a multiplicity of 1 as mentioned below:- > [ dihedral_restraints ] > ; ai aj ak al type phiA dphiA fcA phiB dphiB > fcB > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > 41.840 > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > 41.840 > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > 41.840 > > However, in gromacs manual, I read this:- > > > *Counting transitions only works for dihedrals with multiplicity 3* > Am I doing something wrong? How should I measure dihedral restraint over > time? > > Thanks. > > Sadaf > > > > > ---------- Forwarded message ---------- > From: Sadaf Rani > To: gromacs.org_gmx-users at maillist.sys.kth.se > Cc: > Bcc: > Date: Mon, 2 Mar 2020 17:43:55 +0000 > Subject: [gmx-users] Fwd: regarding dihedral restraints > Dear Gromacs users > I am restraining three dihedral angles between atoms of two > different residues. when I measure it using the following command:- > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > trans.xvg > > I am getting one of my dihedrals graphs as mentioned in the link. > https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0 > My dihedral angles have a multiplicity of 1 as mentioned below:- > [ dihedral_restraints ] > ; ai aj ak al type phiA dphiA fcA phiB dphiB > fcB > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > 41.840 > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > 41.840 > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > 41.840 > > However, in gromacs manual, I read this:- > > > *Counting transitions only works for dihedrals with multiplicity 3* > Am I doing something wrong? How should I measure dihedral restraint over > time? > > Thanks. > > Sadaf > > > > > ---------- Forwarded message ---------- > From: Dallas Warren > To: GROMACS users > Cc: > Bcc: > Date: Tue, 3 Mar 2020 07:36:56 +1100 > Subject: Re: [gmx-users] grompp error : Atomtype CAro not found > You need to use the same forcefield. > > Since you are using ATB to generate the topology for your small molecule, > then it stands to reason that you then should use ATB for the lipid > molecule. > > Search ATB, I'm pretty sure the various lipids will already be there, and > suspect they will be some that the developers of the forcefield added > themselves, rather than a user submitting. > > 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, 2 Mar 2020 at 18:40, Atila Petrosian > wrote: > > > Hi Dallas, > > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB > > server. > > > > My system contains lipid molecules and small molecule. For lipid > molecules, > > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both > > of gromos54a7_atb.ff > > and gromos53a6_lipid.ff in topology file. > > > > Please guide me. > > > > Best, > > Atila > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 Tue Mar 3 17:46:41 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Tue, 03 Mar 2020 16:46:41 -0000 Subject: [gmx-users] GROMACS 2020.1 patch release available Message-ID: Hi GROMACS users, The official release of GROMACS 2020.1 is available! This first patch release fixes several issues found since the initial release of GROMACS 2020. We encourage all users of the 2020 series to update to 2020.1. Please see the link to the release notes below for more details. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.1.tar.gz Documentation: http://manual.gromacs.org/2020.1/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.1.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From johnwhittake at zedat.fu-berlin.de Tue Mar 3 20:53:51 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Tue, 03 Mar 2020 19:53:51 -0000 Subject: [gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs? In-Reply-To: References: Message-ID: <61841.75.166.168.44.1583265227.webmail@webmail.zedat.fu-berlin.de> Hi Ekatherina, I currently develop AdResS (I am the successor to the post-doc who uploaded the files to the e-cam site) and would be happy to help, but since Gromacs no longer supports AdResS, perhaps we should continue the conversation off the user list. If you'd like to talk about the method or some more advanced applications, shoot me an email (johnwhittake at zedat.fu-berlin.de). For posterity's sake, though, just to answer your questions and comment on some things here: > I downloaded and installed Gromacs 5.1.5. (I understand that > GC-AdResS is implemented in this version). Correct, but as you note below, the vanilla Gromacs 5.1.5 distribution implements the AdResS version with a switching function, not the "abrupt" coupling version that is used in (https://www.researchgate.net/publication/326361115_Adaptive_resolution_molecular_dynamics_technique_Down_to_the_essential). Regardless, it should work. > There is a folder (folder attached) for a test run on the site > (https://e-cam.readthedocs.io/en/latest/Meso-Multi-Scale-Modelling-Modules/modules/GC-AdResS/Abrupt_AdResS/readme.html). > When I tried to launch, I got the following error: > Program gmx grompp, VERSION 5.1.5 > Source code file: > /........./gromacs-5.1.5/src/gromacs/gmxpreprocess/readir.c, line: 2690 > Fatal error: > 13824 atoms are not part of any of the T-Coupling groups > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > I had a number of questions: > 1) How can I solve this problem? Hmmm, it looks like the person who uploaded the example files created his index file incorrectly. - First, delete index.ndx - create a new index file (gmx make_ndx -f conf.gro) - enter "a WCG" - enter "!a WCG" - enter "name 4 EXW" - now quit - The index file should now be correct There were a couple issues but namely, he created a group for the explicit water atoms in the index file by choosing the complement of the WCG set (e.g., !WCG), but accidentally did not change the group name to EXW. > 2) Will the smooth GC-address work by default there? I just tested it and it will *work*, but the results won't really make sense. A number of the parameters were created using the abrupt method, so they should only be used with the abrupt patch. > 3) Does it matter that I did not register the existing Source Code > (patch file for Abrupt GC-Address) anywhere? Apply the patch. It makes the code faster and it makes the most sense for the example case given. I apologize for the difficulty... It seems there wasn't much care taken in uploading and outlining the materials on the e-cam website. The AdResS method has gone through many changes since it was last supported in Gromacs, and things can get very complicated without a guide. Again, let me know if you would like more help or to talk about AdResS. Best, John > -- > Sincerely, > Ekatherina > oeg at isc-ras.ru > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-request at gromacs.org. > From jalemkul at vt.edu Tue Mar 3 21:01:00 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 03 Mar 2020 20:01:00 -0000 Subject: [gmx-users] grompp error : Atomtype CAro not found In-Reply-To: References: Message-ID: On 3/3/20 2:47 AM, Atila Petrosian wrote: > Dear Justin and Dallas, > > Thanks for your answers. I am so confused. I am beginner in MD simulation > of lipid + small molecule. > > '' There are far better options for lipids than the old Berger parameters > used in the tutorial. I wrote the tutorial in 2008 and it reflected a > common protocol at the time ''. > Justin, please suggest me better parameter for lipids, exactly (point out > the web site). I suggest you spend some time investigating the literature as many comparison studies have been done. This is a critical choice that you must make in designing your simulation study. The force field you choose needs to adequately cover all the elements of your system, not just the lipids. > '' Since you are using ATB to generate the topology for your small > molecule, then it stands to reason that you then should use ATB for the > lipid molecule. '' Dallas, are you sure ATB can be used for lipids ??? Here I disagree with Dallas. Any robust force field already supports lipids and you should not have to rely on ATB to produce the lipid parameters, which will likely be less accurate than specifically parametrized entities. -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 Tue Mar 3 21:02:41 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 03 Mar 2020 20:02:41 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: References: Message-ID: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> On 3/2/20 9:53 PM, Daniel Kozuch wrote: > Hello, > > I am experimenting with GROMACS 2020. I have compiled the mpi threaded > version and am using the new settings > (GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as > suggested on at the following link: > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. > I am running mdrun with the suggested options: > "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs and > 28 CPUs with "-ntmpi 4 -ntomp 7". > > I am currently running a membrane system with a transmembrane protein in > water solvent. I am using the following settings for COM removal: > > comm_mode = linear > comm_grps = PROT_MEMB SOL_ION > > Here I choose to couple the the protein and the membrane from the advice in > this thread: > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108584.html > > Unfortunately, I still see a large drift in the z-dimension for the entire > membrane/protein group. Currently I have nstcalcenergy/nstcomm set to 100, > as decreasing them leads to poor performance. (Hopefully it is unnecessary > to set them to 1) Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. -Justin > Does anyone have suggestions for avoiding the COM drift? I know this issue > has been discussed before (https://redmine.gromacs.org/issues/2867) but it > looks like it was resolved in earlier GROMACS versions. As a note, I am > using a CHARMM force field with CMAP dihedrals. > > > Here are some other potentially relevant mdp options (from CHARMM) in case > they help: > > integrator = md > dt = 0.002 > nstcalcenergy = 100 > ; > cutoff-scheme = Verlet > nstlist = 20 > rlist = 1.2 > coulombtype = pme > rcoulomb = 1.2 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.2 > ; > tcoupl = v-rescale > tc_grps = PROT_MEMB SOL_ION > tau_t = 1.0 1.0 > ref_t = 303.15 303.15 > ; > pcoupl = Berendsen > pcoupltype = semiisotropic > tau_p = 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > ; > constraints = h-bonds > constraint_algorithm = LINCS > continuation = yes > > Best, > Dan -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 amitkumar879792 at gmail.com Wed Mar 4 05:07:50 2020 From: amitkumar879792 at gmail.com (Amit Kumar) Date: Wed, 04 Mar 2020 04:07:50 -0000 Subject: [gmx-users] Regarding REMD using gromacs4.5.5 Message-ID: Dear Gromacs users, I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent but I am unable to get any output file containing significant data (logfile is obtained with only developers' details) or any error file. I am unable to understand why this is happening and how can I tackle the situation? Kindly, help me out of this situation. ThankYou Amit Kumar From jishrat17 at gmail.com Wed Mar 4 06:58:25 2020 From: jishrat17 at gmail.com (ISHRAT JAHAN) Date: Wed, 04 Mar 2020 05:58:25 -0000 Subject: [gmx-users] Force field for urea and urea-TMAO mixture Message-ID: Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh From jishrat17 at gmail.com Wed Mar 4 07:00:27 2020 From: jishrat17 at gmail.com (ISHRAT JAHAN) Date: Wed, 04 Mar 2020 06:00:27 -0000 Subject: [gmx-users] Force field for urea and urea-TMAO mixture Message-ID: Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh From dburns at iastate.edu Wed Mar 4 15:09:21 2020 From: dburns at iastate.edu (Daniel Burns) Date: Wed, 04 Mar 2020 14:09:21 -0000 Subject: [gmx-users] Regarding REMD using gromacs4.5.5 In-Reply-To: References: Message-ID: Hi Amit, I?m not the best resource for solutions but I?ve been having this issue with gromacs 2018. It seems to be related to the process manager or our open mpi module we are using. The job would hang on some open mpi communication step. I found it would work if each replica was assigned its own entire node but that becomes prohibitively resource expensive with more than a few replicas. I was finally able to get it to work on our least used cluster where things must have been installed correctly. You might have your IT look at what?s happening with the process manager and open mpi or whatever dependencies you have loaded. You might try a small job where you can assign each replica to its own node and see if you get the full output. Our IT dept has been working for two weeks and still haven?t gotten it to work on the other clusters. Dan On Tuesday, March 3, 2020, Amit Kumar wrote: > Dear Gromacs users, > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent > but I am unable to get any output file containing significant data (logfile > is obtained with only developers' details) or any error file. > I am unable to understand why this is happening and how can I tackle the > situation? > Kindly, help me out of this situation. > > ThankYou > Amit Kumar > From dburns at iastate.edu Wed Mar 4 15:09:21 2020 From: dburns at iastate.edu (Daniel Burns) Date: Wed, 04 Mar 2020 14:09:21 -0000 Subject: [gmx-users] Regarding REMD using gromacs4.5.5 In-Reply-To: References: Message-ID: Hi Amit, I?m not the best resource for solutions but I?ve been having this issue with gromacs 2018. It seems to be related to the process manager or our open mpi module we are using. The job would hang on some open mpi communication step. I found it would work if each replica was assigned its own entire node but that becomes prohibitively resource expensive with more than a few replicas. I was finally able to get it to work on our least used cluster where things must have been installed correctly. You might have your IT look at what?s happening with the process manager and open mpi or whatever dependencies you have loaded. You might try a small job where you can assign each replica to its own node and see if you get the full output. Our IT dept has been working for two weeks and still haven?t gotten it to work on the other clusters. Dan On Tuesday, March 3, 2020, Amit Kumar wrote: > Dear Gromacs users, > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent > but I am unable to get any output file containing significant data (logfile > is obtained with only developers' details) or any error file. > I am unable to understand why this is happening and how can I tackle the > situation? > Kindly, help me out of this situation. > > ThankYou > Amit Kumar > From Simone.Schirra at uibk.ac.at Wed Mar 4 16:11:43 2020 From: Simone.Schirra at uibk.ac.at (Schirra, Simone) Date: Wed, 04 Mar 2020 15:11:43 -0000 Subject: [gmx-users] PEG from ATB: No residues in chain Message-ID: <412999B95FB6894AAB9B6283E4C20DA126059CE3@XMBX3.uibk.ac.at> Dear Gromacs users, I'm totally new to GROMACS and I want to simulate a PEG chain in different environment. I found various PEG topologies on the ATB website and tried to use them combined with the force field provided on the website. However, I always get a warning like this: "Warning: No residues in chain starting at YAHE identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct." I have tried different topologies, the residues are always named differently but they are never defined, although I use the force field that ATB specifies for this. Also in other databases I could only find PEG with other residues, but not somewhere defined. Since it is a well known polymer, I guess that it's well defined somewhere and I just need to know the correct name for a r2b file or something like that... I would be very grateful if someone could help me with this! Simone From clarkmaituanh91memory03 at gmail.com Wed Mar 4 16:30:49 2020 From: clarkmaituanh91memory03 at gmail.com (Anh Mai) Date: Wed, 04 Mar 2020 15:30:49 -0000 Subject: [gmx-users] Ellipticity 222 - negative values? Message-ID: Hi all, I have a question about the *positive value* of the output of the *ellipticity 222* ?_222 , as an output from the *gmx helix* package. Specifically, I run "gmx helix -s top.tpr -n index.ndx -f traj.xtc -b 400000 -cz conf.gro" and got the "cd222.xvg" file like this: " # gmx helix is part of G R O M A C S: # # Great Red Oystrich Makes All Chemists Sane # @ title "Ellipticity at 222 nm" @ xaxis label "Time (ps)" @ yaxis label "nm" @TYPE xy 400000 59.57 400050 60.32 400100 57.64 400150 59.94 400200 60.63 400250 56.91 400300 56.67 ... ". Why is the output value of the ellipticity is positive, instead of being negative? According to Hirst and Brooks (1994) (DOI: 10.1006/jmbi.1994.1644 ), the ellipticity is negative (Table 2/ page 176). Any suggestions are greatly appreciated. Thanks, Anh Mai From alessandra.villa.biosim at gmail.com Wed Mar 4 17:25:56 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 04 Mar 2020 16:25:56 -0000 Subject: [gmx-users] PEG from ATB: No residues in chain In-Reply-To: <412999B95FB6894AAB9B6283E4C20DA126059CE3@XMBX3.uibk.ac.at> References: <412999B95FB6894AAB9B6283E4C20DA126059CE3@XMBX3.uibk.ac.at> Message-ID: Hi, On Wed, Mar 4, 2020 at 4:11 PM Schirra, Simone wrote: > Dear Gromacs users, > > I'm totally new to GROMACS and I want to simulate a PEG chain in different > environment. I found various PEG topologies on the ATB website and tried to > use them combined with the force field provided on the website. However, I > always get a warning like this: > > "Warning: No residues in chain starting at YAHE identified as > Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could either > be > correct or a catastrophic error. Please check your structure, and add all > necessary residue names to residuetypes.dat if this was not correct." > > The warning says that you have no Protein/RNA/DNA residues and indeed PEG is polyethylene glycol. Or do you have also protein/DNA/RNA in the system? Is YAHE the molname given to PEG in the topology file? Where do you get the warning? Best regards Alessandra I have tried different topologies, the residues are always named > differently but they are never defined, although I use the force field that > ATB specifies for this. > Also in other databases I could only find PEG with other residues, but not > somewhere defined. Since it is a well known polymer, I guess that it's well > defined somewhere and I just need to know the correct name for a r2b file > or something like that... > I would be very grateful if someone could help me with this! > > Simone > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From mamapcr at gmail.com Wed Mar 4 17:57:49 2020 From: mamapcr at gmail.com (Kunal Dutta) Date: Wed, 04 Mar 2020 16:57:49 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Hello Sir, I hope you are good and doing well. With such settings, I would do the following steps 1. Make up to date the system BIOS. 2. Double Check the appropriate installation of GROMACS dependencies *viz.*, MPI thread, Open MP threads, *etc. * 3. Re-install gmx 4. Re-install Ubuntu and gmx 5. Sudo apt-get update 6. gmx info Just for example, please find a link for MD-Certified systems/engines up to 1000 ns/ day for personal/multi-user environments. I hope it helps. Sincerely, Kunal [Kunal_lifesc at mail.vidyasagar.ac.in] On Mon, 2 Mar 2020 at 22:07, Bogdanov, Vladimir wrote: > Hi Kunal, > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. > > It looks like the reason of my PC shut down is lying in the Bios settings, > but I don't know the version of BIOS, I can look it later, if you need. > ------------------------------ > *From:* gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal > Dutta > *Sent:* Monday, March 2, 2020 8:56 AM > *To:* gmx-users at gromacs.org > *Cc:* gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > *Subject:* Re: [gmx-users] install and mdrun problems > > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > > posting! > > > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > *--------------Every life is precious------------* > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* From mamapcr at gmail.com Wed Mar 4 17:57:51 2020 From: mamapcr at gmail.com (Kunal Dutta) Date: Wed, 04 Mar 2020 16:57:51 -0000 Subject: [gmx-users] install and mdrun problems In-Reply-To: References: Message-ID: Hello Sir, I hope you are good and doing well. With such settings, I would do the following steps 1. Make up to date the system BIOS. 2. Double Check the appropriate installation of GROMACS dependencies *viz.*, MPI thread, Open MP threads, *etc. * 3. Re-install gmx 4. Re-install Ubuntu and gmx 5. Sudo apt-get update 6. gmx info Just for example, please find a link for MD-Certified systems/engines up to 1000 ns/ day for personal/multi-user environments. I hope it helps. Sincerely, Kunal [Kunal_lifesc at mail.vidyasagar.ac.in] On Mon, 2 Mar 2020 at 22:07, Bogdanov, Vladimir wrote: > Hi Kunal, > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. > > It looks like the reason of my PC shut down is lying in the Bios settings, > but I don't know the version of BIOS, I can look it later, if you need. > ------------------------------ > *From:* gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal > Dutta > *Sent:* Monday, March 2, 2020 8:56 AM > *To:* gmx-users at gromacs.org > *Cc:* gromacs.org_gmx-users at maillist.sys.kth.se < > gromacs.org_gmx-users at maillist.sys.kth.se> > *Subject:* Re: [gmx-users] install and mdrun problems > > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > > posting! > > > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > > send a mail to gmx-users-request at gromacs.org. > > > > > -- > *--------------Every life is precious------------* > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or send a mail to gmx-users-request at gromacs.org. > -- *--------------Every life is precious------------* From jdandrade at iq.ufrgs.br Thu Mar 5 03:15:59 2020 From: jdandrade at iq.ufrgs.br (Jones De Andrade) Date: Thu, 05 Mar 2020 02:15:59 -0000 Subject: [gmx-users] =?utf-8?q?Bug_or_Feature=3F_Energy_Minimization_+_Res?= =?utf-8?q?traints_+_Polarization_Possible_Issue=3F?= Message-ID: <8ff748267c3ffe2e2656ea29d75a85c3@ufrgs.br> Hi all. We are trying something a bit really "off" on gromacs here and now: we want to calculate the optimum position (energetic minimum) for Drude Shell particles in a molecule (with longer that 1-4 intramolecular interactions) given conformation. As such, we succeeded on modifying the force field to both place restraints on the atoms positions (easy) and adding the Drude Shell particles (somewhat more difficult). Basically, gmx grompp accepted the topology. Then, we modified the .gro file to add the Drude Shell particles at random positions around the atoms. Again, seems that there are no issues. The next step was to minimize the energy, and as such we tried to use the .mdp options steep and cg. Here is where things got strange: for some reason, no matter the polarizability value chosen, whenever the *atoms* position restraints (we did *not* explicitly placed any restraints on any shell) are activated, the shells are also affected and do not seem to move. We used several different values for polarizability and for the random shell positions, with the same effect. That is a feature, the way gromacs minimization is intended to act under use of restraints in polarizable molecules, or not? Is there any way around this "issue"? We will really need highly (l-BFGS "level" preferably) optimized shell positions for this work, and we really did not expect this specific "roadblock". :) Btw: we are using gromacs version 2018.4 just because it "was already available". If it is a known bug, we will happily upgrade asap. Any suggestion will be really helpful. Thanks a lot in advance, Best Regards. -- Jones de Andrade (jdandrade at iq.ufrgs.br) DFQ/IQ/UFRGS Lattes: http://lattes.cnpq.br/6675936210583999 Orcid: https://orcid.org/0000-0003-3429-8119 ResearcherID: https://publons.com/researcher/AAC-5337-2019/ From jishrat17 at gmail.com Thu Mar 5 07:23:48 2020 From: jishrat17 at gmail.com (ISHRAT JAHAN) Date: Thu, 05 Mar 2020 06:23:48 -0000 Subject: [gmx-users] Fwd: Force field for urea and urea-TMAO mixture In-Reply-To: References: Message-ID: Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest to me which force field would be better for urea and urea tmao mixture? Is the Kast-2016 TMAO model is compatible with the gromos54a5 force field as I have done the simulation of protein with this force field? Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh From alessandra.villa.biosim at gmail.com Thu Mar 5 10:05:56 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 05 Mar 2020 09:05:56 -0000 Subject: [gmx-users] Force field for urea and urea-TMAO mixture In-Reply-To: References: Message-ID: Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: > Dear all, > I want to do MD simulation of protein in urea and urea-TMAO mixture. Can > you suggest me which force field would be better for urea and urea tmao > mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field > as I have done the simulation of protein with this force field. Any > suggestions regarding this will be highly appreciated. > Thank you > Regards > > > -- > Ishrat Jahan > Research Scholar > Department Of Chemistry > A.M.U Aligarh > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From alessandra.villa.biosim at gmail.com Thu Mar 5 10:23:57 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 05 Mar 2020 09:23:57 -0000 Subject: [gmx-users] Amber14SB In-Reply-To: References: Message-ID: Hi, Here a page of force field in GROMACS http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm maybe it helps. I did not fully understand your question Best regards Alessandra On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo wrote: > Hi!! > I'm sorry if is the amber14sb poster on the gromacs download site good?? > I've seen the warning on the page and I don't know what to think. > Thanks in advance. > > On Mon, Mar 2, 2020, 3:38 PM < > gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > > > Send gromacs.org_gmx-users mailing list submissions to > > gromacs.org_gmx-users at maillist.sys.kth.se > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or, via email, send a message with subject or body 'help' to > > gromacs.org_gmx-users-request at maillist.sys.kth.se > > > > You can reach the person managing the list at > > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gromacs.org_gmx-users digest..." > > Today's Topics: > > > > 1. Re: install and mdrun problems (Bogdanov, Vladimir) > > 2. sadaf rani shared "dihedral_angles" with you > > (sadaf rani (via Dropbox)) > > 3. regarding dihedral restraints (Sadaf Rani) > > 4. Fwd: regarding dihedral restraints (Sadaf Rani) > > 5. Re: grompp error : Atomtype CAro not found (Dallas Warren) > > > > > > > > ---------- Forwarded message ---------- > > From: "Bogdanov, Vladimir" > > To: Kunal Dutta , "gmx-users at gromacs.org" < > > gmx-users at gromacs.org> > > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Bcc: > > Date: Mon, 2 Mar 2020 16:36:59 +0000 > > Subject: Re: [gmx-users] install and mdrun problems > > Hi Kunal, > > > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU > Cooler. > > > > It looks like the reason of my PC shut down is lying in the Bios > settings, > > but I don't know the version of BIOS, I can look it later, if you need. > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal > > Dutta > > Sent: Monday, March 2, 2020 8:56 AM > > To: gmx-users at gromacs.org > > Cc: gromacs.org_gmx-users at maillist.sys.kth.se < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Subject: Re: [gmx-users] install and mdrun problems > > > > Hello Sir, > > May I know the detailed configuration of your system. > > Sincerely, > > Kunal > > > > > > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > > wrote: > > > > > Hi all, > > > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > > but > > > when I did make check, my PC turned off. I also tried to install > > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > > tried > > > to do mdrun, my PC also shut down. I also tried the following > > combination: > > > nvidia-smi 440.59, CUDA 9.2. > > > > > > Any ideas would be helpful. > > > > > > Thanks, > > > Vlad > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > > before > > > posting! > > > > > > * Can't post? Read > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > > > * For (un)subscribe requests visit > > > > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > > or > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > *--------------Every life is precious------------* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > > before posting! > > > > * Can't post? Read > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > > or send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > ---------- Forwarded message ---------- > > From: "sadaf rani (via Dropbox)" > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:41:36 +0000 > > Subject: [gmx-users] sadaf rani shared "dihedral_angles" with you > > Hi Nikhil, > > > > sadaf rani (sadafrani6 at gmail.com) invited you to view the folder " > > dihedral_angles " on Dropbox. > > > > sadaf said: > > "Dihedral angles graphs" > > > > Go to folder[1] > > > > Enjoy! > > The Dropbox team > > sadaf and others will be able to see when you view files in this folder. > > Other files shared with you through Dropbox may also show this info. > Learn > > more[2] in our help center. > > > > [1]: https://www.dropbox.com/l/scl/AACA-vmaSSldqrMmtwPiRsCZm4gGyXu3HHY > > [2]: https://www.dropbox.com/l/AAB8qx9y7zEdVmqC5iR2EtvSb49UsMPBKQk > > > > > > > > ---------- Forwarded message ---------- > > From: Sadaf Rani > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:42:19 +0000 > > Subject: [gmx-users] regarding dihedral restraints > > Dear Gromacs users > > I am restraining three dihedral angles between atoms of two > > different residues. when I measure it using the following command:- > > > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > > trans.xvg > > > > I am getting one of my dihedrals graphs as mentioned in the link. > > https://www.dropbox.com/home/dihedral_angles > > My dihedral angles have a multiplicity of 1 as mentioned below:- > > [ dihedral_restraints ] > > ; ai aj ak al type phiA dphiA fcA phiB dphiB > > fcB > > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > > 41.840 > > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > > 41.840 > > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > > 41.840 > > > > However, in gromacs manual, I read this:- > > > > > > *Counting transitions only works for dihedrals with multiplicity 3* > > Am I doing something wrong? How should I measure dihedral restraint over > > time? > > > > Thanks. > > > > Sadaf > > > > > > > > > > ---------- Forwarded message ---------- > > From: Sadaf Rani > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:43:55 +0000 > > Subject: [gmx-users] Fwd: regarding dihedral restraints > > Dear Gromacs users > > I am restraining three dihedral angles between atoms of two > > different residues. when I measure it using the following command:- > > > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > > trans.xvg > > > > I am getting one of my dihedrals graphs as mentioned in the link. > > > https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0 > > My dihedral angles have a multiplicity of 1 as mentioned below:- > > [ dihedral_restraints ] > > ; ai aj ak al type phiA dphiA fcA phiB dphiB > > fcB > > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > > 41.840 > > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > > 41.840 > > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > > 41.840 > > > > However, in gromacs manual, I read this:- > > > > > > *Counting transitions only works for dihedrals with multiplicity 3* > > Am I doing something wrong? How should I measure dihedral restraint over > > time? > > > > Thanks. > > > > Sadaf > > > > > > > > > > ---------- Forwarded message ---------- > > From: Dallas Warren > > To: GROMACS users > > Cc: > > Bcc: > > Date: Tue, 3 Mar 2020 07:36:56 +1100 > > Subject: Re: [gmx-users] grompp error : Atomtype CAro not found > > You need to use the same forcefield. > > > > Since you are using ATB to generate the topology for your small molecule, > > then it stands to reason that you then should use ATB for the lipid > > molecule. > > > > Search ATB, I'm pretty sure the various lipids will already be there, and > > suspect they will be some that the developers of the forcefield added > > themselves, rather than a user submitting. > > > > 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, 2 Mar 2020 at 18:40, Atila Petrosian > > wrote: > > > > > Hi Dallas, > > > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB > > > server. > > > > > > My system contains lipid molecules and small molecule. For lipid > > molecules, > > > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both > > > of gromos54a7_atb.ff > > > and gromos53a6_lipid.ff in topology file. > > > > > > Please guide me. > > > > > > Best, > > > Atila > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 Thu Mar 5 10:23:57 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 05 Mar 2020 09:23:57 -0000 Subject: [gmx-users] Amber14SB In-Reply-To: References: Message-ID: Hi, Here a page of force field in GROMACS http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm maybe it helps. I did not fully understand your question Best regards Alessandra On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo wrote: > Hi!! > I'm sorry if is the amber14sb poster on the gromacs download site good?? > I've seen the warning on the page and I don't know what to think. > Thanks in advance. > > On Mon, Mar 2, 2020, 3:38 PM < > gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote: > > > Send gromacs.org_gmx-users mailing list submissions to > > gromacs.org_gmx-users at maillist.sys.kth.se > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or, via email, send a message with subject or body 'help' to > > gromacs.org_gmx-users-request at maillist.sys.kth.se > > > > You can reach the person managing the list at > > gromacs.org_gmx-users-owner at maillist.sys.kth.se > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gromacs.org_gmx-users digest..." > > Today's Topics: > > > > 1. Re: install and mdrun problems (Bogdanov, Vladimir) > > 2. sadaf rani shared "dihedral_angles" with you > > (sadaf rani (via Dropbox)) > > 3. regarding dihedral restraints (Sadaf Rani) > > 4. Fwd: regarding dihedral restraints (Sadaf Rani) > > 5. Re: grompp error : Atomtype CAro not found (Dallas Warren) > > > > > > > > ---------- Forwarded message ---------- > > From: "Bogdanov, Vladimir" > > To: Kunal Dutta , "gmx-users at gromacs.org" < > > gmx-users at gromacs.org> > > Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Bcc: > > Date: Mon, 2 Mar 2020 16:36:59 +0000 > > Subject: Re: [gmx-users] install and mdrun problems > > Hi Kunal, > > > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU > Cooler. > > > > It looks like the reason of my PC shut down is lying in the Bios > settings, > > but I don't know the version of BIOS, I can look it later, if you need. > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se < > > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal > > Dutta > > Sent: Monday, March 2, 2020 8:56 AM > > To: gmx-users at gromacs.org > > Cc: gromacs.org_gmx-users at maillist.sys.kth.se < > > gromacs.org_gmx-users at maillist.sys.kth.se> > > Subject: Re: [gmx-users] install and mdrun problems > > > > Hello Sir, > > May I know the detailed configuration of your system. > > Sincerely, > > Kunal > > > > > > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > > wrote: > > > > > Hi all, > > > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > > but > > > when I did make check, my PC turned off. I also tried to install > > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > > tried > > > to do mdrun, my PC also shut down. I also tried the following > > combination: > > > nvidia-smi 440.59, CUDA 9.2. > > > > > > Any ideas would be helpful. > > > > > > Thanks, > > > Vlad > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > > before > > > posting! > > > > > > * Can't post? Read > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > > > * For (un)subscribe requests visit > > > > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > > or > > > send a mail to gmx-users-request at gromacs.org. > > > > > > > > > -- > > *--------------Every life is precious------------* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > > before posting! > > > > * Can't post? Read > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > > or send a mail to gmx-users-request at gromacs.org. > > > > > > > > > > ---------- Forwarded message ---------- > > From: "sadaf rani (via Dropbox)" > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:41:36 +0000 > > Subject: [gmx-users] sadaf rani shared "dihedral_angles" with you > > Hi Nikhil, > > > > sadaf rani (sadafrani6 at gmail.com) invited you to view the folder " > > dihedral_angles " on Dropbox. > > > > sadaf said: > > "Dihedral angles graphs" > > > > Go to folder[1] > > > > Enjoy! > > The Dropbox team > > sadaf and others will be able to see when you view files in this folder. > > Other files shared with you through Dropbox may also show this info. > Learn > > more[2] in our help center. > > > > [1]: https://www.dropbox.com/l/scl/AACA-vmaSSldqrMmtwPiRsCZm4gGyXu3HHY > > [2]: https://www.dropbox.com/l/AAB8qx9y7zEdVmqC5iR2EtvSb49UsMPBKQk > > > > > > > > ---------- Forwarded message ---------- > > From: Sadaf Rani > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:42:19 +0000 > > Subject: [gmx-users] regarding dihedral restraints > > Dear Gromacs users > > I am restraining three dihedral angles between atoms of two > > different residues. when I measure it using the following command:- > > > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > > trans.xvg > > > > I am getting one of my dihedrals graphs as mentioned in the link. > > https://www.dropbox.com/home/dihedral_angles > > My dihedral angles have a multiplicity of 1 as mentioned below:- > > [ dihedral_restraints ] > > ; ai aj ak al type phiA dphiA fcA phiB dphiB > > fcB > > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > > 41.840 > > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > > 41.840 > > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > > 41.840 > > > > However, in gromacs manual, I read this:- > > > > > > *Counting transitions only works for dihedrals with multiplicity 3* > > Am I doing something wrong? How should I measure dihedral restraint over > > time? > > > > Thanks. > > > > Sadaf > > > > > > > > > > ---------- Forwarded message ---------- > > From: Sadaf Rani > > To: gromacs.org_gmx-users at maillist.sys.kth.se > > Cc: > > Bcc: > > Date: Mon, 2 Mar 2020 17:43:55 +0000 > > Subject: [gmx-users] Fwd: regarding dihedral restraints > > Dear Gromacs users > > I am restraining three dihedral angles between atoms of two > > different residues. when I measure it using the following command:- > > > > gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of > > trans.xvg > > > > I am getting one of my dihedrals graphs as mentioned in the link. > > > https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0 > > My dihedral angles have a multiplicity of 1 as mentioned below:- > > [ dihedral_restraints ] > > ; ai aj ak al type phiA dphiA fcA phiB dphiB > > fcB > > 72 74 31 33 1 146.72 0.0 0 146.72 0.0 > > 41.840 > > 75 74 31 27 1 173.10 0.0 0 173.10 0.0 > > 41.840 > > 75 74 31 25 1 158.21 0.0 0 158.21 0.0 > > 41.840 > > > > However, in gromacs manual, I read this:- > > > > > > *Counting transitions only works for dihedrals with multiplicity 3* > > Am I doing something wrong? How should I measure dihedral restraint over > > time? > > > > Thanks. > > > > Sadaf > > > > > > > > > > ---------- Forwarded message ---------- > > From: Dallas Warren > > To: GROMACS users > > Cc: > > Bcc: > > Date: Tue, 3 Mar 2020 07:36:56 +1100 > > Subject: Re: [gmx-users] grompp error : Atomtype CAro not found > > You need to use the same forcefield. > > > > Since you are using ATB to generate the topology for your small molecule, > > then it stands to reason that you then should use ATB for the lipid > > molecule. > > > > Search ATB, I'm pretty sure the various lipids will already be there, and > > suspect they will be some that the developers of the forcefield added > > themselves, rather than a user submitting. > > > > 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, 2 Mar 2020 at 18:40, Atila Petrosian > > wrote: > > > > > Hi Dallas, > > > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB > > > server. > > > > > > My system contains lipid molecules and small molecule. For lipid > > molecules, > > > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both > > > of gromos54a7_atb.ff > > > and gromos53a6_lipid.ff in topology file. > > > > > > Please guide me. > > > > > > Best, > > > Atila > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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 amitkumar879792 at gmail.com Thu Mar 5 11:07:36 2020 From: amitkumar879792 at gmail.com (Amit Kumar) Date: Thu, 05 Mar 2020 10:07:36 -0000 Subject: [gmx-users] Regarding REMD using gromacs4.5.5 In-Reply-To: References: Message-ID: Thank You Daniel Burns, Actually, right now I am looking at the installation and trying to install fresh as I found some error and created mess again while rectifying each one. At the time of installation "mdrun_mpi -h" worked perfectly so I thought installation is fine. But really thank you for your valuable inputs. Amit Kumar On Wed, Mar 4, 2020 at 7:39 PM Daniel Burns wrote: > Hi Amit, > > I?m not the best resource for solutions but I?ve been having this issue > with gromacs 2018. It seems to be related to the process manager or our > open mpi module we are using. The job would hang on some open mpi > communication step. > > I found it would work if each replica was assigned its own entire node but > that becomes prohibitively resource expensive with more than a few > replicas. > > I was finally able to get it to work on our least used cluster where things > must have been installed correctly. > > You might have your IT look at what?s happening with the process manager > and open mpi or whatever dependencies you have loaded. You might try a > small job where you can assign each replica to its own node and see if you > get the full output. Our IT dept has been working for two weeks and still > haven?t gotten it to work on the other clusters. > > > Dan > > > On Tuesday, March 3, 2020, Amit Kumar wrote: > > > Dear Gromacs users, > > > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent > > but I am unable to get any output file containing significant data > (logfile > > is obtained with only developers' details) or any error file. > > I am unable to understand why this is happening and how can I tackle the > > situation? > > Kindly, help me out of this situation. > > > > ThankYou > > Amit Kumar > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From Simone.Schirra at uibk.ac.at Thu Mar 5 11:16:01 2020 From: Simone.Schirra at uibk.ac.at (Schirra, Simone) Date: Thu, 05 Mar 2020 10:16:01 -0000 Subject: [gmx-users] PEG from ATB: No residues in chain In-Reply-To: References: <412999B95FB6894AAB9B6283E4C20DA126059CE3@XMBX3.uibk.ac.at> Message-ID: <412999B95FB6894AAB9B6283E4C20DA12605AD63@XMBX3.uibk.ac.at> Yes, there is no protein/DNA/RNA in my system. Do I have to define this somewhere? I get the warning when executing pdb2gmx. -----Urspr?ngliche Nachricht----- Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se Im Auftrag von Alessandra Villa Gesendet: Mittwoch, 4. M?rz 2020 17:26 An: gmx-users at gromacs.org Betreff: Re: [gmx-users] PEG from ATB: No residues in chain Hi, On Wed, Mar 4, 2020 at 4:11 PM Schirra, Simone wrote: > Dear Gromacs users, > > I'm totally new to GROMACS and I want to simulate a PEG chain in > different environment. I found various PEG topologies on the ATB > website and tried to use them combined with the force field provided > on the website. However, I always get a warning like this: > > "Warning: No residues in chain starting at YAHE identified as > Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could > either be correct or a catastrophic error. Please check your > structure, and add all necessary residue names to residuetypes.dat if > this was not correct." > > The warning says that you have no Protein/RNA/DNA residues and indeed PEG is polyethylene glycol. Or do you have also protein/DNA/RNA in the system? Is YAHE the molname given to PEG in the topology file? Where do you get the warning? Best regards Alessandra I have tried different topologies, the residues are always named > differently but they are never defined, although I use the force field > that ATB specifies for this. > Also in other databases I could only find PEG with other residues, but > not somewhere defined. Since it is a well known polymer, I guess that > it's well defined somewhere and I just need to know the correct name > for a r2b file or something like that... > I would be very grateful if someone could help me with this! > > Simone > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests 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 Thu Mar 5 13:52:42 2020 From: smithmd at ornl.gov (Smith, Micholas D.) Date: Thu, 05 Mar 2020 12:52:42 -0000 Subject: [gmx-users] Odd temperature spikes during T-REMD? Message-ID: Good morning, I am experiencing a very bizarre problem during my T-REMD simulations of a (single-glycosylated residue) protein in water. During my T-REMD simulations, I find that my temperatures jumps from the expected range (my replicas are spaces between 310 to 350K) to 1000K or higher for 10 to 15 steps at a time and then fall back to the expected temperatures, and this occurs for all of the replicas. The system contains ~25k atoms, so it isn't that large, and exchanges are occurring with -replex 500 (and I did test at -replex 1000 as well, same behavior). I've tried using both Nose-Hoover and V-Rescale for the termostats, and I get the same behaviour. I ran additional relaxation simulations at each replicate independently without replex (where I don't see this spiking behavior) and tried again after the relaxations, and still no luck. Energy minimization of the original system looks fine, and simulating a similar sized system (almost the same protein actually) without the glycosylation didn't have this problem. I am using gromacs2018.3 and my mdp options are the defaults you would obtain from CHARMM-GUI for a standard NPT simulation (with modified temperatures for the different replicas). Any ideas? I am still trying to get to the bottom of why it is doing this, but was wondering if anyone else has had this happen them before. =================== Micholas Dean Smith, PhD. MRSC From dkozuch at princeton.edu Thu Mar 5 15:31:31 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Thu, 05 Mar 2020 14:31:31 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: <926e2e8bac6b49d3ae9a1912df22c59c@MN2PR04MB6798.namprd04.prod.outlook.com> References: <926e2e8bac6b49d3ae9a1912df22c59c@MN2PR04MB6798.namprd04.prod.outlook.com> Message-ID: I agree, but this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with GROMACS 2019.6 using all the same settings (but without the new ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. Best, Dan On Tue, Mar 3, 2020 at 3:03 PM Justin Lemkul wrote: > > > On 3/2/20 9:53 PM, Daniel Kozuch wrote: > > Hello, > > > > I am experimenting with GROMACS 2020. I have compiled the mpi threaded > > version and am using the new settings > > (GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as > > suggested on at the following link: > > > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ > . > > I am running mdrun with the suggested options: > > "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs and > > 28 CPUs with "-ntmpi 4 -ntomp 7". > > > > I am currently running a membrane system with a transmembrane protein in > > water solvent. I am using the following settings for COM removal: > > > > comm_mode = linear > > comm_grps = PROT_MEMB SOL_ION > > > > Here I choose to couple the the protein and the membrane from the advice > in > > this thread: > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108584.html > > > > Unfortunately, I still see a large drift in the z-dimension for the > entire > > membrane/protein group. Currently I have nstcalcenergy/nstcomm set to > 100, > > as decreasing them leads to poor performance. (Hopefully it is > unnecessary > > to set them to 1) > > Removing artificial contributions to COM motion does not mean that the > entities cannot diffuse over time. Depending on the length of your > simulation, drift in absolute position can be perfectly normal. > > -Justin > > > Does anyone have suggestions for avoiding the COM drift? I know this > issue > > has been discussed before (https://redmine.gromacs.org/issues/2867) but > it > > looks like it was resolved in earlier GROMACS versions. As a note, I am > > using a CHARMM force field with CMAP dihedrals. > > > > > > Here are some other potentially relevant mdp options (from CHARMM) in > case > > they help: > > > > integrator = md > > dt = 0.002 > > nstcalcenergy = 100 > > ; > > cutoff-scheme = Verlet > > nstlist = 20 > > rlist = 1.2 > > coulombtype = pme > > rcoulomb = 1.2 > > vdwtype = Cut-off > > vdw-modifier = Force-switch > > rvdw_switch = 1.0 > > rvdw = 1.2 > > ; > > tcoupl = v-rescale > > tc_grps = PROT_MEMB SOL_ION > > tau_t = 1.0 1.0 > > ref_t = 303.15 303.15 > > ; > > pcoupl = Berendsen > > pcoupltype = semiisotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > ; > > constraints = h-bonds > > constraint_algorithm = LINCS > > continuation = yes > > > > Best, > > Dan > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 rabetayeasmin at gmail.com Thu Mar 5 16:48:55 2020 From: rabetayeasmin at gmail.com (Rabeta Yeasmin) Date: Thu, 05 Mar 2020 15:48:55 -0000 Subject: [gmx-users] how to add c-terminal to the coarse-grained structure Message-ID: Hi, I am trying to convert all-atom system to coarse grained system using martini. I am encountering a problem with the C terminal of the protein. *Atom OT1 in residue LYS 45 was not found in rtp entry LYS with 22 atomswhile sorting atoms.* This is because Lysine 45 is at the end of C-terminal and it has 23 atoms due to -COOH, while in the rtp file of charmm36.ff, lysine has 22 atoms. I am wondering how could I add n and c-terminal. Thanks. Rabeta Yeasmin From soumadwipghosh at gmail.com Thu Mar 5 18:40:50 2020 From: soumadwipghosh at gmail.com (soumadwip ghosh) Date: Thu, 05 Mar 2020 17:40:50 -0000 Subject: [gmx-users] PEG from ATB: No residues in chain Message-ID: Hi, Why do you need to execute gmx pdb2gmx if you already retrieved parameters from ATB? ATB should be able to provide you the coordinate and topology files (.gro and .itp respectively) compatible with GROMACS. Soumadwip From haolun.wu at ucdconnect.ie Thu Mar 5 18:41:34 2020 From: haolun.wu at ucdconnect.ie (HaoLun Wu) Date: Thu, 05 Mar 2020 17:41:34 -0000 Subject: [gmx-users] gmx hbond -life Message-ID: Dear Gromacs users I am analyzing the hbond lifetime between two residues by using gmx hbond -life. I attached the result xvg file and would like to know the explanation of the second column. I made different ndx file to check it but found both the sum of the second column is 0.01. Could you give me some suggestions to understand it. Thank you. Best regards, Haolun From m.b.abdelaal at gmail.com Thu Mar 5 20:53:52 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Thu, 05 Mar 2020 19:53:52 -0000 Subject: [gmx-users] core dump Message-ID: Hello everybody I have been using GROMACS 2018.1 in the last month and I got an error "core dumped" while running the simulation. Accordingly, I have installed the 2020.1 version and while I am doing pressure equilibration (npt), I had the same error again (I paste it below) which is core dumped. Is it a problem in this version or I might have done something wrong while running the equilibration ? I would really appreciate it, if anyone can guide me. I have pasted the error below Thanks Mohamed :-) GROMACS - gmx mdrun, 2020.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, 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 2020.1 Executable: /home/abdelaal/build2/gromacs-2020.1/build/bin/gmx Data prefix: /home/abdelaal/build2/gromacs-2020.1 (source tree) Working dir: /home/abdelaal/Desktop/GROMACS/C60:TAPC/C60_GRM/22 Command line: gmx mdrun -v -deffnm npt Reading file npt.tpr, VERSION 2020.1 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 8 OpenMP threads starting mdrun 'GRM in vacuum' 50000 steps, 25.0 ps. step 44700, remaining wall clock time: 137 s Step 44790 Warning: pressure scaling more than 1%, mu: 1.01937 1.01937 1.01937 Segmentation fault (core dumped) From m.b.abdelaal at gmail.com Thu Mar 5 20:53:52 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Thu, 05 Mar 2020 19:53:52 -0000 Subject: [gmx-users] core dump Message-ID: Hello everybody I have been using GROMACS 2018.1 in the last month and I got an error "core dumped" while running the simulation. Accordingly, I have installed the 2020.1 version and while I am doing pressure equilibration (npt), I had the same error again (I paste it below) which is core dumped. Is it a problem in this version or I might have done something wrong while running the equilibration ? I would really appreciate it, if anyone can guide me. I have pasted the error below Thanks Mohamed :-) GROMACS - gmx mdrun, 2020.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, 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 2020.1 Executable: /home/abdelaal/build2/gromacs-2020.1/build/bin/gmx Data prefix: /home/abdelaal/build2/gromacs-2020.1 (source tree) Working dir: /home/abdelaal/Desktop/GROMACS/C60:TAPC/C60_GRM/22 Command line: gmx mdrun -v -deffnm npt Reading file npt.tpr, VERSION 2020.1 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 8 OpenMP threads starting mdrun 'GRM in vacuum' 50000 steps, 25.0 ps. step 44700, remaining wall clock time: 137 s Step 44790 Warning: pressure scaling more than 1%, mu: 1.01937 1.01937 1.01937 Segmentation fault (core dumped) From dallas.warren at monash.edu Thu Mar 5 23:36:09 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Thu, 05 Mar 2020 22:36:09 -0000 Subject: [gmx-users] core dump In-Reply-To: References: Message-ID: http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25 System is unstable, there is a problem with with your topology or coordinates. On Fri, 6 Mar. 2020, 6:53 am Mohamed Abdelaal, wrote: > Hello everybody > > I have been using GROMACS 2018.1 in the last month and I got an error "core > dumped" while running the simulation. Accordingly, I have installed the > 2020.1 version and while I am doing pressure equilibration (npt), I had the > same error again (I paste it below) which is core dumped. Is it a problem > in this version or I might have done something wrong while running the > equilibration ? > > I would really appreciate it, if anyone can guide me. I have pasted the > error below > > Thanks > Mohamed > > :-) GROMACS - gmx mdrun, 2020.1 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > Karkoulis > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > Christian Wennberg Maarten Wolf Artem Zhmurov > 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) 2001-2019, 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 2020.1 > Executable: /home/abdelaal/build2/gromacs-2020.1/build/bin/gmx > Data prefix: /home/abdelaal/build2/gromacs-2020.1 (source tree) > Working dir: /home/abdelaal/Desktop/GROMACS/C60:TAPC/C60_GRM/22 > Command line: > gmx mdrun -v -deffnm npt > > Reading file npt.tpr, VERSION 2020.1 (single precision) > Changing nstlist from 10 to 100, rlist from 1 to 1 > > Using 1 MPI thread > > Non-default thread affinity set, disabling internal thread affinity > > Using 8 OpenMP threads > > starting mdrun 'GRM in vacuum' > 50000 steps, 25.0 ps. > step 44700, remaining wall clock time: 137 s > Step 44790 Warning: pressure scaling more than 1%, mu: 1.01937 1.01937 > 1.01937 > Segmentation fault (core dumped) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Fri Mar 6 00:00:40 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 05 Mar 2020 23:00:40 -0000 Subject: [gmx-users] how to generate average structure from trajectory Message-ID: Dear Gromacs users I want to get the average structure of a 10ns simulation by discarding earlier 1ns run. What is the best way to get the average structure? Thanks in advance. Sadaf From rabetayeasmin at gmail.com Fri Mar 6 00:10:06 2020 From: rabetayeasmin at gmail.com (Rabeta Yeasmin) Date: Thu, 05 Mar 2020 23:10:06 -0000 Subject: [gmx-users] 12 bead mapping of lipid Message-ID: How, The mapping that is available for POPS lipid contains 13 beads. But I think the newest mapping has 12 bead. I am wondering how can I get this? Thanks. Rabeta Yeasmin From dave.gromax at gmail.com Fri Mar 6 01:22:31 2020 From: dave.gromax at gmail.com (Dave M) Date: Fri, 06 Mar 2020 00:22:31 -0000 Subject: [gmx-users] 12 bead mapping of lipid In-Reply-To: References: Message-ID: I believe you are looking for Martini CG models. You should be able to download the itp file for all Martini lipids here: http://cgmartini.nl/index.php/force-field-parameters/lipids It has old and current itp files. I think the 'current' file has 12 beads for POPS you are looking for. On Thu, Mar 5, 2020 at 3:10 PM Rabeta Yeasmin wrote: > How, > > The mapping that is available for POPS lipid contains 13 beads. But I think > the newest mapping has 12 bead. I am wondering how can I get this? > Thanks. > > Rabeta Yeasmin > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From dave.gromax at gmail.com Fri Mar 6 01:22:31 2020 From: dave.gromax at gmail.com (Dave M) Date: Fri, 06 Mar 2020 00:22:31 -0000 Subject: [gmx-users] 12 bead mapping of lipid In-Reply-To: References: Message-ID: I believe you are looking for Martini CG models. You should be able to download the itp file for all Martini lipids here: http://cgmartini.nl/index.php/force-field-parameters/lipids It has old and current itp files. I think the 'current' file has 12 beads for POPS you are looking for. On Thu, Mar 5, 2020 at 3:10 PM Rabeta Yeasmin wrote: > How, > > The mapping that is available for POPS lipid contains 13 beads. But I think > the newest mapping has 12 bead. I am wondering how can I get this? > Thanks. > > Rabeta Yeasmin > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sranjan at iiserb.ac.in Fri Mar 6 05:22:26 2020 From: sranjan at iiserb.ac.in (Shashank Ranjan Srivastava) Date: Fri, 06 Mar 2020 04:22:26 -0000 Subject: [gmx-users] Regarding use of harmonic wall model Message-ID: Hello everyone, I want to use harmonic wall model in gromacs. So, I have generated an input file using charmm-gui and and using its production file (production.mdp) to run the simulation but i am getting that how can use harmonic wall model in it. My want to make gap between beta-barrel where i want to open up barrel by distorting the bonds between first and last strand so that I can put new strand in between. Please kindly help me for this query if anybody has any idea regarding this. Thank you -- Shashank Ranjan Srivastava Molecular Biophysics Laboratory Department of Biological Sciences, IISER-Bhopal, Madhya Pradesh From johannes.hermann at tum.de Fri Mar 6 08:53:20 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Fri, 06 Mar 2020 07:53:20 -0000 Subject: [gmx-users] mdp option periodic molecules Message-ID: <0c800120-90a6-334a-ba10-5657d8edd19d@tum.de> Dear all, could you please confirm if I understood the periodic molecules entry (I already browsed through the manual and mailing list): I need "periodic molecules = yes", if a molecule interacts=connects to itself via covalent bonds over the periodic boundary. I do NOT need "periodic molecules = yes", if a molecule interacts via non-covalent interactions to itself via PBs. In this case "periodic molecules = no" is the right choice. Is that right? Thanks in advance! All the best Johannes From blau at kth.se Fri Mar 6 09:00:18 2020 From: blau at kth.se (Christian Blau) Date: Fri, 06 Mar 2020 08:00:18 -0000 Subject: [gmx-users] mdp option periodic molecules In-Reply-To: <0c800120-90a6-334a-ba10-5657d8edd19d@tum.de> References: <0c800120-90a6-334a-ba10-5657d8edd19d@tum.de> Message-ID: <497751cf-20ce-7d1e-da40-28cbafb91496@kth.se> Hi Johannnes, That is correct. Another confirmation of what you already suspect is found in the manual in http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html "Molecules can be made infinitely long by connecting to themselves over periodic boundaries. When such periodic molecules are present, an option in the mdp file needs to be set to tell GROMACS not to attempt to make molecules that are broken over periodic boundaries whole again." Best, Christian On 2020-03-06 08:52, Johannes Hermann wrote: > Dear all, > > could you please confirm if I understood the periodic molecules entry (I already browsed through the manual and > mailing list): > > I need "periodic molecules = yes", if a molecule interacts=connects to itself via covalent bonds over the periodic > boundary. > > I do NOT need "periodic molecules = yes", if a molecule interacts via non-covalent interactions to itself via PBs. In > this case "periodic molecules = no" is the right choice. > > Is that right? > > Thanks in advance! > > All the best > > Johannes > > > From johannes.hermann at tum.de Fri Mar 6 09:13:23 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Fri, 06 Mar 2020 08:13:23 -0000 Subject: [gmx-users] mdp option periodic molecules In-Reply-To: <497751cf-20ce-7d1e-da40-28cbafb91496@kth.se> References: <0c800120-90a6-334a-ba10-5657d8edd19d@tum.de> <497751cf-20ce-7d1e-da40-28cbafb91496@kth.se> Message-ID: Perfect, Thanks! On 06.03.20 09:00, Christian Blau wrote: > Hi Johannnes, > > > That is correct. > > Another confirmation of what you already suspect is found in the > manual in > > http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html > > > > "Molecules can be made infinitely long by connecting to themselves > over periodic boundaries. When such periodic molecules are present, an > option in the mdp file needs to be set to tell GROMACS not to attempt > to make molecules that are broken over periodic boundaries whole again." > > > Best, > > Christian > > On 2020-03-06 08:52, Johannes Hermann wrote: >> Dear all, >> >> could you please confirm if I understood the periodic molecules entry >> (I already browsed through the manual and mailing list): >> >> I need "periodic molecules = yes", if a molecule interacts=connects >> to itself via covalent bonds over the periodic boundary. >> >> I do NOT need "periodic molecules = yes", if a molecule interacts via >> non-covalent interactions to itself via PBs. In this case "periodic >> molecules = no" is the right choice. >> >> Is that right? >> >> Thanks in advance! >> >> All the best >> >> Johannes >> >> >> -- ______________________________________ *Technische Universit?t M?nchen* *Johannes Hermann, M.Sc.* Lehrstuhl f?r Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 89289 15730 Fax: +49 89289 15714 Email: j.hermann at lrz.tum.de http://www.biovt.mw.tum.de/ From subhomoy.bk at gmail.com Fri Mar 6 12:12:22 2020 From: subhomoy.bk at gmail.com (Subhomoi Borkotoky) Date: Fri, 06 Mar 2020 11:12:22 -0000 Subject: [gmx-users] how to generate average structure from trajectory In-Reply-To: References: Message-ID: Hi, For discarding first 1ns , modify the trajectory with *trjconv* with *-b* flag. Use the modified trajectory for cluster analysis with *gmx cluster* to get an average structure from a highly populated cluster. 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 On Fri, Mar 6, 2020 at 4:31 AM Sadaf Rani wrote: > Dear Gromacs users > I want to get the average structure of a 10ns simulation by discarding > earlier 1ns run. What is the best way to get the average structure? > > Thanks in advance. > > 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 yangli2021 at u.northwestern.edu Fri Mar 6 15:40:25 2020 From: yangli2021 at u.northwestern.edu (Yang Li) Date: Fri, 06 Mar 2020 14:40:25 -0000 Subject: [gmx-users] Minimize energy of protein in CCl4 Message-ID: Hi! I am trying to minimize two proteins in CCl4 solvent. When I do mdrun -v -deffnm em, gromacs says too many LINCS warnings I have tried the following: 1. use smaller time step 2. turn off temperature/pressure coupling 3. play around the lincs entries Does this mean the minimization is just unachievable? Below is the entries I used for bonds. ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = yes ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 40 ; Convert harmonic bonds to morse potentials morse = no Thank you! From dkozuch at princeton.edu Fri Mar 6 16:00:53 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Fri, 06 Mar 2020 15:00:53 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> Message-ID: [Somehow my response got put in a different thread - hopefully this works] Justin, Thanks for your reply. I agree that some COM motion is normal. However, this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with GROMACS 2019.6 using all the same settings (but without the new ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. Best, Dan -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Tuesday, March 3, 2020 3:02 PM To: gmx-users at gromacs.org Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue On 3/2/20 9:53 PM, Daniel Kozuch wrote: > Hello, > > I am experimenting with GROMACS 2020. I have compiled the mpi threaded > version and am using the new settings (GMX_GPU_DD_COMMS, > GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on at > the following link: > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. > I am running mdrun with the suggested options: > "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs > and > 28 CPUs with "-ntmpi 4 -ntomp 7". > > I am currently running a membrane system with a transmembrane protein > in water solvent. I am using the following settings for COM removal: > > comm_mode = linear > comm_grps = PROT_MEMB SOL_ION > > Here I choose to couple the the protein and the membrane from the > advice in this thread: > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Sept > ember/108584.html > > Unfortunately, I still see a large drift in the z-dimension for the > entire membrane/protein group. Currently I have nstcalcenergy/nstcomm > set to 100, as decreasing them leads to poor performance. (Hopefully > it is unnecessary to set them to 1) Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. -Justin > Does anyone have suggestions for avoiding the COM drift? I know this > issue has been discussed before > (https://redmine.gromacs.org/issues/2867) but it looks like it was > resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. > > > Here are some other potentially relevant mdp options (from CHARMM) in > case they help: > > integrator = md > dt = 0.002 > nstcalcenergy = 100 > ; > cutoff-scheme = Verlet > nstlist = 20 > rlist = 1.2 > coulombtype = pme > rcoulomb = 1.2 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.2 > ; > tcoupl = v-rescale > tc_grps = PROT_MEMB SOL_ION > tau_t = 1.0 1.0 > ref_t = 303.15 303.15 > ; > pcoupl = Berendsen > pcoupltype = semiisotropic > tau_p = 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > ; > constraints = h-bonds > constraint_algorithm = LINCS > continuation = yes > > Best, > Dan -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Fri Mar 6 17:02:36 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 06 Mar 2020 16:02:36 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> Message-ID: <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> On 3/6/20 10:00 AM, Daniel Kozuch wrote: > [Somehow my response got put in a different thread - hopefully this works] > > Justin, > > Thanks for your reply. I agree that some COM motion is normal. However, this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with GROMACS 2019.6 using all the same settings (but without the new > ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. Does a membrane system (no protein) also cause the same issue? -Justin > Best, > Dan > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul > Sent: Tuesday, March 3, 2020 3:02 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue > > > > On 3/2/20 9:53 PM, Daniel Kozuch wrote: >> Hello, >> >> I am experimenting with GROMACS 2020. I have compiled the mpi threaded >> version and am using the new settings (GMX_GPU_DD_COMMS, >> GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on at >> the following link: >> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. >> I am running mdrun with the suggested options: >> "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs >> and >> 28 CPUs with "-ntmpi 4 -ntomp 7". >> >> I am currently running a membrane system with a transmembrane protein >> in water solvent. I am using the following settings for COM removal: >> >> comm_mode = linear >> comm_grps = PROT_MEMB SOL_ION >> >> Here I choose to couple the the protein and the membrane from the >> advice in this thread: >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Sept >> ember/108584.html >> >> Unfortunately, I still see a large drift in the z-dimension for the >> entire membrane/protein group. Currently I have nstcalcenergy/nstcomm >> set to 100, as decreasing them leads to poor performance. (Hopefully >> it is unnecessary to set them to 1) > Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. > > -Justin > >> Does anyone have suggestions for avoiding the COM drift? I know this >> issue has been discussed before >> (https://redmine.gromacs.org/issues/2867) but it looks like it was >> resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. >> >> >> Here are some other potentially relevant mdp options (from CHARMM) in >> case they help: >> >> integrator = md >> dt = 0.002 >> nstcalcenergy = 100 >> ; >> cutoff-scheme = Verlet >> nstlist = 20 >> rlist = 1.2 >> coulombtype = pme >> rcoulomb = 1.2 >> vdwtype = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> ; >> tcoupl = v-rescale >> tc_grps = PROT_MEMB SOL_ION >> tau_t = 1.0 1.0 >> ref_t = 303.15 303.15 >> ; >> pcoupl = Berendsen >> pcoupltype = semiisotropic >> tau_p = 5.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> ; >> constraints = h-bonds >> constraint_algorithm = LINCS >> continuation = yes >> >> Best, >> Dan > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 rabetayeasmin at gmail.com Fri Mar 6 18:22:15 2020 From: rabetayeasmin at gmail.com (Rabeta Yeasmin) Date: Fri, 06 Mar 2020 17:22:15 -0000 Subject: [gmx-users] 12 bead mapping of lipid Message-ID: Hi Dave, Thanks for your reply. I have seen the new topology file. But I am wondering how can I get the mapping of the new POPS. Is there any way that I can do it myself? Rabeta Yeasmin From dkozuch at princeton.edu Fri Mar 6 18:38:35 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Fri, 06 Mar 2020 17:38:35 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> Message-ID: Yes, a smaller system with only membrane/solvent (no protein) causes the same issue. Best, Dan -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Friday, March 6, 2020 11:02 AM To: gmx-users at gromacs.org Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue On 3/6/20 10:00 AM, Daniel Kozuch wrote: > [Somehow my response got put in a different thread - hopefully this > works] > > Justin, > > Thanks for your reply. I agree that some COM motion is normal. > However, this was a very short simulation (1 ns), so the size of the > drift (several nm) was unexpected. To test, I repeated the simulation > with GROMACS 2019.6 using all the same settings (but without the new > ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. Does a membrane system (no protein) also cause the same issue? -Justin > Best, > Dan > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of > Justin Lemkul > Sent: Tuesday, March 3, 2020 3:02 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue > > > > On 3/2/20 9:53 PM, Daniel Kozuch wrote: >> Hello, >> >> I am experimenting with GROMACS 2020. I have compiled the mpi >> threaded version and am using the new settings (GMX_GPU_DD_COMMS, >> GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on >> at the following link: >> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. >> I am running mdrun with the suggested options: >> "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs >> and >> 28 CPUs with "-ntmpi 4 -ntomp 7". >> >> I am currently running a membrane system with a transmembrane protein >> in water solvent. I am using the following settings for COM removal: >> >> comm_mode = linear >> comm_grps = PROT_MEMB SOL_ION >> >> Here I choose to couple the the protein and the membrane from the >> advice in this thread: >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Sep >> t >> ember/108584.html >> >> Unfortunately, I still see a large drift in the z-dimension for the >> entire membrane/protein group. Currently I have nstcalcenergy/nstcomm >> set to 100, as decreasing them leads to poor performance. (Hopefully >> it is unnecessary to set them to 1) > Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. > > -Justin > >> Does anyone have suggestions for avoiding the COM drift? I know this >> issue has been discussed before >> (https://redmine.gromacs.org/issues/2867) but it looks like it was >> resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. >> >> >> Here are some other potentially relevant mdp options (from CHARMM) in >> case they help: >> >> integrator = md >> dt = 0.002 >> nstcalcenergy = 100 >> ; >> cutoff-scheme = Verlet >> nstlist = 20 >> rlist = 1.2 >> coulombtype = pme >> rcoulomb = 1.2 >> vdwtype = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> ; >> tcoupl = v-rescale >> tc_grps = PROT_MEMB SOL_ION >> tau_t = 1.0 1.0 >> ref_t = 303.15 303.15 >> ; >> pcoupl = Berendsen >> pcoupltype = semiisotropic >> tau_p = 5.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> ; >> constraints = h-bonds >> constraint_algorithm = LINCS >> continuation = yes >> >> Best, >> Dan > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 dkozuch at princeton.edu Fri Mar 6 18:58:24 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Fri, 06 Mar 2020 17:58:24 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> Message-ID: Additional (good) news, the problem appears to be resolved in the 2020.1 update (at least for the membrane only system). I'll conduct some additional tests to see if there is any lingering problems. Dan -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: Friday, March 6, 2020 11:02 AM To: gmx-users at gromacs.org Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue On 3/6/20 10:00 AM, Daniel Kozuch wrote: > [Somehow my response got put in a different thread - hopefully this > works] > > Justin, > > Thanks for your reply. I agree that some COM motion is normal. > However, this was a very short simulation (1 ns), so the size of the > drift (several nm) was unexpected. To test, I repeated the simulation > with GROMACS 2019.6 using all the same settings (but without the new > ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. Does a membrane system (no protein) also cause the same issue? -Justin > Best, > Dan > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of > Justin Lemkul > Sent: Tuesday, March 3, 2020 3:02 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue > > > > On 3/2/20 9:53 PM, Daniel Kozuch wrote: >> Hello, >> >> I am experimenting with GROMACS 2020. I have compiled the mpi >> threaded version and am using the new settings (GMX_GPU_DD_COMMS, >> GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on >> at the following link: >> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. >> I am running mdrun with the suggested options: >> "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs >> and >> 28 CPUs with "-ntmpi 4 -ntomp 7". >> >> I am currently running a membrane system with a transmembrane protein >> in water solvent. I am using the following settings for COM removal: >> >> comm_mode = linear >> comm_grps = PROT_MEMB SOL_ION >> >> Here I choose to couple the the protein and the membrane from the >> advice in this thread: >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Sep >> t >> ember/108584.html >> >> Unfortunately, I still see a large drift in the z-dimension for the >> entire membrane/protein group. Currently I have nstcalcenergy/nstcomm >> set to 100, as decreasing them leads to poor performance. (Hopefully >> it is unnecessary to set them to 1) > Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. > > -Justin > >> Does anyone have suggestions for avoiding the COM drift? I know this >> issue has been discussed before >> (https://redmine.gromacs.org/issues/2867) but it looks like it was >> resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. >> >> >> Here are some other potentially relevant mdp options (from CHARMM) in >> case they help: >> >> integrator = md >> dt = 0.002 >> nstcalcenergy = 100 >> ; >> cutoff-scheme = Verlet >> nstlist = 20 >> rlist = 1.2 >> coulombtype = pme >> rcoulomb = 1.2 >> vdwtype = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> ; >> tcoupl = v-rescale >> tc_grps = PROT_MEMB SOL_ION >> tau_t = 1.0 1.0 >> ref_t = 303.15 303.15 >> ; >> pcoupl = Berendsen >> pcoupltype = semiisotropic >> tau_p = 5.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> ; >> constraints = h-bonds >> constraint_algorithm = LINCS >> continuation = yes >> >> Best, >> Dan > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 paul.bauer.q at gmail.com Fri Mar 6 19:00:17 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Fri, 06 Mar 2020 18:00:17 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> Message-ID: Hello, we resolved some issues with COM removal in the latest release (please see the patch notes for more details). So it might be that you where affected by this before. Please let us know if the issue shows up again. Cheers Paul On 06/03/2020 18:58, Daniel Kozuch wrote: > Additional (good) news, the problem appears to be resolved in the 2020.1 update (at least for the membrane only system). I'll conduct some additional tests to see if there is any lingering problems. > > Dan > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Justin Lemkul > Sent: Friday, March 6, 2020 11:02 AM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue > > > > On 3/6/20 10:00 AM, Daniel Kozuch wrote: >> [Somehow my response got put in a different thread - hopefully this >> works] >> >> Justin, >> >> Thanks for your reply. I agree that some COM motion is normal. >> However, this was a very short simulation (1 ns), so the size of the >> drift (several nm) was unexpected. To test, I repeated the simulation >> with GROMACS 2019.6 using all the same settings (but without the new >> ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. > Does a membrane system (no protein) also cause the same issue? > > -Justin > >> Best, >> Dan >> >> -----Original Message----- >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se >> On Behalf Of >> Justin Lemkul >> Sent: Tuesday, March 3, 2020 3:02 PM >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue >> >> >> >> On 3/2/20 9:53 PM, Daniel Kozuch wrote: >>> Hello, >>> >>> I am experimenting with GROMACS 2020. I have compiled the mpi >>> threaded version and am using the new settings (GMX_GPU_DD_COMMS, >>> GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on >>> at the following link: >>> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. >>> I am running mdrun with the suggested options: >>> "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs >>> and >>> 28 CPUs with "-ntmpi 4 -ntomp 7". >>> >>> I am currently running a membrane system with a transmembrane protein >>> in water solvent. I am using the following settings for COM removal: >>> >>> comm_mode = linear >>> comm_grps = PROT_MEMB SOL_ION >>> >>> Here I choose to couple the the protein and the membrane from the >>> advice in this thread: >>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Sep >>> t >>> ember/108584.html >>> >>> Unfortunately, I still see a large drift in the z-dimension for the >>> entire membrane/protein group. Currently I have nstcalcenergy/nstcomm >>> set to 100, as decreasing them leads to poor performance. (Hopefully >>> it is unnecessary to set them to 1) >> Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. >> >> -Justin >> >>> Does anyone have suggestions for avoiding the COM drift? I know this >>> issue has been discussed before >>> (https://redmine.gromacs.org/issues/2867) but it looks like it was >>> resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. >>> >>> >>> Here are some other potentially relevant mdp options (from CHARMM) in >>> case they help: >>> >>> integrator = md >>> dt = 0.002 >>> nstcalcenergy = 100 >>> ; >>> cutoff-scheme = Verlet >>> nstlist = 20 >>> rlist = 1.2 >>> coulombtype = pme >>> rcoulomb = 1.2 >>> vdwtype = Cut-off >>> vdw-modifier = Force-switch >>> rvdw_switch = 1.0 >>> rvdw = 1.2 >>> ; >>> tcoupl = v-rescale >>> tc_grps = PROT_MEMB SOL_ION >>> tau_t = 1.0 1.0 >>> ref_t = 303.15 303.15 >>> ; >>> pcoupl = Berendsen >>> pcoupltype = semiisotropic >>> tau_p = 5.0 >>> compressibility = 4.5e-5 4.5e-5 >>> ref_p = 1.0 1.0 >>> ; >>> constraints = h-bonds >>> constraint_algorithm = LINCS >>> continuation = yes >>> >>> Best, >>> Dan >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel 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. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From slall at ncbs.res.in Fri Mar 6 19:37:04 2020 From: slall at ncbs.res.in (Sahil Lall) Date: Fri, 06 Mar 2020 18:37:04 -0000 Subject: [gmx-users] 12 bead mapping of lipid In-Reply-To: References: Message-ID: <6fd27312d37735feb92fc8109700bfca@ncbs.res.in> Hello, Do you want to include the 12 bead POPS model in your Martini CG simulations? That is straightforward : Download the "itp" file to the directory with the "top" file and enter #include "martini_v2.0_POPS_02.itp" with the hash in the header of the ".top" file. That should be enough to be given as input to grompp. Sahil On 2020-03-06 22:52, Rabeta Yeasmin wrote: > Hi Dave, > > Thanks for your reply. I have seen the new topology file. But I am > wondering how can I get the mapping of the new POPS. Is there any way that > I can do it myself? > > Rabeta Yeasmin From dkozuch at princeton.edu Fri Mar 6 20:35:58 2020 From: dkozuch at princeton.edu (Daniel Kozuch) Date: Fri, 06 Mar 2020 19:35:58 -0000 Subject: [gmx-users] GMX 2020 - COMM Removal Issue In-Reply-To: References: <01024ca8-ccca-c520-f2f5-447b8113c41d@vt.edu> <0d937b02-0a57-5948-26ba-1a3d1b952b0b@vt.edu> Message-ID: Thanks Paul! Unfortunately while 2020.1 seems to work for the membrane system (no protein), for the protein-membrane system I am still having significant COM motion in the xy plane (i.e. the membrane translates several nm/ns sideways in its own plane). This happens regardless of coupling the membrane and protein independently (3 COMM groups: protein, membrane, solvent) or together (2 COMM groups: protein-membrane, solvent). Any suggestions on how to track down why a protein imbedded in the membrane is causing this problem? Best, Dan -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of Paul bauer Sent: Friday, March 6, 2020 1:02 PM To: gmx-users at gromacs.org Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue Hello, we resolved some issues with COM removal in the latest release (please see the patch notes for more details). So it might be that you where affected by this before. Please let us know if the issue shows up again. Cheers Paul On 06/03/2020 18:58, Daniel Kozuch wrote: > Additional (good) news, the problem appears to be resolved in the 2020.1 update (at least for the membrane only system). I'll conduct some additional tests to see if there is any lingering problems. > > Dan > > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of > Justin Lemkul > Sent: Friday, March 6, 2020 11:02 AM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue > > > > On 3/6/20 10:00 AM, Daniel Kozuch wrote: >> [Somehow my response got put in a different thread - hopefully this >> works] >> >> Justin, >> >> Thanks for your reply. I agree that some COM motion is normal. >> However, this was a very short simulation (1 ns), so the size of the >> drift (several nm) was unexpected. To test, I repeated the simulation >> with GROMACS 2019.6 using all the same settings (but without the new >> ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift. > Does a membrane system (no protein) also cause the same issue? > > -Justin > >> Best, >> Dan >> >> -----Original Message----- >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se >> On Behalf Of >> Justin Lemkul >> Sent: Tuesday, March 3, 2020 3:02 PM >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue >> >> >> >> On 3/2/20 9:53 PM, Daniel Kozuch wrote: >>> Hello, >>> >>> I am experimenting with GROMACS 2020. I have compiled the mpi >>> threaded version and am using the new settings (GMX_GPU_DD_COMMS, >>> GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as suggested on >>> at the following link: >>> https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/. >>> I am running mdrun with the suggested options: >>> "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 >>> GPUs and >>> 28 CPUs with "-ntmpi 4 -ntomp 7". >>> >>> I am currently running a membrane system with a transmembrane >>> protein in water solvent. I am using the following settings for COM removal: >>> >>> comm_mode = linear >>> comm_grps = PROT_MEMB SOL_ION >>> >>> Here I choose to couple the the protein and the membrane from the >>> advice in this thread: >>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-Se >>> p >>> t >>> ember/108584.html >>> >>> Unfortunately, I still see a large drift in the z-dimension for the >>> entire membrane/protein group. Currently I have >>> nstcalcenergy/nstcomm set to 100, as decreasing them leads to poor >>> performance. (Hopefully it is unnecessary to set them to 1) >> Removing artificial contributions to COM motion does not mean that the entities cannot diffuse over time. Depending on the length of your simulation, drift in absolute position can be perfectly normal. >> >> -Justin >> >>> Does anyone have suggestions for avoiding the COM drift? I know this >>> issue has been discussed before >>> (https://redmine.gromacs.org/issues/2867) but it looks like it was >>> resolved in earlier GROMACS versions. As a note, I am using a CHARMM force field with CMAP dihedrals. >>> >>> >>> Here are some other potentially relevant mdp options (from CHARMM) >>> in case they help: >>> >>> integrator = md >>> dt = 0.002 >>> nstcalcenergy = 100 >>> ; >>> cutoff-scheme = Verlet >>> nstlist = 20 >>> rlist = 1.2 >>> coulombtype = pme >>> rcoulomb = 1.2 >>> vdwtype = Cut-off >>> vdw-modifier = Force-switch >>> rvdw_switch = 1.0 >>> rvdw = 1.2 >>> ; >>> tcoupl = v-rescale >>> tc_grps = PROT_MEMB SOL_ION >>> tau_t = 1.0 1.0 >>> ref_t = 303.15 303.15 >>> ; >>> pcoupl = Berendsen >>> pcoupltype = semiisotropic >>> tau_p = 5.0 >>> compressibility = 4.5e-5 4.5e-5 >>> ref_p = 1.0 1.0 >>> ; >>> constraints = h-bonds >>> constraint_algorithm = LINCS >>> continuation = yes >>> >>> Best, >>> Dan >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel 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. -- 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 rabetayeasmin at gmail.com Fri Mar 6 21:09:16 2020 From: rabetayeasmin at gmail.com (Rabeta Yeasmin) Date: Fri, 06 Mar 2020 20:09:16 -0000 Subject: [gmx-users] 12 bead mapping of lipid Message-ID: Hi, I have run some coarse-grained simulations in GROMACS and now I am trying to learn converting back the system to all-atom. I have set up the coarse-grained system in CHARMM-GUI, They did not provide the mapping files and the mapping files all I found in MARTINI website has 13 beads for POPS, but my system POPS has 12 beads. That's why I am looking for newest mapping of POPS lipid. Thanks. Rabeta Yeasmin From sadafrani6 at gmail.com Fri Mar 6 21:21:21 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Fri, 06 Mar 2020 20:21:21 -0000 Subject: [gmx-users] how to generate average structure from trajectory Message-ID: Dear Subhomoi Thanks for your reply. I was doing the following:- discarding 1 ns trajectory by the following command:- gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o md_1000ps.xtc Extracting average structure by the following command:- gmx rmsf -s md.tpr -f md_1000ps.xtc -o rmsf1000ps.xvg -ox average1000ps.pdb -res -n index.ndx I am confused between using gmx rmsf and gmx cluster for getting average structure for clustering should I do the following? gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb Can you please correct me. Thanks in advance. Sadaf From jalemkul at vt.edu Fri Mar 6 21:41:13 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 06 Mar 2020 20:41:13 -0000 Subject: [gmx-users] how to generate average structure from trajectory In-Reply-To: References: Message-ID: <17209cba-a3ba-255f-0929-00bcc6ad96f6@vt.edu> On 3/6/20 3:21 PM, Sadaf Rani wrote: > Dear Subhomoi > Thanks for your reply. > I was doing the following:- > discarding 1 ns trajectory by the following command:- > gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o > md_1000ps.xtc If your simulation is longer than 2 ns, you are not just discarding the first 1 ns, you're also discarding everything after 2 ns by doing this. > Extracting average structure by the following command:- > > gmx rmsf -s md.tpr -f md_1000ps.xtc -o rmsf1000ps.xvg -ox > average1000ps.pdb -res -n index.ndx > I am confused between using gmx rmsf and gmx cluster for getting average > structure > > for clustering should I do the following? > gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb > > Can you please correct me. gmx rmsf produces an average structure, which has no physical meaning. gmx cluster gives you the central structures of the cluster, which are physically real (directly from the trajectory) and reflect the structure with the lowest RMSD relative to the cluster membership. -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 jdandrade at iq.ufrgs.br Fri Mar 6 22:01:08 2020 From: jdandrade at iq.ufrgs.br (Jones De Andrade) Date: Fri, 06 Mar 2020 21:01:08 -0000 Subject: [gmx-users] =?utf-8?q?Can_drude_shell_positions_be_minimized_with?= =?utf-8?q?_keeping_atoms_positions_restrained=3F?= Message-ID: <29a27de706862559509350684920c358@ufrgs.br> Hi everybody. Since my first email seemed to be not following the list's nettiquete rules (sorry for that), I'm trying again. First, I was not successful in solving this issue on gromacs versions 2018.4, 2019.6 and 2020.1: so, it is consistent among them. What we are trying to do is to make the energy optimization only for the Drude shells of the molecules we are using. At this point we tried both steepest-descent and conjugated-gradient, but when it is working successfully we will probably need to go all the way to l-BFGS under double precision. Let me point out that the molecules we are trying have longer than 1-4 intramolecular interactions, and our [defaults ] section reads "1 2 yes 0.5 0.8333", while the exclusion number in the [ moleculetype ] section is 3: as such, 1-4 interactions are scaled while longer ones should be fully taken into account. As a first step, we made the energy optimization of a molecule, atoms+shells, without any restraint applied. So we just had to add the [ polarization ] section to the topology: [ polarization ] ; ai sj type alpha (nm^3) 1 10 1 500 2 11 1 300 3 12 1 500 (...) We verified that the shells were moving related to "their" atoms because we made the calculations with different values of polarizability in the topology file (its magnitude was changed from e-3 to e+2 nm^3 for this testing purposes) and measured the shell distances respective to its atom. As expected, the distances between both runs were different (e-2 to e-3 nm) despite starting at the same initial positions, and as such we concluded that the minimization is acting over both atoms and shells due to only intramolecular interactions and in the absence of outer fields. The second step was then to apply position restraints to all atoms, and *not* to any of the shells. [ position_restraints ] ; ai funct fcx fcy fcz restrains to a point 1 1 10000000000 10000000000 10000000000 2 1 10000000000 10000000000 10000000000 3 1 10000000000 10000000000 10000000000 (...) 9 1 10000000000 10000000000 10000000000 Then when we ran the energy optimization again, no matter the polarizability value applied (same range of magnitude, from e-3 to e+2 nm^3), both atoms (as expected) and shells (reason of concern) did not move in absolute. From our point of view, applying the restraints to the atoms positions should not affect the shells that are (freely) bonded to them. However, we do not know if this was intentional from the developers for some reason, since we can understand that this is not a commonplace calculation. We wish to know if this behavior is to be expected from the developers point of view (in which case, we will definitely move ahead towards studying and rewriting this piece of code by ourselves). If it is not, we will look forward to fill in a bug report (btw, http://bugzilla.gromacs.org/ seems to be offline right now, so we could not check if this is a known issue of some sort) and help each other. Any ideas? Thanks a lot in advance. Best Regards, Jones From slall at ncbs.res.in Sat Mar 7 07:34:04 2020 From: slall at ncbs.res.in (Sahil Lall) Date: Sat, 07 Mar 2020 06:34:04 -0000 Subject: [gmx-users] 12 bead mapping of lipid In-Reply-To: References: Message-ID: <4fe9f4fc5f12a73989d9ba7c36e669f1@ncbs.res.in> Hello, I see the problem now. You are right, the backmapping files have the 13 bead POPS rather that the latest 12 bead POPS. As far as I know the backmapping files have not been publicly updated but you could try the Martini forum. If the exact lipid coordinates are absolutely essential to your results, I guess you might have to create a new map file yourself. Otherwise, if a lipid bilayer is all you seek, you could always add newer all atom lipids in the process of transformation. - Sahil On 2020-03-07 01:39, Rabeta Yeasmin wrote: > Hi, > > I have run some coarse-grained simulations in GROMACS and now I am trying > to learn converting back the system to all-atom. I have set up the > coarse-grained system in CHARMM-GUI, They did not provide the mapping files > and the mapping files all I found in MARTINI website has 13 beads for POPS, > but my system POPS has 12 beads. That's why I am looking for newest mapping > of POPS lipid. > Thanks. > > Rabeta Yeasmin From ranadeepu2017 at gmail.com Sat Mar 7 11:20:35 2020 From: ranadeepu2017 at gmail.com (Rana Ali) Date: Sat, 07 Mar 2020 10:20:35 -0000 Subject: [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2 Message-ID: Hi I was running water on graphene using PBC =xy by keeping the graphene fixed in y direction. It was running in gromacs version 4.6 but failed to run in 5.1.2. This is the error. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# ERROR 1 [file nvt.mdp]: With Verlet lists only full pbc or pbc=xy with walls is supported ERROR 2 [file nvt.mdp]: With Verlet lists rcoulomb!=rvdw is not supported NOTE 2 [file nvt.mdp]: Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off and vdw_modifier=Potential-switch ERROR 3 [file nvt.mdp]: The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1. Setting the LD random seed to 1821932621 Generated 371091 of the 371091 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 371091 of the 371091 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'GRA' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Setting gen_seed to 925853613 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet There were 2 notes ------------------------------------------------------- Program gmx grompp, VERSION 5.1.2 Source code file: /home/usr01/gromacs/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738 Fatal error: There were 3 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Here is the NVT.mdp ; Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.001 nsteps = 50000 ; 100 ps nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 0 xtc-precision = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xy rlist = 1.20 ; Electrostatics coulombtype = cut-off rcoulomb = 1.20 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 1.0 ref_t = 300 gen_vel = yes gen_temp = 300 gen_seed = -1 periodic_molecules=yes freezegrps = LIG freezedim = Y Y Y ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Could you please help to sort out the problem from version 4.6 to 5.1.2 in NVT.mdp Thanks in advance From rollyng at gmail.com Sat Mar 7 17:02:33 2020 From: rollyng at gmail.com (Rolly Ng) Date: Sat, 07 Mar 2020 16:02:33 -0000 Subject: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites Message-ID: <002e01d5f499$bb9670f0$32c352d0$@gmail.com> Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites and adh_dodec_vsites failed at grompp. Could you please have a look at the following output log? Thanks, Rolly Ng PhD, Former Research Fellow, Department of Materials Science and Engineering City University of Hong Kong :-) GROMACS - gmx grompp, 2020-UNCHECKED (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, 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 2020-UNCHECKED Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi Data prefix: /home/rolly/Gromacs/gromacs-2020/install Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites Command line: gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top Ignoring obsolete mdp entry 'ns_type' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Setting the LD random seed to -1974193353 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_D' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... WARNING 1 [file topol.top, line 55]: The following macros were defined in the 'define' mdp field with the -D prefix, but were not used in the topology: VSITE If you haven't made a spelling error, either use the macro you defined, or don't define the macro Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Analysing residue names: There are: 1408 Protein residues There are: 37600 Water residues There are: 12 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 247713.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K NOTE 1 [file pme_verlet_vsites.mdp]: There are 9592 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.113 nm Set rlist, assuming 4x4 atom pair-list, to 0.935 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 100x100x100, spacing 0.110 0.110 0.110 Estimate for the relative computational load of the PME mesh part: 0.28 This run will generate roughly 10 Mb of data There was 1 note There was 1 warning ------------------------------------------------------- Program: gmx grompp, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2352) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor :-) GROMACS - gmx mdrun, 2020-UNCHECKED (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: srun: Job step aborted: Waiting up to 32 seconds for job step to finish. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, 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 2020-UNCHECKED Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi Data prefix: /home/rolly/Gromacs/gromacs-2020/install Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites Command line: gmx_mpi mdrun -g adh_cubic_vsites.log -pin on -v -noconfout -nsteps 10000 -s topol.tpr -ntomp 1 ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 0 (out of 176) Error in user input: Invalid command-line options In command-line option -s File 'topol.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- srun: error: node11: tasks 0-8,10-11,14,18-19,22-24,29,35,37,46,48,53-54,58-59,64,66-69,71,73-74,76,78- 79,85,90,93,95,98,101-103,105-106,108-109,111-113,115,118-121,123-124,126,12 8-129,131,135-136,138-142,144-145,147,152,154-156,158-159: Exited with exit code 1 ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 1 (out of 176) Error in user input: Invalid command-line options srun: error: node11: tasks 9,12-13,15-17,20-21,25-28,30-34,36,38-45,47,49-52,55-57,60-63,65,70,72,75,77 ,80-84,86-89,91-92,94,96-97,99-100,104,107,110,114,116-117,122,125,127,130,1 32-134,137,143,146,148-151,153,157,160-175: Killed ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 3 (out of 176) Error in user input: Invalid command-line options In command-line option -s ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 4 (out of 176) Error in user input: Invalid command-line options In command-line option -s File 'topol.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory From rollyng at gmail.com Sat Mar 7 17:04:46 2020 From: rollyng at gmail.com (Rolly Ng) Date: Sat, 07 Mar 2020 16:04:46 -0000 Subject: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites In-Reply-To: <002e01d5f499$bb9670f0$32c352d0$@gmail.com> References: <002e01d5f499$bb9670f0$32c352d0$@gmail.com> Message-ID: <003501d5f49a$1b0c75c0$51256140$@gmail.com> Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites and adh_dodec_vsites failed at grompp. Could you please have a look at the following output log? Thanks, Rolly Ng PhD, Former Research Fellow, Department of Materials Science and Engineering City University of Hong Kong :-) GROMACS - gmx grompp, 2020-UNCHECKED (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov 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) 2001-2019, 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 2020-UNCHECKED Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi Data prefix: /home/rolly/Gromacs/gromacs-2020/install Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites Command line: gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top Ignoring obsolete mdp entry 'ns_type' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Setting the LD random seed to -1974193353 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_D' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... WARNING 1 [file topol.top, line 55]: The following macros were defined in the 'define' mdp field with the -D prefix, but were not used in the topology: VSITE If you haven't made a spelling error, either use the macro you defined, or don't define the macro Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1683 Angles with virtual sites, 8136 left Removed 1587 Proper Dih.s with virtual sites, 16689 left Converted 2918 Constraints with virtual sites to connections, 2473 left Warning: removed 896 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Analysing residue names: There are: 1408 Protein residues There are: 37600 Water residues There are: 12 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 247713.00 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K NOTE 1 [file pme_verlet_vsites.mdp]: There are 9592 non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly. Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.113 nm Set rlist, assuming 4x4 atom pair-list, to 0.935 nm, buffer size 0.035 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 100x100x100, spacing 0.110 0.110 0.110 Estimate for the relative computational load of the PME mesh part: 0.28 This run will generate roughly 10 Mb of data There was 1 note There was 1 warning ------------------------------------------------------- Program: gmx grompp, version 2020-UNCHECKED Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2352) Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor :-) GROMACS - gmx mdrun, 2020-UNCHECKED (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: srun: Job step aborted: Waiting up to 32 seconds for job step to finish. Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, 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 2020-UNCHECKED Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi Data prefix: /home/rolly/Gromacs/gromacs-2020/install Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites Command line: gmx_mpi mdrun -g adh_cubic_vsites.log -pin on -v -noconfout -nsteps 10000 -s topol.tpr -ntomp 1 ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 0 (out of 176) Error in user input: Invalid command-line options In command-line option -s File 'topol.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- srun: error: node11: tasks 0-8,10-11,14,18-19,22-24,29,35,37,46,48,53-54,58-59,64,66-69,71,73-74,76,78- 79,85,90,93,95,98,101-103,105-106,108-109,111-113,115,118-121,123-124,126,12 8-129,131,135-136,138-142,144-145,147,152,154-156,158-159: Exited with exit code 1 ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 1 (out of 176) Error in user input: Invalid command-line options srun: error: node11: tasks 9,12-13,15-17,20-21,25-28,30-34,36,38-45,47,49-52,55-57,60-63,65,70,72,75,77 ,80-84,86-89,91-92,94,96-97,99-100,104,107,110,114,116-117,122,125,127,130,1 32-134,137,143,146,148-151,153,157,160-175: Killed ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 3 (out of 176) Error in user input: Invalid command-line options In command-line option -s ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 4 (out of 176) Error in user input: Invalid command-line options In command-line option -s File 'topol.tpr' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory From spoel at xray.bmc.uu.se Sat Mar 7 17:46:58 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 07 Mar 2020 16:46:58 -0000 Subject: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites In-Reply-To: <003501d5f49a$1b0c75c0$51256140$@gmail.com> References: <002e01d5f499$bb9670f0$32c352d0$@gmail.com> <003501d5f49a$1b0c75c0$51256140$@gmail.com> Message-ID: <4cef1359-f567-4ee2-e5d0-b7cb650bd301@xray.bmc.uu.se> Den 2020-03-07 kl. 17:04, skrev Rolly Ng: > Dear Gromacs developers, > > > > I am new to Gromacs and I have recently compiled Gromacs 2020. > > > > I tried to run the ADH benchmarks from > ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz > > > > The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites > and adh_dodec_vsites failed at grompp. > > > > Could you please have a look at the following output log? > It actually tells you what is wrong in the input. -maxwarn 1 is your friend. > > > Thanks, > > Rolly Ng > > > > PhD, Former Research Fellow, > > Department of Materials Science and Engineering > > City University of Hong Kong > > > > :-) GROMACS - gmx grompp, 2020-UNCHECKED (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > Karkoulis > > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > > Christian Wennberg Maarten Wolf Artem Zhmurov > > 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) 2001-2019, 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 2020-UNCHECKED > > Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi > > Data prefix: /home/rolly/Gromacs/gromacs-2020/install > > Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites > > Command line: > > gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top > > > > Ignoring obsolete mdp entry 'ns_type' > > Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' > > Setting the LD random seed to -1974193353 > > Generated 2145 of the 2145 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 2145 of the 2145 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_B' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_C' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_D' > > turning all bonds into constraints... > > Excluding 2 bonded neighbours molecule type 'SOL' > > turning all bonds into constraints... > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 1 bonded neighbours molecule type 'NA' > > turning all bonds into constraints... > > > > WARNING 1 [file topol.top, line 55]: > > The following macros were defined in the 'define' mdp field with the -D > > prefix, but were not used in the topology: > > VSITE > > If you haven't made a spelling error, either use the macro you defined, > > or don't define the macro > > > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Analysing residue names: > > There are: 1408 Protein residues > > There are: 37600 Water residues > > There are: 12 Ion residues > > Analysing Protein... > > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > Number of degrees of freedom in T-Coupling group System is 247713.00 > > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > > > > NOTE 1 [file pme_verlet_vsites.mdp]: > > There are 9592 non-linear virtual site constructions. Their contribution > > to the energy error is approximated. In most cases this does not affect > > the error significantly. > > > > Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.113 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.935 nm, buffer size 0.035 nm > > Note that mdrun will redetermine rlist based on the actual pair-list setup > > Calculating fourier grid dimensions for X Y Z > > Using a fourier grid of 100x100x100, spacing 0.110 0.110 0.110 > > Estimate for the relative computational load of the PME mesh part: 0.28 > > This run will generate roughly 10 Mb of data > > > > There was 1 note > > > > There was 1 warning > > > > ------------------------------------------------------- > > Program: gmx grompp, version 2020-UNCHECKED > > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2352) > > > > Fatal error: > > Too many warnings (1). > > If you are sure all warnings are harmless, use the -maxwarn option. > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 > > : > > system msg for write_line failure : Bad file descriptor > > :-) GROMACS - gmx mdrun, 2020-UNCHECKED (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > Karkoulis > > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > > Christian Wennberg Maarten Wolf Artem Zhmurov > > and the project leaders: > > srun: Job step aborted: Waiting up to 32 seconds for job step to finish. > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2019, 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 2020-UNCHECKED > > Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi > > Data prefix: /home/rolly/Gromacs/gromacs-2020/install > > Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites > > Command line: > > gmx_mpi mdrun -g adh_cubic_vsites.log -pin on -v -noconfout -nsteps 10000 > -s topol.tpr -ntomp 1 > > > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 0 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > File 'topol.tpr' does not exist or is not accessible. > > The file could not be opened. > > Reason: No such file or directory > > (call to fopen() returned error code 2) > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > srun: error: node11: tasks > 0-8,10-11,14,18-19,22-24,29,35,37,46,48,53-54,58-59,64,66-69,71,73-74,76,78- > 79,85,90,93,95,98,101-103,105-106,108-109,111-113,115,118-121,123-124,126,12 > 8-129,131,135-136,138-142,144-145,147,152,154-156,158-159: Exited with exit > code 1 > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 1 (out of 176) > > > > Error in user input: > > Invalid command-line options > > srun: error: node11: tasks > 9,12-13,15-17,20-21,25-28,30-34,36,38-45,47,49-52,55-57,60-63,65,70,72,75,77 > ,80-84,86-89,91-92,94,96-97,99-100,104,107,110,114,116-117,122,125,127,130,1 > 32-134,137,143,146,148-151,153,157,160-175: Killed > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 3 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 4 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > File 'topol.tpr' does not exist or is not accessible. > > The file could not be opened. > > Reason: No such file or directory > > > -- 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 apdapbbau at gmail.com Sat Mar 7 19:12:21 2020 From: apdapbbau at gmail.com (Anwesh Pandey) Date: Sat, 07 Mar 2020 18:12:21 -0000 Subject: [gmx-users] MMGBSA for GROMACS Message-ID: Dear GROMACS Team, I have done a drug-DNA molecular dynamics, I now wish to perform MMGBSA for it, but I do not find any tutorial, script, etc. for it. Please help! *Anwesh Pandey*, Research Scholar (Computational Biophysics), Department of Physics, School for Physical & Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow-226025, UP, India. +91-9452444164 https://www.researchgate.net/profile/Anwesh_Pandey3 From rollyng at gmail.com Sat Mar 7 19:13:20 2020 From: rollyng at gmail.com (Rolly Ng) Date: Sat, 07 Mar 2020 18:13:20 -0000 Subject: [gmx-users] =?gb2312?b?u9i4tDogIEdyb21hY3MgMjAyMCBmYWlscyB0byBy?= =?gb2312?b?dW4gYWRoX2N1YmljX3ZzaXRlcw==?= In-Reply-To: <4cef1359-f567-4ee2-e5d0-b7cb650bd301@xray.bmc.uu.se> References: <002e01d5f499$bb9670f0$32c352d0$@gmail.com> <003501d5f49a$1b0c75c0$51256140$@gmail.com> <4cef1359-f567-4ee2-e5d0-b7cb650bd301@xray.bmc.uu.se> Message-ID: <003c01d5f4ab$0784b420$168e1c60$@gmail.com> Dear Prof. Van der Spoel, Thank you for the quick reply. I just found that it works with 8, 16, 32, 64 and 128 threads but not 176 threads. Best, Rolly Ng -----????----- ???: gromacs.org_gmx-users-bounces at maillist.sys.kth.se ?? David van der Spoel ????: 2020?3?8???? ??12:47 ???: gmx-users at gromacs.org ??: Re: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites Den 2020-03-07 kl. 17:04, skrev Rolly Ng: > Dear Gromacs developers, > > > > I am new to Gromacs and I have recently compiled Gromacs 2020. > > > > I tried to run the ADH benchmarks from > ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz > > > > The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites > and adh_dodec_vsites failed at grompp. > > > > Could you please have a look at the following output log? > It actually tells you what is wrong in the input. -maxwarn 1 is your friend. > > > Thanks, > > Rolly Ng > > > > PhD, Former Research Fellow, > > Department of Materials Science and Engineering > > City University of Hong Kong > > > > :-) GROMACS - gmx grompp, 2020-UNCHECKED (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > Karkoulis > > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > > Christian Wennberg Maarten Wolf Artem Zhmurov > > 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) 2001-2019, 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 2020-UNCHECKED > > Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi > > Data prefix: /home/rolly/Gromacs/gromacs-2020/install > > Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites > > Command line: > > gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top > > > > Ignoring obsolete mdp entry 'ns_type' > > Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' > > Setting the LD random seed to -1974193353 > > Generated 2145 of the 2145 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 2145 of the 2145 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_B' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_C' > > turning all bonds into constraints... > > Excluding 3 bonded neighbours molecule type 'Protein_chain_D' > > turning all bonds into constraints... > > Excluding 2 bonded neighbours molecule type 'SOL' > > turning all bonds into constraints... > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 2 bonded neighbours molecule type 'SOL' > > Excluding 1 bonded neighbours molecule type 'NA' > > turning all bonds into constraints... > > > > WARNING 1 [file topol.top, line 55]: > > The following macros were defined in the 'define' mdp field with the -D > > prefix, but were not used in the topology: > > VSITE > > If you haven't made a spelling error, either use the macro you defined, > > or don't define the macro > > > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Cleaning up constraints and constant bonded interactions with virtual sites > > Removed 1683 Angles with virtual sites, 8136 left > > Removed 1587 Proper Dih.s with virtual sites, 16689 left > > Converted 2918 Constraints with virtual sites to connections, 2473 left > > Warning: removed 896 Constraints with vsite with Virtual site 3out > construction > > This vsite construction does not guarantee constant bond-length > > If the constructions were generated by pdb2gmx ignore this warning > > Analysing residue names: > > There are: 1408 Protein residues > > There are: 37600 Water residues > > There are: 12 Ion residues > > Analysing Protein... > > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > Number of degrees of freedom in T-Coupling group System is 247713.00 > > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K > > > > NOTE 1 [file pme_verlet_vsites.mdp]: > > There are 9592 non-linear virtual site constructions. Their contribution > > to the energy error is approximated. In most cases this does not affect > > the error significantly. > > > > Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.113 nm > > Set rlist, assuming 4x4 atom pair-list, to 0.935 nm, buffer size 0.035 nm > > Note that mdrun will redetermine rlist based on the actual pair-list setup > > Calculating fourier grid dimensions for X Y Z > > Using a fourier grid of 100x100x100, spacing 0.110 0.110 0.110 > > Estimate for the relative computational load of the PME mesh part: 0.28 > > This run will generate roughly 10 Mb of data > > > > There was 1 note > > > > There was 1 warning > > > > ------------------------------------------------------- > > Program: gmx grompp, version 2020-UNCHECKED > > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2352) > > > > Fatal error: > > Too many warnings (1). > > If you are sure all warnings are harmless, use the -maxwarn option. > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 > > : > > system msg for write_line failure : Bad file descriptor > > :-) GROMACS - gmx mdrun, 2020-UNCHECKED (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > > Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd > > Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray > > Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang > > Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > Karkoulis > > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson > > Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund > > Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall > > Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov > > Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen > > Christian Wennberg Maarten Wolf Artem Zhmurov > > and the project leaders: > > srun: Job step aborted: Waiting up to 32 seconds for job step to finish. > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2019, 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 2020-UNCHECKED > > Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi > > Data prefix: /home/rolly/Gromacs/gromacs-2020/install > > Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites > > Command line: > > gmx_mpi mdrun -g adh_cubic_vsites.log -pin on -v -noconfout -nsteps 10000 > -s topol.tpr -ntomp 1 > > > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 0 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > File 'topol.tpr' does not exist or is not accessible. > > The file could not be opened. > > Reason: No such file or directory > > (call to fopen() returned error code 2) > > > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > srun: error: node11: tasks > 0-8,10-11,14,18-19,22-24,29,35,37,46,48,53-54,58-59,64,66-69,71,73-74,76,78- > 79,85,90,93,95,98,101-103,105-106,108-109,111-113,115,118-121,123-124,126, 12 > 8-129,131,135-136,138-142,144-145,147,152,154-156,158-159: Exited with exit > code 1 > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 1 (out of 176) > > > > Error in user input: > > Invalid command-line options > > srun: error: node11: tasks > 9,12-13,15-17,20-21,25-28,30-34,36,38-45,47,49-52,55-57,60-63,65,70,72,75, 77 > ,80-84,86-89,91-92,94,96-97,99-100,104,107,110,114,116-117,122,125,127,130,1 > 32-134,137,143,146,148-151,153,157,160-175: Killed > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 3 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > > > ------------------------------------------------------- > > Program: gmx mdrun, version 2020-UNCHECKED > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275) > > Function: void gmx::CommandLineParser::parse(int *, char **) > > MPI rank: 4 (out of 176) > > > > Error in user input: > > Invalid command-line options > > In command-line option -s > > File 'topol.tpr' does not exist or is not accessible. > > The file could not be opened. > > Reason: No such file or directory > > > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From subhomoy.bk at gmail.com Sat Mar 7 19:18:47 2020 From: subhomoy.bk at gmail.com (Borkotoky Speaks) Date: Sat, 07 Mar 2020 18:18:47 -0000 Subject: [gmx-users] MMGBSA for GROMACS In-Reply-To: References: Message-ID: https://rashmikumari.github.io/g_mmpbsa/Tutorial.html 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 On Sat, Mar 7, 2020 at 11:42 PM Anwesh Pandey wrote: > Dear GROMACS Team, > I have done a drug-DNA molecular dynamics, I now wish to perform MMGBSA for > it, but I do not find any tutorial, script, etc. for it. Please help! > > *Anwesh Pandey*, > > Research Scholar (Computational Biophysics), > > Department of Physics, > > School for Physical & Decision Sciences, > > Babasaheb Bhimrao Ambedkar University, > > Lucknow-226025, UP, India. > > +91-9452444164 > > https://www.researchgate.net/profile/Anwesh_Pandey3 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From eduardomayoyanes at gmail.com Sat Mar 7 20:10:17 2020 From: eduardomayoyanes at gmail.com (Eduardo Mayo) Date: Sat, 07 Mar 2020 19:10:17 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 10 In-Reply-To: References: Message-ID: > > > > Hi!, > I mean the page http://www.gromacs.org/Downloads/User_contributions/Force_fields has a amber14sb.ff.tar.gz amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz but at the top of the page it is a warning that say "These force fields are provided by volunteer contributors on an as-is basis. The GROMACS team implies no warranty by hosting them here. If you plan to use any of these force fields, you should make sure you test them for correctness on your system. Please let people know what you observe (good or bad!)." So I was wondering if this force field is realable, like is the any publication which validate it's results?? Can I use them for my simulation? Everyone who report Amberff14SB using gromacs use this forcefield file?? > ---------- Forwarded message ---------- > From: Alessandra Villa > To: gmx-users at gromacs.org, "gromacs.org_gmx-users" < > gromacs.org_gmx-users at maillist.sys.kth.se> > Cc: > Bcc: > Date: Thu, 5 Mar 2020 10:23:42 +0100 > Subject: Re: [gmx-users] Amber14SB > Hi, > > Here a page of force field in GROMACS > http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm > maybe it helps. I did not fully understand your question > > Best regards > Alessandra > > On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo > wrote: > > > Hi!! > > I'm sorry if is the amber14sb poster on the gromacs download site good?? > > I've seen the warning on the page and I don't know what to think. > > Thanks in advance. > > From adarsh_p130085bt at nitc.ac.in Mon Mar 9 06:40:34 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Mon, 09 Mar 2020 05:40:34 -0000 Subject: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4? Message-ID: Dear all, How to solve this error ? gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 The command returns following errors while suing ions.mdp ----------------------------------------------------- NOTE 1 [file ions.mdp] ERROR 1 [file lig.prm, line 49]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ----------------------------------------------------- Can I use the the mdp files used in Gromacs 5.1.4? em.mdp followed by em_real.mdp? From adarsh_p130085bt at nitc.ac.in Mon Mar 9 06:56:47 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Mon, 09 Mar 2020 05:56:47 -0000 Subject: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4? In-Reply-To: References: Message-ID: Dear all, How to solve this error ? gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 The command returns following errors while using " ions.mdp " ----------------------------------------------------- NOTE 1 [file ions.mdp] ERROR 1 [file lig.prm, line 49]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ----------------------------------------------------- Can I use the the mdp files used in Gromacs 5.1.4? em.mdp followed by em_real.mdp? From S.Turega at shu.ac.uk Mon Mar 9 10:55:07 2020 From: S.Turega at shu.ac.uk (Turega, Simon) Date: Mon, 09 Mar 2020 09:55:07 -0000 Subject: [gmx-users] Gromacs 2020 Message-ID: Hi all After attempting to install GROMACS 2020 on new system, I get the error below. The system details & other details are below the error. cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=gcc -DGMX_GPU=ON -Wno-dev make [ 84%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o In file included from /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:48:0, from /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161: /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h: In instantiation of 'std::unique_ptr gmx::SimulatorBuilder::build(bool, Args&& ...) [with Args = {_IO_FILE*&, t_commrec*&, gmx_multisim_t*&, gmx::MDLogger&, int, const t_filenm*, gmx_output_env_t*&, gmx::MdrunOptions&, gmx::StartingBehavior&, gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*&, gmx::ImdSession*, pull_t*&, t_swap*&, gmx_mtop_t*, t_fcdata*&, t_state*, ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*&, t_forcerec*&, gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, ReplicaExchangeParameters&, gmx_membed_t*&, gmx_walltime_accounting*&, std::unique_ptr >, const bool&}]': /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:1612:77: required from here /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h:94:23: error: use of deleted function 'std::unique_ptr<_Tp, _Dp>::unique_ptr(const std::unique_ptr<_Tp, _Dp>&) [with _Tp = gmx::StopHandlerBuilder; _Dp = std::default_delete]' using ISimulator::ISimulator; ^~~~~~~~~~ In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0, from /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.h:48, from /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:46: /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: declared here unique_ptr(const unique_ptr&) = delete; ^~~~~~~~~~ In file included from /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:0: /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:123:45: note: synthesized method 'gmx::LegacySimulator::LegacySimulator(FILE*, t_commrec*, const gmx_multisim_t*, const gmx::MDLogger&, int, const t_filenm*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior, gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*, gmx::ImdSession*, pull_t*, t_swap*, gmx_mtop_t*, t_fcdata*, t_state*, ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*, t_forcerec*, gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, const ReplicaExchangeParameters&, gmx_membed_t*, gmx_walltime_accounting*, std::unique_ptr, bool)' first required here return std::unique_ptr(new LegacySimulator(std::forward(args)...)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o] Error 1 make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [all] Error 2 System details Architecture: x86_64 CPU op modes: 32-bit, 64-bit OS details CentOS Linux release 7.3.1611 (Core) Linux 3.10.0-327.22.2.el7.x86_64 Compiler/ nvcc details openmpi/intel-ofed/gcc/64/1.10.4 Cuda 90 toolkit/9.0.176 gcc version 6.1.0 Thanks in advance for your help Simon Turega From sadafrani6 at gmail.com Mon Mar 9 11:42:27 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 09 Mar 2020 10:42:27 -0000 Subject: [gmx-users] Negative Pressure during equilibration Message-ID: Dear Gromacs users I am running a free energy test calculation and using position restraints for all of the system. At the end of pressure equilibration I am getting negative average pressure as below:- Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure -0.292343 1.3 60.9244 8.84635 (bar) I selected 1 bar ref pressure. Why is it going negative how should I fix it? I need your kind suggestions. Thanks in advance. Sadaf From mark.j.abraham at gmail.com Mon Mar 9 13:08:12 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 09 Mar 2020 12:08:12 -0000 Subject: [gmx-users] Negative Pressure during equilibration In-Reply-To: References: Message-ID: Hi, Check out the GROMACS FAQs - this question is a very frequent one! :-) Mark On Mon, 9 Mar 2020 at 11:42, Sadaf Rani wrote: > Dear Gromacs users > > I am running a free energy test calculation and using position restraints > for all of the system. At the end of pressure equilibration I am > getting negative average pressure as below:- > > > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Pressure -0.292343 1.3 60.9244 8.84635 (bar) > > I selected 1 bar ref pressure. Why is it going negative how should I fix > it? I need your kind suggestions. > > Thanks in advance. > > 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 mark.j.abraham at gmail.com Mon Mar 9 13:08:12 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 09 Mar 2020 12:08:12 -0000 Subject: [gmx-users] Negative Pressure during equilibration In-Reply-To: References: Message-ID: Hi, Check out the GROMACS FAQs - this question is a very frequent one! :-) Mark On Mon, 9 Mar 2020 at 11:42, Sadaf Rani wrote: > Dear Gromacs users > > I am running a free energy test calculation and using position restraints > for all of the system. At the end of pressure equilibration I am > getting negative average pressure as below:- > > > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Pressure -0.292343 1.3 60.9244 8.84635 (bar) > > I selected 1 bar ref pressure. Why is it going negative how should I fix > it? I need your kind suggestions. > > Thanks in advance. > > 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 mark.j.abraham at gmail.com Mon Mar 9 13:26:52 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 09 Mar 2020 12:26:52 -0000 Subject: [gmx-users] Gromacs 2020 In-Reply-To: References: Message-ID: Hi, The code is tested extensively on a range of compilers, so we believe it is correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS tests with 6.4.0, so the issue might have been fixed in the meantime. As newer versions of gcc and cuda will give better performance, I suggest you get cuda 10.2 and gcc 8 and try again. Sorry! Mark On Mon, 9 Mar 2020 at 10:56, Turega, Simon wrote: > Hi all > > After attempting to install GROMACS 2020 on new system, I get the error > below. The system details & other details are below the error. > > cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020 > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=gcc -DGMX_GPU=ON -Wno-dev > > make > > [ 84%] Building CXX object > src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o > In file included from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:48:0, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161: > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h: In > instantiation of 'std::unique_ptr > gmx::SimulatorBuilder::build(bool, Args&& ...) [with Args = {_IO_FILE*&, > t_commrec*&, gmx_multisim_t*&, gmx::MDLogger&, int, const t_filenm*, > gmx_output_env_t*&, gmx::MdrunOptions&, gmx::StartingBehavior&, > gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, > gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*&, > gmx::ImdSession*, pull_t*&, t_swap*&, gmx_mtop_t*, t_fcdata*&, t_state*, > ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*&, t_forcerec*&, > gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, > ReplicaExchangeParameters&, gmx_membed_t*&, gmx_walltime_accounting*&, > std::unique_ptr std::default_delete >, const bool&}]': > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:1612:77: > required from here > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h:94:23: > error: use of deleted function 'std::unique_ptr<_Tp, _Dp>::unique_ptr(const > std::unique_ptr<_Tp, _Dp>&) [with _Tp = gmx::StopHandlerBuilder; _Dp = > std::default_delete]' > using ISimulator::ISimulator; > ^~~~~~~~~~ > In file included from > /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.h:48, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:46: > /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: > declared here > unique_ptr(const unique_ptr&) = delete; > ^~~~~~~~~~ > In file included from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:0: > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:123:45: > note: synthesized method 'gmx::LegacySimulator::LegacySimulator(FILE*, > t_commrec*, const gmx_multisim_t*, const gmx::MDLogger&, int, const > t_filenm*, const gmx_output_env_t*, const gmx::MdrunOptions&, > gmx::StartingBehavior, gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, > gmx::BoxDeformation*, gmx::IMDOutputProvider*, const > gmx::MdModulesNotifier&, t_inputrec*, gmx::ImdSession*, pull_t*, t_swap*, > gmx_mtop_t*, t_fcdata*, t_state*, ObservablesHistory*, gmx::MDAtoms*, > t_nrnb*, gmx_wallcycle*, t_forcerec*, gmx_enerdata_t*, gmx_ekindata_t*, > gmx::MdrunScheduleWorkload*, const ReplicaExchangeParameters&, > gmx_membed_t*, gmx_walltime_accounting*, > std::unique_ptr, bool)' first required here > return std::unique_ptr(new > LegacySimulator(std::forward(args)...)); > > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o] > Error 1 > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > make: *** [all] Error 2 > > System details > > Architecture: x86_64 > CPU op modes: 32-bit, 64-bit > > OS details > > CentOS Linux release 7.3.1611 (Core) > Linux 3.10.0-327.22.2.el7.x86_64 > > Compiler/ nvcc details > > openmpi/intel-ofed/gcc/64/1.10.4 > Cuda 90 toolkit/9.0.176 > gcc version 6.1.0 > > Thanks in advance for your help > > Simon Turega > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mar 9 13:26:53 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 09 Mar 2020 12:26:53 -0000 Subject: [gmx-users] Gromacs 2020 In-Reply-To: References: Message-ID: Hi, The code is tested extensively on a range of compilers, so we believe it is correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS tests with 6.4.0, so the issue might have been fixed in the meantime. As newer versions of gcc and cuda will give better performance, I suggest you get cuda 10.2 and gcc 8 and try again. Sorry! Mark On Mon, 9 Mar 2020 at 10:56, Turega, Simon wrote: > Hi all > > After attempting to install GROMACS 2020 on new system, I get the error > below. The system details & other details are below the error. > > cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020 > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=gcc -DGMX_GPU=ON -Wno-dev > > make > > [ 84%] Building CXX object > src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o > In file included from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:48:0, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161: > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h: In > instantiation of 'std::unique_ptr > gmx::SimulatorBuilder::build(bool, Args&& ...) [with Args = {_IO_FILE*&, > t_commrec*&, gmx_multisim_t*&, gmx::MDLogger&, int, const t_filenm*, > gmx_output_env_t*&, gmx::MdrunOptions&, gmx::StartingBehavior&, > gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, > gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*&, > gmx::ImdSession*, pull_t*&, t_swap*&, gmx_mtop_t*, t_fcdata*&, t_state*, > ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*&, t_forcerec*&, > gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, > ReplicaExchangeParameters&, gmx_membed_t*&, gmx_walltime_accounting*&, > std::unique_ptr std::default_delete >, const bool&}]': > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:1612:77: > required from here > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h:94:23: > error: use of deleted function 'std::unique_ptr<_Tp, _Dp>::unique_ptr(const > std::unique_ptr<_Tp, _Dp>&) [with _Tp = gmx::StopHandlerBuilder; _Dp = > std::default_delete]' > using ISimulator::ISimulator; > ^~~~~~~~~~ > In file included from > /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.h:48, > from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:46: > /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: > declared here > unique_ptr(const unique_ptr&) = delete; > ^~~~~~~~~~ > In file included from > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:0: > /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:123:45: > note: synthesized method 'gmx::LegacySimulator::LegacySimulator(FILE*, > t_commrec*, const gmx_multisim_t*, const gmx::MDLogger&, int, const > t_filenm*, const gmx_output_env_t*, const gmx::MdrunOptions&, > gmx::StartingBehavior, gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, > gmx::BoxDeformation*, gmx::IMDOutputProvider*, const > gmx::MdModulesNotifier&, t_inputrec*, gmx::ImdSession*, pull_t*, t_swap*, > gmx_mtop_t*, t_fcdata*, t_state*, ObservablesHistory*, gmx::MDAtoms*, > t_nrnb*, gmx_wallcycle*, t_forcerec*, gmx_enerdata_t*, gmx_ekindata_t*, > gmx::MdrunScheduleWorkload*, const ReplicaExchangeParameters&, > gmx_membed_t*, gmx_walltime_accounting*, > std::unique_ptr, bool)' first required here > return std::unique_ptr(new > LegacySimulator(std::forward(args)...)); > > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o] > Error 1 > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > make: *** [all] Error 2 > > System details > > Architecture: x86_64 > CPU op modes: 32-bit, 64-bit > > OS details > > CentOS Linux release 7.3.1611 (Core) > Linux 3.10.0-327.22.2.el7.x86_64 > > Compiler/ nvcc details > > openmpi/intel-ofed/gcc/64/1.10.4 > Cuda 90 toolkit/9.0.176 > gcc version 6.1.0 > > Thanks in advance for your help > > Simon Turega > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mon Mar 9 14:47:34 2020 From: 272699575 at qq.com (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) Date: Mon, 09 Mar 2020 13:47:34 -0000 Subject: [gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa" Message-ID: Dear Gromacs, There seems to be very little explanation on the "-surface" and "-output" options of "gmx sasa": -surface: This should always consist of all non-solvent atoms in the system. The area of this group is always calculated -output: can specify additional selections, which should be subsets of the calculation group. Can I understand in this way: 1. The "-surface" will calculate the surface area of the suppiled group. Regardless the group is inside or outside of the protein, the "sasa" will always assume the group to be fully solvent-exposed. So actually, it is not "Solvent Accessible Surface Area" of the group; it is "taking the group out from the protein, and put it in solvent, then calculate its surface".  2. When all the residues are supplied to the "-output" option, I have tested that the sum of "-output" equals to the "-surface": gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output 'resnr 1; resnr 2; resnr 3; ...; resnr n' This is good. However, I saw many residues having area of 0 even though they locate on the very outer surface. I think the explanation could be, their side-chains are totally shielded by their neighbouring side-chains. Is that correct? (I just feel SASA value of 0 is almost impossible) Thank you! Yours sincerely Cheng From pall.szilard at gmail.com Mon Mar 9 16:53:30 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 09 Mar 2020 15:53:30 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> Message-ID: Hi Andreas, Sorry for the delay. I can confirm the regression. This affects the energy calculation steps where the GPU bonded computational did get significantly slower (as a side-effect of optimizations that mainly targeted the force-only kernels). Can you please file an issue on redmine.gromacs.org and upload the data you shared with me? As a workaround you should consider using an nstcalcenergy>1; bumping it to just ~10 would eliminate most of the regression and would improve the performance of other computation too (the nonbonded F-only kernels are also at least 1.5x faster than the force+energy kernels). Alternatively, I recall you had decent CPU, so you could run the bonded interactions on the CPU Side-note: you are using an overly fine PME grid that you did not scale along the (overly accurate) the rather long cut-offs (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-fourierspacing ). Cheers, -- Szil?rd On Fri, Feb 28, 2020 at 11:10 AM Andreas Baer wrote: > 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 si.papadatos at edu.cut.ac.cy Mon Mar 9 17:00:49 2020 From: si.papadatos at edu.cut.ac.cy (Sotirios Dionysios I. Papadatos) Date: Mon, 09 Mar 2020 16:00:49 -0000 Subject: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4? In-Reply-To: References: , Message-ID: In most cases this means that the exact same line is given more than once. I would start from there. ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Adarsh V. K. Sent: Monday, March 9, 2020 1:26 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4? Dear all, How to solve this error ? gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 The command returns following errors while using " ions.mdp " ----------------------------------------------------- NOTE 1 [file ions.mdp] ERROR 1 [file lig.prm, line 49]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ----------------------------------------------------- Can I use the the mdp files used in Gromacs 5.1.4? em.mdp followed by em_real.mdp? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests 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 Mar 9 17:01:01 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 09 Mar 2020 16:01:01 -0000 Subject: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5 In-Reply-To: <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> References: <5ec24c10-4f71-fe0e-4e26-8958ef8366e6@gmail.com> <33dec4f3-93a9-0f2a-ad87-672eee24a3b4@fau.de> <150df543-9084-3adb-50c3-4276818dbf61@fau.de> <192c7610-a044-50e4-a4f1-718dabeab621@fau.de> Message-ID: Hi Andreas, Sorry for the delay. I can confirm the regression. This affects the energy calculation steps where the GPU bonded computational did get significantly slower (as a side-effect of optimizations that mainly targeted the force-only kernels). Can you please file an issue on redmine.gromacs.org and upload the data you shared with me? As a workaround you should consider using an nstcalcenergy>1; bumping it to just ~10 would eliminate most of the regression and would improve the performance of other computation too (the nonbonded F-only kernels are also at least 1.5x faster than the force+energy kernels). Alternatively, I recall you had decent CPU, so you could run the bonded interactions on the CPU Side-note: you are using an overly fine PME grid that you did not scale along the (overly accurate) the rather long cut-offs (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-fourierspacing ). Cheers, -- Szil?rd On Fri, Feb 28, 2020 at 11:10 AM Andreas Baer wrote: > 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 jalemkul at vt.edu Mon Mar 9 18:36:40 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 09 Mar 2020 17:36:40 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 10 In-Reply-To: References: Message-ID: <029e646c-eac2-59cb-1aed-1cf7a1945d56@vt.edu> On 3/7/20 2:10 PM, Eduardo Mayo wrote: >> >> >> Hi!, >> > I mean the page > http://www.gromacs.org/Downloads/User_contributions/Force_fields > has > a amber14sb.ff.tar.gz amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz > but at the top of the page it is a warning that say "These force fields are > provided by volunteer contributors on an as-is basis. The GROMACS team > implies no warranty by hosting them here. If you plan to use any of these > force fields, you should make sure you test them for correctness on your > system. Please let people know what you observe (good or bad!)." > So I was wondering if this force field is realable, like is the any > publication which validate it's results?? Can I use them for my simulation? > Everyone who report Amberff14SB using gromacs use this forcefield file?? You should ask the corresponding authors how the implemented the force field. As with any user contribution, unless explicit validation has been done (e.g. comparing forces and energies of identical configurations in AMBER vs. GROMACS), you should be wary about using the force field files. Or do the validation yourself before basing your whole project on the contributed files. Some of the parameter sets have been validated, but most haven't. -Justin > >> ---------- Forwarded message ---------- >> From: Alessandra Villa >> To: gmx-users at gromacs.org, "gromacs.org_gmx-users" < >> gromacs.org_gmx-users at maillist.sys.kth.se> >> Cc: >> Bcc: >> Date: Thu, 5 Mar 2020 10:23:42 +0100 >> Subject: Re: [gmx-users] Amber14SB >> Hi, >> >> Here a page of force field in GROMACS >> http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm >> maybe it helps. I did not fully understand your question >> >> Best regards >> Alessandra >> >> On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo >> wrote: >> >>> Hi!! >>> I'm sorry if is the amber14sb poster on the gromacs download site good?? >>> I've seen the warning on the page and I don't know what to think. >>> Thanks in advance. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Mon Mar 9 18:38:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 09 Mar 2020 17:38:05 -0000 Subject: [gmx-users] ERROR 1 [file lig.prm, line 49] - Can I use the the mdp files -> em.mdp followed by em_real.mdp used for Gromacs 5.1.4? In-Reply-To: References: Message-ID: On 3/9/20 7:10 AM, Adarsh V. K. wrote: > Dear all, > > How to solve this error ? > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1 > > The command returns following errors while suing ions.mdp > ----------------------------------------------------- > NOTE 1 [file ions.mdp] > ERROR 1 [file lig.prm, line 49]: > Encountered a second block of parameters for dihedral type 9 for the same > atoms, with either different parameters and/or the first block has > multiple lines. This is not supported. > ----------------------------------------------------- This is a consequence of the CGenFF server having an older (4.0) version of CGenFF but our force field ports have the newest (4.1). Eliminate the offending line(s) from lig.prm because you want to use the parameters in the force field already (which have been explicitly refined) rather than the guessed parameters in the .prm file (which may not be suitable). > Can I use the the mdp files used in Gromacs 5.1.4? Why use outdated software? -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 travis.meyer at rutgers.edu Mon Mar 9 20:32:34 2020 From: travis.meyer at rutgers.edu (Travis Meyer) Date: Mon, 09 Mar 2020 19:32:34 -0000 Subject: [gmx-users] Troubleshooting Generic Floating Point Exception Errors Message-ID: Hello all, I am a very new user to GROMACS and MD simulations in general. While going through some tutorials and other test simulations I've been getting some floating point exception errors. I recognize that there are a vast number of problems that could be causing this - I am not looking for any solutions to a specific problem, but am mostly wondering if there is a good procedure for troubleshooting these errors. Are there a couple of most-likely culprits which I should check first? Thanks in advance! Travis Travis Meyer, Ph.D. INSPIRE Postdoctoral Fellow Gormley Lab, Rutgers University From spoel at xray.bmc.uu.se Mon Mar 9 21:36:20 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 09 Mar 2020 20:36:20 -0000 Subject: [gmx-users] Troubleshooting Generic Floating Point Exception Errors In-Reply-To: References: Message-ID: <2f4ab16c-1eaa-0dca-2b45-9cf6f6b87823@xray.bmc.uu.se> Den 2020-03-09 kl. 20:14, skrev Travis Meyer: > Hello all, > > I am a very new user to GROMACS and MD simulations in general. While going through some tutorials and other test simulations I've been getting some floating point exception errors. I recognize that there are a vast number of problems that could be causing this - I am not looking for any solutions to a specific problem, but am mostly wondering if there is a good procedure for troubleshooting these errors. Are there a couple of most-likely culprits which I should check first? > > Thanks in advance! > Travis > > > Travis Meyer, Ph.D. > INSPIRE Postdoctoral Fellow > Gormley Lab, Rutgers University > These are rather uncommon unless you have truly unphysical setups (e.g. due to a unit problem) or broken hardware. Hard to tell based on your mail unfortunately. -- 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 mark.j.abraham at gmail.com Mon Mar 9 22:30:17 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Mon, 09 Mar 2020 21:30:17 -0000 Subject: [gmx-users] Troubleshooting Generic Floating Point Exception Errors In-Reply-To: References: Message-ID: Hi, Depends when you see them. From mdrun, you're generally blowing up (see user guide and FAQ list). From tools, maybe your input data is somehow bad (or bad in part, so try different parts), or you ran into a silent size limitation in the code (see if a smaller data set works and if so file a bug). Always visualize trajectories to check for sanity before you do any numerical analysis. Countless millions of simulation hours have been wasted by people too lazy for that! Mark On Mon., 9 Mar. 2020, 20:32 Travis Meyer, wrote: > Hello all, > > I am a very new user to GROMACS and MD simulations in general. While going > through some tutorials and other test simulations I've been getting some > floating point exception errors. I recognize that there are a vast number > of problems that could be causing this - I am not looking for any solutions > to a specific problem, but am mostly wondering if there is a good procedure > for troubleshooting these errors. Are there a couple of most-likely > culprits which I should check first? > > Thanks in advance! > Travis > > > Travis Meyer, Ph.D. > INSPIRE Postdoctoral Fellow > Gormley Lab, Rutgers University > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Tue Mar 10 03:18:10 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Tue, 10 Mar 2020 02:18:10 -0000 Subject: [gmx-users] Setting a electric field in a simulation Message-ID: Dear GMX users, I would like to perform MD simulations of solutions applying electric fields such as the microwave heating process. Is it possible to perform in gromacs? 1. How can I set the external electric field in the simulations? (from the user guide, I understood that I need to set 4 values electric-field-x = 2.0 150 5 0 How can I adjust the 2.45 GHz frequency? If you do not mind, please guide me. Best regards, Mijiddorj From devargyachakraborty.kgp at gmail.com Tue Mar 10 05:05:03 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Tue, 10 Mar 2020 04:05:03 -0000 Subject: [gmx-users] Replicate a structure Message-ID: I have an equilibrated droplet of water. What I want to do is replicate that droplet in the x direction. So that my simulation box will carry two water droplets. Is that possible in gromacs. If yes please guide me. Thank you Devargya Chakraborty From 177cy500.bratin at nitk.edu.in Tue Mar 10 06:47:56 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Tue, 10 Mar 2020 05:47:56 -0000 Subject: [gmx-users] Replicate a structure In-Reply-To: References: Message-ID: Gmx editconf you can use with -translate flag...after that merz the coordinates of two water droplets. I hope this may help you. On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < devargyachakraborty.kgp at gmail.com> wrote: > I have an equilibrated droplet of water. What I want to do is replicate > that droplet in the x direction. So that my simulation box will carry two > water droplets. Is that possible in gromacs. If yes please guide me. > > Thank you > Devargya Chakraborty > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Tue Mar 10 09:09:54 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 10 Mar 2020 08:09:54 -0000 Subject: [gmx-users] Setting a electric field in a simulation In-Reply-To: References: Message-ID: <92e46fbb-adf6-de46-5391-c8dc509bb4f5@xray.bmc.uu.se> Den 2020-03-10 kl. 03:17, skrev Mijiddorj B: > Dear GMX users, > > I would like to perform MD simulations of solutions applying electric > fields such as the microwave heating process. Is it possible to perform in > gromacs? > > 1. How can I set the external electric field in the simulations? > (from the user guide, I understood that I need to set 4 values > > electric-field-x = 2.0 150 5 0 > > How can I adjust the 2.45 GHz frequency? > > If you do not mind, please guide me. > > Best regards, > > Mijiddorj > Why don't you try to play around and check the output file field.xvg to see what frequency you get? -- 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 alessandra.villa.biosim at gmail.com Tue Mar 10 13:07:25 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 10 Mar 2020 12:07:25 -0000 Subject: [gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa" In-Reply-To: References: Message-ID: On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699575 at qq.com> wrote: > Dear Gromacs, > > > There seems to be very little explanation on the "-surface" and "-output" > options of "gmx sasa": > -surface: This should always consist of all non-solvent atoms in the > system. The area of this group is always calculated > -output: can specify additional selections, which should be subsets of the > calculation group. > > > Can I understand in this way: > > > 1. The "-surface" will calculate the surface area of the suppiled group. > Regardless the group is inside or outside of the protein, the "sasa" will > always assume the group to be fully solvent-exposed. So actually, it is not > "Solvent Accessible Surface Area" of the group; it is "taking the group out > from the protein, and put it in solvent, then calculate its surface".  > > > 2. When all the residues are supplied to the "-output" option, I have > tested that the sum of "-output" equals to the "-surface": > gmx sasa -s protein.pdb -o area.xvg -tu ns -surface 'group 1' -output > 'resnr 1; resnr 2; resnr 3; ...; resnr n' > This is good. However, I saw many residues having area of 0 even though > they locate on the very outer surface. I think the explanation could be, > their side-chains are totally shielded by their neighbouring side-chains. > Is that correct? (I just feel SASA value of 0 is almost impossible) > > To calculate the surface a radii of 0.14 nm is used for the solvent probe, and also a radii is associated to each atom belonging the surface (for the values of the radii see the reference Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284). Thus it could be that atoms are shielded by other atoms volume or not accessible to the water bead. Best regards Alessandra > > Thank you! > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From johnwhittake at zedat.fu-berlin.de Tue Mar 10 13:30:40 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Tue, 10 Mar 2020 12:30:40 -0000 Subject: [gmx-users] Replicate a structure In-Reply-To: References: Message-ID: <54542.160.45.109.123.1583843437.webmail@webmail.zedat.fu-berlin.de> Probably better to use gmx genconf; This situation is probably its main purpose. - John > Gmx editconf you can use with -translate flag...after that merz the > coordinates of two water droplets. I hope this may help you. > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < > devargyachakraborty.kgp at gmail.com> wrote: > >> I have an equilibrated droplet of water. What I want to do is replicate >> that droplet in the x direction. So that my simulation box will carry >> two >> water droplets. Is that possible in gromacs. If yes please guide me. >> >> Thank you >> Devargya Chakraborty >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 devargyachakraborty.kgp at gmail.com Tue Mar 10 15:45:03 2020 From: devargyachakraborty.kgp at gmail.com (Devargya Chakraborty) Date: Tue, 10 Mar 2020 14:45:03 -0000 Subject: [gmx-users] Replicate a structure In-Reply-To: <54542.160.45.109.123.1583843437.webmail@webmail.zedat.fu-berlin.de> References: <54542.160.45.109.123.1583843437.webmail@webmail.zedat.fu-berlin.de> Message-ID: Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o new_system.gro right?? On Tue, Mar 10, 2020, 6:01 PM John Whittaker < johnwhittake at zedat.fu-berlin.de> wrote: > Probably better to use gmx genconf; This situation is probably its main > purpose. > > - John > > > Gmx editconf you can use with -translate flag...after that merz the > > coordinates of two water droplets. I hope this may help you. > > > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < > > devargyachakraborty.kgp at gmail.com> wrote: > > > >> I have an equilibrated droplet of water. What I want to do is replicate > >> that droplet in the x direction. So that my simulation box will carry > >> two > >> water droplets. Is that possible in gromacs. If yes please guide me. > >> > >> Thank you > >> Devargya Chakraborty > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe 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 Tue Mar 10 15:51:43 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Tue, 10 Mar 2020 14:51:43 -0000 Subject: [gmx-users] Replicate a structure In-Reply-To: References: <54542.160.45.109.123.1583843437.webmail@webmail.zedat.fu-berlin.de> Message-ID: <57226.160.45.109.123.1583851900.webmail@webmail.zedat.fu-berlin.de> > Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o > new_system.gro right?? Based on what you described, I'd say that's correct. Try it out and then visualize the resulting .gro file to see if things are how you want them to be. > > On Tue, Mar 10, 2020, 6:01 PM John Whittaker < > johnwhittake at zedat.fu-berlin.de> wrote: > >> Probably better to use gmx genconf; This situation is probably its main >> purpose. >> >> - John >> >> > Gmx editconf you can use with -translate flag...after that merz the >> > coordinates of two water droplets. I hope this may help you. >> > >> > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < >> > devargyachakraborty.kgp at gmail.com> wrote: >> > >> >> I have an equilibrated droplet of water. What I want to do is >> replicate >> >> that droplet in the x direction. So that my simulation box will carry >> >> two >> >> water droplets. Is that possible in gromacs. If yes please guide me. >> >> >> >> Thank you >> >> Devargya Chakraborty >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe 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 Mar 10 18:15:21 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 10 Mar 2020 17:15:21 -0000 Subject: [gmx-users] [gmx-developers] The setup of gpu_id has a bug? In-Reply-To: <1557959f.841b.170c558cf16.Coremail.dxli75@126.com> References: <1557959f.841b.170c558cf16.Coremail.dxli75@126.com> Message-ID: Hi, Please sue the user's mailing list for questions not related to GROMACS development. By default. the "-gpu_id" option takes a sequence of digits corresponding to the numeric identifiers of GPUs. In cases where there are >10 GPUs in a system, a comma-separated string should be used, see http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node Cheers, -- Szil?rd On Tue, Mar 10, 2020 at 5:51 PM dxli75 wrote: > everyone, > When I set the gpu_id as 10-15, the GMX always give the message of PP:1,PME:1. > And the job run on GPU No.1 instead of No.10-15. > Is there a bug? > > GROMACS: gmx mdrun, version 2020.1 > > Executable: > /raid/data/dxli/projects/ncovs-1rpb/../../gromacs-2020.1/bin/gmx > Data prefix: /raid/data/dxli/projects/ncovs-1rpb/../../gromacs-2020.1 > Working dir: /raid/data/dxli/projects/ncovs-1rpb > Command line: > gmx mdrun -deffnm test -gpu_id 10 -ntmpi 1 -ntomp 8 > > Reading file test.tpr, VERSION 2020 (single precision) > 1 GPU selected for this run. > Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: > PP:1,PME:1 > PP tasks will do (non-perturbed) short-ranged interactions on the GPU > PP task will update and constrain coordinates on the CPUPME tasks will do > all aspects on the GPU > Using 1 MPI thread > > Non-default thread affinity set, disabling internal thread affinity > > Using 8 OpenMP threads > > > > > > > -- > *Daixi Li * > *Ph.D., Associated Professor**P.I.*, Laboratory of Computational Biology > > > > -- > Gromacs Developers mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers > or send a mail to gmx-developers-request at gromacs.org. From neena.susaneappen at mail.utoronto.ca Tue Mar 10 20:20:07 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Tue, 10 Mar 2020 19:20:07 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: , , Message-ID: Hi Justin, I tried that script out, but I want the output in a different way. So I have n log files (.log), and I want to extract potential energy value say from line x from all n log files. Is there a way I can export all these potential energy values into one text file with one script? Many thanks, Neena ________________________________ From: Neena Susan Eappen Sent: Saturday, February 22, 2020 4:28 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] Script for looping n simulations 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 Tue Mar 10 20:22:28 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 10 Mar 2020 19:22:28 -0000 Subject: [gmx-users] Script for looping n simulations In-Reply-To: References: Message-ID: <04675030-1d1f-c9fa-bc9c-5982ac7e10d6@vt.edu> On 3/10/20 3:20 PM, Neena Susan Eappen wrote: > Hi Justin, > > I tried that script out, but I want the output in a different way. So I have n log files (.log), and I want to extract potential energy value say from line x from all n log files. Is there a way I can export all these potential energy values into one text file with one script? Yes, this is easy to do with standard Linux tools, but that is a topic for other forums. It is easier to get this information from .edr files directly from gmx energy. -Justin > Many thanks, > Neena > ________________________________ > From: Neena Susan Eappen > Sent: Saturday, February 22, 2020 4:28 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] Script for looping n simulations > > 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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 alfredo at ices.utexas.edu Tue Mar 10 21:29:48 2020 From: alfredo at ices.utexas.edu (Cardenas, Alfredo E) Date: Tue, 10 Mar 2020 20:29:48 -0000 Subject: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells Message-ID: Hi, I am using gromacs-2019.4. I have been running simulations box that contains a peptide embedded in a DOPC bilayer membrane, using all atom simulations. I have been running for weeks in a TACC computer that has 4 gpu in a single node, so I usually run 4 trajectories in a single node using the -multidir option. My submission script is: #!/bin/bash #SBATCH -J sb16 # Job name #SBATCH -o test.o%j # Job name #SBATCH -e test.e%j # Job name #SBATCH -N 1 # Total number of nodes requested #SBATCH -n 4 # Total number of mpi tasks requested #SBATCH -p rtx # Queue (partition) name -- normal, development, etc. #SBATCH -t 48:00:00 # Run time (hh:mm:ss) - 1.5 hours module load cuda/10.1 module use -a /home1/01247/alfredo/Software/ForGPU/plumed-2.5.3/MyInstall/lib/plumed/ModuleFile module load plumed_gpu export OMP_NUM_THREADS=4 ibrun /home1/01247/alfredo/Software/gromacs-2019.4_gpu/build-gpu-mpi-plumed/My_install/bin/mdrun_mpi -s topol.tpr -plumed plumed.dat -multidir 1 2 3 4 Because the system is going to be down for a week I want to do continuation runs in a slower computer system, also using gpus. Because the system is slower I want to run it using two nodes. A script that I have used successfully in that old machine is: #!/bin/bash #SBATCH -J SB9_pi1 # Job name #SBATCH -o test.o%j # Job name #SBATCH -N 2 # Total number of nodes requested #SBATCH -n 2 # Total number of mpi tasks requested #SBATCH -p gpu # Queue (partition) name -- normal, development, etc. #SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 1.5 hours module load gcc/5.2.0 module load cray_mpich/7.7.3 module load cuda/9.0 # Launc hMPI-based executable export OMP_NUM_THREADS=6 ibrun /home1/01247/alfredo/gromacs-2019.4/build_MPI/My_install/bin/mdrun_mpi -s topol2.tpr -pin on -cpi state.cpt -noappend It works great if I setup a new simulation of the same molecular system (create a new tpr file). But if I attempt to run a continuation run coming from the other machine (that used 4 threads). I get Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond of 10801 missing -5 U-B of 53187 missing 22 Proper Dih. of 89703 missing 119 LJ-14 of 73729 missing 3 srun: Job step aborted: Waiting up to 32 seconds for job step to finish. And it stops. If I modified the script for the old machine to use 1 nodes, 1 task and 4 thread, it runs well but it is a lot slower. My question is if there is any way to avoid this error, so I can do a continuation run using state.cpt with a different domain decomposition. I have seen in the list that is suggested to use -rdd. The value printed in the log file is 1.595 nm. I increased to 2.0 and gave a similar error. Thanks, Alfredo From alessandra.villa.biosim at gmail.com Wed Mar 11 10:27:50 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 11 Mar 2020 09:27:50 -0000 Subject: [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2 In-Reply-To: References: Message-ID: Hi, mdp option may have been changed going from 4.6 to 5.1 , you should update your mdp file according to the 5.1 option (see http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html ) If you do not have any special reason to use 5.1, I will suggest to move to the newest version of GROMACS (GROMACS-2020.1 http://manual.gromacs.org/current/index.html), since you are on the way to change version. Best regards Alessandra On Sat, Mar 7, 2020 at 11:21 AM Rana Ali wrote: > Hi > I was running water on graphene using PBC =xy by keeping the graphene > fixed in y direction. > It was running in gromacs version 4.6 but failed to run in 5.1.2. > This is the error. > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# > > ERROR 1 [file nvt.mdp]: > With Verlet lists only full pbc or pbc=xy with walls is supported > > > ERROR 2 [file nvt.mdp]: > With Verlet lists rcoulomb!=rvdw is not supported > > > NOTE 2 [file nvt.mdp]: > Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off > and vdw_modifier=Potential-switch > > > ERROR 3 [file nvt.mdp]: > The box volume is required for calculating rlist from the energy drift > with verlet-buffer-tolerance > 0. You are using at least one unbounded > dimension, so no volume can be computed. Either use a finite box, or set > rlist yourself together with verlet-buffer-tolerance = -1. > > Setting the LD random seed to 1821932621 > Generated 371091 of the 371091 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 371091 of the 371091 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'GRA' > turning H bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning H bonds into constraints... > Setting gen_seed to 925853613 > Velocities were taken from a Maxwell distribution at 300 K > Removing all charge groups because cutoff-scheme=Verlet > > There were 2 notes > > ------------------------------------------------------- > Program gmx grompp, VERSION 5.1.2 > Source code file: > /home/usr01/gromacs/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: > 1738 > > Fatal error: > There were 3 errors in input file(s) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > Here is the NVT.mdp > ; Run control > integrator = sd ; Langevin dynamics > tinit = 0 > dt = 0.001 > nsteps = 50000 ; 100 ps > nstcomm = 100 > ; Output control > nstxout = 500 > nstvout = 500 > nstfout = 0 > nstlog = 500 > nstenergy = 500 > nstxtcout = 0 > xtc-precision = 1000 > ; Neighborsearching and short-range nonbonded interactions > nstlist = 10 > ns_type = grid > pbc = xy > rlist = 1.20 > ; Electrostatics > coulombtype = cut-off > rcoulomb = 1.20 > ; van der Waals > vdw-type = switch > rvdw-switch = 0.8 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = no > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; EWALD/PME/PPPM parameters > pme_order = 6 > ewald_rtol = 1e-06 > epsilon_surface = 0 > optimize_fft = no > ; Temperature coupling > ; tcoupl is implicitly handled by the sd integrator > tc_grps = system > tau_t = 1.0 > ref_t = 300 > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > > periodic_molecules=yes > > freezegrps = LIG > freezedim = Y Y Y > ; options for bonds > constraints = h-bonds ; we only have C-H bonds here > ; Type of constraint algorithm > constraint-algorithm = lincs > ; Do not constrain the starting configuration > continuation = no > ; Highest order in the expansion of the constraint coupling matrix > lincs-order = 12 > > Could you please help to sort out the problem from version 4.6 to 5.1.2 > in NVT.mdp > Thanks 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 m.b.abdelaal at gmail.com Wed Mar 11 14:07:42 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 11 Mar 2020 13:07:42 -0000 Subject: [gmx-users] GROMACS automation Message-ID: Hello everybody, I am trying to insert molecules into a box but I have to insert one single molecule at a time reaching 3000 molecule in total. Is there a way to automate this process ? Thanks Mohamed From m.b.abdelaal at gmail.com Wed Mar 11 14:07:42 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 11 Mar 2020 13:07:42 -0000 Subject: [gmx-users] GROMACS automation Message-ID: Hello everybody, I am trying to insert molecules into a box but I have to insert one single molecule at a time reaching 3000 molecule in total. Is there a way to automate this process ? Thanks Mohamed From johnwhittake at zedat.fu-berlin.de Wed Mar 11 14:42:45 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 11 Mar 2020 13:42:45 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: References: Message-ID: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> Write a script that calls gmx insert-molecules 3000 times and uses the previous output as input for each call. http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html Is there something you have to do in between each insertion? - John > Hello everybody, > > I am trying to insert molecules into a box but I have to insert one single > molecule at a time reaching 3000 molecule in total. Is there a way to > automate this process ? > > 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 m.b.abdelaal at gmail.com Wed Mar 11 14:56:49 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Wed, 11 Mar 2020 13:56:49 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> Message-ID: I want to insert an atom with a velocity moving downwards toward the graphene sheet in my box. Yes I need to remove any atom moving away from my substrate or the deposited atoms and far by 0.4 nm. Then repeat the process until I have inserted 3000 atoms. Thanks for your reply. Mohamed On Wed, Mar 11, 2020 at 13:43 John Whittaker < johnwhittake at zedat.fu-berlin.de> wrote: > Write a script that calls gmx insert-molecules 3000 times and uses the > previous output as input for each call. > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > > Is there something you have to do in between each insertion? > > - John > > > Hello everybody, > > > > I am trying to insert molecules into a box but I have to insert one > single > > molecule at a time reaching 3000 molecule in total. Is there a way to > > automate this process ? > > > > 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 snehasis.chatterjee18 at gmail.com Wed Mar 11 16:33:34 2020 From: snehasis.chatterjee18 at gmail.com (Snehasis Chatterjee) Date: Wed, 11 Mar 2020 15:33:34 -0000 Subject: [gmx-users] query regarding running simulation using GPU Message-ID: Dear Gromacs users, I am trying to perform a simulation for a relatively large system using GROMACS 2019. I was using CPU for running simulation and now, I have 100 ns data. But, now I have a access to use good quality GPU machine. I want to continue my simulation (after 100ns) using GPU. Is it possible to do that? I am bit confused regarding this issue. Any kind of advice/ suggestions will be deeply appreciated. Thanks in advance, Snehasis Chatterjee From nedomacho at gmail.com Wed Mar 11 19:14:39 2020 From: nedomacho at gmail.com (Alex) Date: Wed, 11 Mar 2020 18:14:39 -0000 Subject: [gmx-users] gmx traj Message-ID: Hi all, I have an aqueous system featuring a membrane and a bunch of ions driven by a constant field in the z-direction (PBC). In order to look at current fluctuations in time, for every frame, I represent current as proportional to for the whole ion group (K, CL, for instance), so I run gmx traj with -ov and -com options. This does yield the velocities. Here is the fun part: there is a long-standing simple formula for getting the actual average current, which goes something like the time-average of per-frame q*/L_z, which is nothing but the ion charge, times the effective frequency it crosses the entire box. This produces a number. In order to cross-check this number, we use a much more reliable current calculation based on the ion fluxes -- this is completely independent and is a script that processes the ion trajectories. That also produces a number. The two numbers are vastly different -- the current from gmx traj is 20 times smaller than the flux-based estimate. The average is over 250 ns, which I believe is 2500 velocity frames. Is there anything PBC-related I am missing, or is the -based method is simply unreliable, given the noise and the velocity output frequency (which I am obviously happy to increase)? Thank you, Alex From sam.rudinsky at steaminstruments.com Wed Mar 11 19:59:56 2020 From: sam.rudinsky at steaminstruments.com (Samantha Rudinsky) Date: Wed, 11 Mar 2020 18:59:56 -0000 Subject: [gmx-users] Chlorine atom displacement Message-ID: I have followed the lysosome in water tutorial and I would like to know if it is normal that the Cl atoms at some points instantaneously jump. I've attached a graph of their position as a function of time. Is this an artefact or numerical error? Thanks, Sam Samantha Rudinsky, PhD Steam Instruments From jalemkul at vt.edu Wed Mar 11 20:05:15 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 11 Mar 2020 19:05:15 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> Message-ID: <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: > I want to insert an atom with a velocity moving downwards toward the > graphene sheet in my box. > Yes I need to remove any atom moving away from my substrate or the > deposited atoms and far by 0.4 nm. > Then repeat the process until I have inserted 3000 atoms. gmx insert-molecules has no knowledge of velocities, and atoms are not inserted with any velocity, only a position. Removal of atoms is handled with gmx trjconv and a suitable index file generated by gmx select (in this case, since you're specifying a geometric criterion). -Justin > Thanks for your reply. > Mohamed > > On Wed, Mar 11, 2020 at 13:43 John Whittaker < > johnwhittake at zedat.fu-berlin.de> wrote: > >> Write a script that calls gmx insert-molecules 3000 times and uses the >> previous output as input for each call. >> >> >> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html >> >> Is there something you have to do in between each insertion? >> >> - John >> >>> Hello everybody, >>> >>> I am trying to insert molecules into a box but I have to insert one >> single >>> molecule at a time reaching 3000 molecule in total. Is there a way to >>> automate this process ? >>> >>> 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. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 Mar 11 20:06:22 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 11 Mar 2020 19:06:22 -0000 Subject: [gmx-users] Chlorine atom displacement In-Reply-To: References: Message-ID: <04c80793-2c65-0b74-a94f-15a4c3c9ac43@vt.edu> On 3/11/20 2:58 PM, Samantha Rudinsky wrote: > I have followed the lysosome in water tutorial and I would like to know if > it is normal that the Cl atoms at some points instantaneously jump. I've > attached a graph of their position as a function of time. Is this an > artefact or numerical error? The mailing list does not accept attachments, but likely any kind of sudden jump is a simple PBC issue. Any massive displacement would be accompanied by gigantic forces that would cause mdrun to halt. -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 Wed Mar 11 21:29:43 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 11 Mar 2020 20:29:43 -0000 Subject: [gmx-users] query regarding running simulation using GPU In-Reply-To: References: Message-ID: Hi, Sure. With a GPU-enabled build, you can just continue running almost all kinds of simulations. Mark On Wed, 11 Mar 2020 at 16:33, Snehasis Chatterjee < snehasis.chatterjee18 at gmail.com> wrote: > Dear Gromacs users, > > I am trying to perform a simulation for a relatively large system using > GROMACS 2019. I was using CPU for running simulation and now, I have 100 ns > data. But, now I have a access to use good quality GPU machine. I want to > continue my simulation (after 100ns) using GPU. Is it possible to do > that? I > am bit confused regarding this issue. > > Any kind of advice/ suggestions will be deeply appreciated. > > Thanks in advance, > Snehasis Chatterjee > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 11 21:29:43 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 11 Mar 2020 20:29:43 -0000 Subject: [gmx-users] query regarding running simulation using GPU In-Reply-To: References: Message-ID: Hi, Sure. With a GPU-enabled build, you can just continue running almost all kinds of simulations. Mark On Wed, 11 Mar 2020 at 16:33, Snehasis Chatterjee < snehasis.chatterjee18 at gmail.com> wrote: > Dear Gromacs users, > > I am trying to perform a simulation for a relatively large system using > GROMACS 2019. I was using CPU for running simulation and now, I have 100 ns > data. But, now I have a access to use good quality GPU machine. I want to > continue my simulation (after 100ns) using GPU. Is it possible to do > that? I > am bit confused regarding this issue. > > Any kind of advice/ suggestions will be deeply appreciated. > > Thanks in advance, > Snehasis Chatterjee > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From prathegreat2204 at gmail.com Thu Mar 12 05:25:53 2020 From: prathegreat2204 at gmail.com (Pranav BVN) Date: Thu, 12 Mar 2020 04:25:53 -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 this? From ha.rahmaani at gmail.com Thu Mar 12 07:14:19 2020 From: ha.rahmaani at gmail.com (Hadi Rahmaninejad) Date: Thu, 12 Mar 2020 06:14:19 -0000 Subject: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale Message-ID: Hello Gromacs users, I hope you are well. I am doing a simulation to get the diffusion coefficient of some gas molecules in a material structure. After minimization and solvation, I run NVT and then NPT to equilibrate the system, and then for production again I am running NPT step. My first question is that which system (NVT vs NPT) is more suitable for diffusion of gas molecule in a solvent? Second, does this point affect my result which 'temperature coupling' I am using? I highly appreciate if you can help me with this. Warm regards, Hadi From alessandra.villa.biosim at gmail.com Thu Mar 12 10:15:50 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 12 Mar 2020 09:15:50 -0000 Subject: [gmx-users] Parametrization of Mn(ii) in charmm force field In-Reply-To: References: Message-ID: Hi, You have to search in literature for parameters for Mn ions compatible with CHARMM36 and with the water model (some ions are parameterized to reproduce structural, thermodynamics, kinetic properties in water solution). For example Mn non-bonded parameters can be found *J. Phys. Chem. A* 2006, 110, 2, 691-699, but you should check if they are compatible with your setting Best regards Alessandra On Thu, Mar 12, 2020 at 5:26 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 this? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mar 12 10:15:53 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 12 Mar 2020 09:15:53 -0000 Subject: [gmx-users] Parametrization of Mn(ii) in charmm force field In-Reply-To: References: Message-ID: Hi, You have to search in literature for parameters for Mn ions compatible with CHARMM36 and with the water model (some ions are parameterized to reproduce structural, thermodynamics, kinetic properties in water solution). For example Mn non-bonded parameters can be found *J. Phys. Chem. A* 2006, 110, 2, 691-699, but you should check if they are compatible with your setting Best regards Alessandra On Thu, Mar 12, 2020 at 5:26 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 this? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Thu Mar 12 10:50:36 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 12 Mar 2020 09:50:36 -0000 Subject: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale In-Reply-To: References: Message-ID: Hi, It's very likely a good idea to get the velocity distribution right, for the situation you're trying to model. Check out https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 (and the other great LiveComsJ material!) Mark On Thu, 12 Mar 2020 at 07:14, Hadi Rahmaninejad wrote: > Hello Gromacs users, > > I hope you are well. I am doing a simulation to get the diffusion > coefficient of some gas molecules in a material structure. After > minimization and solvation, I run NVT and then NPT to equilibrate the > system, and then for production again I am running NPT step. My first > question is that which system (NVT vs NPT) is more suitable for diffusion > of gas molecule in a solvent? Second, does this point affect my result > which 'temperature coupling' I am using? I highly appreciate if you can > help me with this. > > Warm regards, > Hadi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From mark.j.abraham at gmail.com Thu Mar 12 10:50:36 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 12 Mar 2020 09:50:36 -0000 Subject: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale In-Reply-To: References: Message-ID: Hi, It's very likely a good idea to get the velocity distribution right, for the situation you're trying to model. Check out https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 (and the other great LiveComsJ material!) Mark On Thu, 12 Mar 2020 at 07:14, Hadi Rahmaninejad wrote: > Hello Gromacs users, > > I hope you are well. I am doing a simulation to get the diffusion > coefficient of some gas molecules in a material structure. After > minimization and solvation, I run NVT and then NPT to equilibrate the > system, and then for production again I am running NPT step. My first > question is that which system (NVT vs NPT) is more suitable for diffusion > of gas molecule in a solvent? Second, does this point affect my result > which 'temperature coupling' I am using? I highly appreciate if you can > help me with this. > > Warm regards, > Hadi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From aishwaryshivgan55 at gmail.com Thu Mar 12 10:56:44 2020 From: aishwaryshivgan55 at gmail.com (Aishwary Shivgan) Date: Thu, 12 Mar 2020 09:56:44 -0000 Subject: [gmx-users] Vacuum simulations with Gromacs 2018 Message-ID: Dear all, I want to do vacuum simulations for calculating partition coefficients. I found the appropriate options for gromacs 5 through one of the previous threads. cutoff-scheme = group ns_type = grid rlist = 0 nstlist = 0 vdwtype = cutoff rvdw = 0 coulombtype = cutoff rcoulomb = 0 pbc = no I get a warning error and a warning while running these with gromacs 2018 Fatal error: Domain decomposition does not work with nstlist=0 NOTE 1 [file ti_31.mdp]: The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. with verlet scheme nstlist = 0 is not supported. What would be correct options to for running these vacuum simulations with 2018 and above versions? Regards, Aishwary From m.b.abdelaal at gmail.com Thu Mar 12 12:35:13 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Thu, 12 Mar 2020 11:35:13 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> Message-ID: I was planning to put the velocities in the .gro file from which I am inserting the molecules. If the gmx insert-molecules will ignore the velocities of the atoms, can you please guide me how can I insert the molecules with a velocity ? I have read a paper which mentions that they inserted the molecules and the velocities of the ATOMS were sampled from a distribution with standard deviation =xx and mean = xxx. On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: > > > On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: > > I want to insert an atom with a velocity moving downwards toward the > > graphene sheet in my box. > > Yes I need to remove any atom moving away from my substrate or the > > deposited atoms and far by 0.4 nm. > > Then repeat the process until I have inserted 3000 atoms. > > gmx insert-molecules has no knowledge of velocities, and atoms are not > inserted with any velocity, only a position. > > Removal of atoms is handled with gmx trjconv and a suitable index file > generated by gmx select (in this case, since you're specifying a > geometric criterion). > > -Justin > > > Thanks for your reply. > > Mohamed > > > > On Wed, Mar 11, 2020 at 13:43 John Whittaker < > > johnwhittake at zedat.fu-berlin.de> wrote: > > > >> Write a script that calls gmx insert-molecules 3000 times and uses the > >> previous output as input for each call. > >> > >> > >> > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > >> > >> Is there something you have to do in between each insertion? > >> > >> - John > >> > >>> Hello everybody, > >>> > >>> I am trying to insert molecules into a box but I have to insert one > >> single > >>> molecule at a time reaching 3000 molecule in total. Is there a way to > >>> automate this process ? > >>> > >>> 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. > >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 atila.petrosian at gmail.com Thu Mar 12 12:40:52 2020 From: atila.petrosian at gmail.com (Atila Petrosian) Date: Thu, 12 Mar 2020 11:40:52 -0000 Subject: [gmx-users] slurm and gromacs Message-ID: Dear gromacs users I am doing md simulation of protein in a cluster system with Slurm Workload Manager using following job file: --------------------------------------------------------------------------- #! /bin/bash #SBATCH --job-name Pr_lig #SBATCH -n 28 #SBATCH --time 300:30:00 #SBATCH --mem 50000 #SBATCH --partition gpu module load gnu8 module load openmpi3 module load gromacs #gmx grompp -f nvt.mdp -c em2.gro -p topol.top -o nvt.tpr -n index.ndx #gmx mdrun -v -nb gpu -deffnm nvt >& nvt.job & gmx energy -f nvt.edr -o temperature.xvg --------------------------------------------------------------------------- After runing job file, How to select temperature to compute using gmx energy? In clusters without Slurm Workload Manager, for gmx energy analysis, there was a list of parameters to select by user. Please guide me. Best, Atila From johnwhittake at zedat.fu-berlin.de Thu Mar 12 12:45:31 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Thu, 12 Mar 2020 11:45:31 -0000 Subject: [gmx-users] slurm and gromacs In-Reply-To: References: Message-ID: <41244.160.45.109.123.1584013528.webmail@webmail.zedat.fu-berlin.de> This link should help: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts - John > Dear gromacs users > > I am doing md simulation of protein in a cluster system with > Slurm Workload Manager using following job file: > --------------------------------------------------------------------------- > #! /bin/bash > #SBATCH --job-name Pr_lig > #SBATCH -n 28 > #SBATCH --time 300:30:00 > #SBATCH --mem 50000 > #SBATCH --partition gpu > > module load gnu8 > module load openmpi3 > module load gromacs > > #gmx grompp -f nvt.mdp -c em2.gro -p topol.top -o nvt.tpr -n index.ndx > #gmx mdrun -v -nb gpu -deffnm nvt >& nvt.job & > gmx energy -f nvt.edr -o temperature.xvg > --------------------------------------------------------------------------- > After runing job file, How to select temperature to compute using gmx > energy? > > In clusters without Slurm Workload Manager, for gmx energy analysis, > there was a list of parameters to select by user. > > Please guide me. > > Best, > Atila > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Thu Mar 12 12:49:58 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Thu, 12 Mar 2020 11:49:58 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> Message-ID: <41274.160.45.109.123.1584013795.webmail@webmail.zedat.fu-berlin.de> > I was planning to put the velocities in the .gro file from which I am > inserting the molecules. If the gmx insert-molecules will ignore the > velocities of the atoms, can you please guide me how can I insert the > molecules with a velocity ? > I have read a paper which mentions that they inserted the molecules and > the velocities of the ATOMS were sampled from a distribution with standard > deviation =xx and mean = xxx. Which paper? You probably have to add the velocities yourself with a script that samples from the Maxwell-Boltzmann distribution at the appropriate temperature and adds those velocities to the atoms in your .gro file. Perhaps there is an easier way that someone can shed some light on, but that's what immediately comes to mind. - John > > > On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: > >> >> >> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: >> > I want to insert an atom with a velocity moving downwards toward the >> > graphene sheet in my box. >> > Yes I need to remove any atom moving away from my substrate or the >> > deposited atoms and far by 0.4 nm. >> > Then repeat the process until I have inserted 3000 atoms. >> >> gmx insert-molecules has no knowledge of velocities, and atoms are not >> inserted with any velocity, only a position. >> >> Removal of atoms is handled with gmx trjconv and a suitable index file >> generated by gmx select (in this case, since you're specifying a >> geometric criterion). >> >> -Justin >> >> > Thanks for your reply. >> > Mohamed >> > >> > On Wed, Mar 11, 2020 at 13:43 John Whittaker < >> > johnwhittake at zedat.fu-berlin.de> wrote: >> > >> >> Write a script that calls gmx insert-molecules 3000 times and uses >> the >> >> previous output as input for each call. >> >> >> >> >> >> >> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html >> >> >> >> Is there something you have to do in between each insertion? >> >> >> >> - John >> >> >> >>> Hello everybody, >> >>> >> >>> I am trying to insert molecules into a box but I have to insert one >> >> single >> >>> molecule at a time reaching 3000 molecule in total. Is there a way >> to >> >>> automate this process ? >> >>> >> >>> 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. >> >> >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel 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 m.b.abdelaal at gmail.com Thu Mar 12 13:10:21 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Thu, 12 Mar 2020 12:10:21 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: <41274.160.45.109.123.1584013795.webmail@webmail.zedat.fu-berlin.de> References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> <41274.160.45.109.123.1584013795.webmail@webmail.zedat.fu-berlin.de> Message-ID: The paper information is as below : Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. Powell https://doi.org/10.1002/anie.201610727 in the supporting documents page 9 they mentioned how they simulated the evaporation process. Regarding the automation and the script writing, I need to insert one molecule with the required velocity and then remove the atom if moving in the opposite direction and repeat the process until I have 3000 atom. you told me to write a script and make each step's output the input to the next step and so on. how can I do this part linking the step's output to the next step input. for example I want: insert molecule remove the molecule if moving in the opposite direction insert remove if . . . Do I need just to write it and copy it 3000 time or how can I do it ? Many Thankss Mohamed On Thu, Mar 12, 2020 at 11:51 AM John Whittaker < johnwhittake at zedat.fu-berlin.de> wrote: > > I was planning to put the velocities in the .gro file from which I am > > inserting the molecules. If the gmx insert-molecules will ignore the > > velocities of the atoms, can you please guide me how can I insert the > > molecules with a velocity ? > > I have read a paper which mentions that they inserted the molecules and > > the velocities of the ATOMS were sampled from a distribution with > standard > > deviation =xx and mean = xxx. > > Which paper? > > You probably have to add the velocities yourself with a script that > samples from the Maxwell-Boltzmann distribution at the appropriate > temperature and adds those velocities to the atoms in your .gro file. > > Perhaps there is an easier way that someone can shed some light on, but > that's what immediately comes to mind. > > - John > > > > > > > On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: > > > >> > >> > >> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: > >> > I want to insert an atom with a velocity moving downwards toward the > >> > graphene sheet in my box. > >> > Yes I need to remove any atom moving away from my substrate or the > >> > deposited atoms and far by 0.4 nm. > >> > Then repeat the process until I have inserted 3000 atoms. > >> > >> gmx insert-molecules has no knowledge of velocities, and atoms are not > >> inserted with any velocity, only a position. > >> > >> Removal of atoms is handled with gmx trjconv and a suitable index file > >> generated by gmx select (in this case, since you're specifying a > >> geometric criterion). > >> > >> -Justin > >> > >> > Thanks for your reply. > >> > Mohamed > >> > > >> > On Wed, Mar 11, 2020 at 13:43 John Whittaker < > >> > johnwhittake at zedat.fu-berlin.de> wrote: > >> > > >> >> Write a script that calls gmx insert-molecules 3000 times and uses > >> the > >> >> previous output as input for each call. > >> >> > >> >> > >> >> > >> > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > >> >> > >> >> Is there something you have to do in between each insertion? > >> >> > >> >> - John > >> >> > >> >>> Hello everybody, > >> >>> > >> >>> I am trying to insert molecules into a box but I have to insert one > >> >> single > >> >>> molecule at a time reaching 3000 molecule in total. Is there a way > >> to > >> >>> automate this process ? > >> >>> > >> >>> 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. > >> >> > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalemkul at vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-request at gromacs.org. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From johnwhittake at zedat.fu-berlin.de Thu Mar 12 14:32:47 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Thu, 12 Mar 2020 13:32:47 -0000 Subject: [gmx-users] GROMACS automation In-Reply-To: References: <34334.160.45.109.123.1583934162.webmail@webmail.zedat.fu-berlin.de> <150fee14-0fb8-281a-bdc9-425289118282@vt.edu> <41274.160.45.109.123.1584013795.webmail@webmail.zedat.fu-berlin.de> Message-ID: <42050.160.45.109.123.1584019964.webmail@webmail.zedat.fu-berlin.de> > The paper information is as below : > Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic > Light-Emitting Diode Films > Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. > Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R. > Gentle, Alan E. Mark,* and Benjamin J. Powell > https://doi.org/10.1002/anie.201610727 > in the supporting documents page 9 they mentioned how they simulated the > evaporation process. > > Regarding the automation and the script writing, I need to insert one > molecule with the required velocity and then remove the atom if moving in > the opposite direction and repeat the process until I have 3000 atom. you > told me to write a script and make each step's output the input to the > next > step and so on. how can I do this part linking the step's output to the > next step input. Well, for example, you would insert a molecule using gmx insert-molecule and specify the output file with the -o flag (we'll call the file conf1.gro) then, use gmx insert-molecule with conf1.gro as the input and specify the output file as conf2.gro, and so on... > for example I want: > insert molecule > remove the molecule if moving in the opposite direction There's no need to remove the molecule. The supporting information you mentioned says that the z-direction velocities were taken to be the absolute value, which gets rid of the problem of molecules traveling in the wrong direction (if the +z direction is where you want the molecules to travel towards). > insert > remove if > . > . > . > Do I need just to write it and copy it 3000 time or how can I do it ? Definitely do not copy it 3000 times. Use a simple for loop: https://www.cyberciti.biz/faq/bash-for-loop/ On the other hand, maybe you should contact the corresponding author of the paper you linked and ask if they have any advice or leftover scripts they used to set up the system. It will probably save you some time, although you won't necessarily learn something new. Best, - John > > Many Thankss > Mohamed > > On Thu, Mar 12, 2020 at 11:51 AM John Whittaker < > johnwhittake at zedat.fu-berlin.de> wrote: > >> > I was planning to put the velocities in the .gro file from which I am >> > inserting the molecules. If the gmx insert-molecules will ignore the >> > velocities of the atoms, can you please guide me how can I insert the >> > molecules with a velocity ? >> > I have read a paper which mentions that they inserted the molecules >> and >> > the velocities of the ATOMS were sampled from a distribution with >> standard >> > deviation =xx and mean = xxx. >> >> Which paper? >> >> You probably have to add the velocities yourself with a script that >> samples from the Maxwell-Boltzmann distribution at the appropriate >> temperature and adds those velocities to the atoms in your .gro file. >> >> Perhaps there is an easier way that someone can shed some light on, but >> that's what immediately comes to mind. >> >> - John >> >> > >> > >> > On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: >> > >> >> >> >> >> >> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: >> >> > I want to insert an atom with a velocity moving downwards toward >> the >> >> > graphene sheet in my box. >> >> > Yes I need to remove any atom moving away from my substrate or the >> >> > deposited atoms and far by 0.4 nm. >> >> > Then repeat the process until I have inserted 3000 atoms. >> >> >> >> gmx insert-molecules has no knowledge of velocities, and atoms are >> not >> >> inserted with any velocity, only a position. >> >> >> >> Removal of atoms is handled with gmx trjconv and a suitable index >> file >> >> generated by gmx select (in this case, since you're specifying a >> >> geometric criterion). >> >> >> >> -Justin >> >> >> >> > Thanks for your reply. >> >> > Mohamed >> >> > >> >> > On Wed, Mar 11, 2020 at 13:43 John Whittaker < >> >> > johnwhittake at zedat.fu-berlin.de> wrote: >> >> > >> >> >> Write a script that calls gmx insert-molecules 3000 times and uses >> >> the >> >> >> previous output as input for each call. >> >> >> >> >> >> >> >> >> >> >> >> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html >> >> >> >> >> >> Is there something you have to do in between each insertion? >> >> >> >> >> >> - John >> >> >> >> >> >>> Hello everybody, >> >> >>> >> >> >>> I am trying to insert molecules into a box but I have to insert >> one >> >> >> single >> >> >>> molecule at a time reaching 3000 molecule in total. Is there a >> way >> >> to >> >> >>> automate this process ? >> >> >>> >> >> >>> 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. >> >> >> >> >> >> >> -- >> >> ================================================== >> >> >> >> Justin A. Lemkul, Ph.D. >> >> Assistant Professor >> >> Office: 301 Fralin Hall >> >> Lab: 303 Engel Hall >> >> >> >> Virginia Tech Department of Biochemistry >> >> 340 West Campus Dr. >> >> Blacksburg, VA 24061 >> >> >> >> jalemkul at vt.edu | (540) 231-3129 >> >> http://www.thelemkullab.com >> >> >> >> ================================================== >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >> send a mail to gmx-users-request at gromacs.org. >> >> >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send >> > a mail to gmx-users-request at gromacs.org. >> > >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-request at gromacs.org. > From afsane_farhadi at yahoo.com Thu Mar 12 15:59:25 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Thu, 12 Mar 2020 14:59:25 -0000 Subject: [gmx-users] (no subject) References: <1025791582.562403.1584025159462.ref@mail.yahoo.com> Message-ID: <1025791582.562403.1584025159462@mail.yahoo.com> afsane_farhadi at yahoo.com Sent from Yahoo Mail on Android From afsane_farhadi at yahoo.com Thu Mar 12 16:03:55 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Thu, 12 Mar 2020 15:03:55 -0000 Subject: [gmx-users] pressure fluctuation and actual density References: <991308016.2550910.1584025425585.ref@mail.yahoo.com> Message-ID: <991308016.2550910.1584025425585@mail.yahoo.com> ?hiI want to simulate a box of methyldiethanol amine and see the ?actual density . I set 100 amine molecules in a cubic box 4?4?4 (nm^3)I first used energy minimization for 400ps . then I used npt for 2ns. I saw a lot fluctuation in pressure .pressure is 1bar.I used Rahman ....barostat. is my procedure correct? what is the suitable fluctuation around pressure?what is the number of compressibility isotherm of MDEA?? Sent from Yahoo Mail on Android From jalemkul at vt.edu Thu Mar 12 16:34:27 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 12 Mar 2020 15:34:27 -0000 Subject: [gmx-users] Parametrization of Mn(ii) in charmm force field In-Reply-To: References: Message-ID: <5a9ed79f-fa55-b427-c55f-ce3ab455abb0@vt.edu> On 3/12/20 5:15 AM, Alessandra Villa wrote: > Hi, > > You have to search in literature for parameters for Mn ions compatible > with CHARMM36 and with the water model (some ions are parameterized to > reproduce structural, thermodynamics, kinetic properties in water solution). > > For example Mn non-bonded parameters can be found *J. Phys. Chem. A* 2006, > 110, 2, 691-699, but you should check if they are compatible with your > setting We have used parameters for Mn2+ from dx.doi.org/10.1021/jp309150r with some specific modifications for interactions with His residues given in the SI of one of our recent articles (https://aac.asm.org/content/aac/suppl/2017/10/13/AAC.01572-17.DCSupplemental/zac011176653s1.pdf) -Justin > Best regards > Alessandra > > > On Thu, Mar 12, 2020 at 5:26 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 this? >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From dburns at iastate.edu Thu Mar 12 20:38:57 2020 From: dburns at iastate.edu (Daniel Burns) Date: Thu, 12 Mar 2020 19:38:57 -0000 Subject: [gmx-users] checkpoint files with replica exchange/ -multidir Message-ID: Hello, I'm using 2 replicas to test exchange conditions. I restarted a run and included the checkpoint file name (which is identical in each directory provided under the -multidir option). After the restart, I'm getting 100% exchange when before it was 50%. Does the -cpi option work properly for replica exchange/ multidir runs? The only thing I changed was the exchange attempt frequency from every 4ps to 1ps. Thank you, Dan From mark.j.abraham at gmail.com Thu Mar 12 20:44:12 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 12 Mar 2020 19:44:12 -0000 Subject: [gmx-users] checkpoint files with replica exchange/ -multidir In-Reply-To: References: Message-ID: Hi, On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > Hello, > > I'm using 2 replicas to test exchange conditions. I restarted a run and > included the checkpoint file name (which is identical in each directory > provided under the -multidir option). After the restart, I'm getting 100% > exchange when before it was 50%. > > Does the -cpi option work properly for replica exchange/ multidir runs? > As far as we know :-) The only thing I changed was the exchange attempt frequency from every 4ps > to 1ps. > What happens if you start at 4 and stay there? Start at 1 and stay there? Mark > 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 Thu Mar 12 20:44:15 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 12 Mar 2020 19:44:15 -0000 Subject: [gmx-users] checkpoint files with replica exchange/ -multidir In-Reply-To: References: Message-ID: Hi, On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > Hello, > > I'm using 2 replicas to test exchange conditions. I restarted a run and > included the checkpoint file name (which is identical in each directory > provided under the -multidir option). After the restart, I'm getting 100% > exchange when before it was 50%. > > Does the -cpi option work properly for replica exchange/ multidir runs? > As far as we know :-) The only thing I changed was the exchange attempt frequency from every 4ps > to 1ps. > What happens if you start at 4 and stay there? Start at 1 and stay there? Mark > 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 Thu Mar 12 20:49:25 2020 From: dburns at iastate.edu (Daniel Burns) Date: Thu, 12 Mar 2020 19:49:25 -0000 Subject: [gmx-users] checkpoint files with replica exchange/ -multidir In-Reply-To: References: Message-ID: Thanks Mark, >From my experience so far if I stayed at 4ps, I would continue to get lower exchange rates. As for starting at 1ps, my system must not have been equilibrated because it was blowing up on the first exchange attempt which Is why I decided to restart with the checkpoint file. Dan On Thu, Mar 12, 2020 at 2:44 PM Mark Abraham wrote: > Hi, > > On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > > > Hello, > > > > I'm using 2 replicas to test exchange conditions. I restarted a run and > > included the checkpoint file name (which is identical in each directory > > provided under the -multidir option). After the restart, I'm getting > 100% > > exchange when before it was 50%. > > > > Does the -cpi option work properly for replica exchange/ multidir runs? > > > > As far as we know :-) > > The only thing I changed was the exchange attempt frequency from every 4ps > > to 1ps. > > > > What happens if you start at 4 and stay there? Start at 1 and stay there? > > Mark > > > > 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 dallas.warren at monash.edu Thu Mar 12 22:33:12 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Thu, 12 Mar 2020 21:33:12 -0000 Subject: [gmx-users] pressure fluctuation and actual density In-Reply-To: <991308016.2550910.1584025425585@mail.yahoo.com> References: <991308016.2550910.1584025425585.ref@mail.yahoo.com> <991308016.2550910.1584025425585@mail.yahoo.com> Message-ID: Some examples of the pressure fluctuations that you can get can be seen here: https://twitter.com/dr_dbw/status/968624615063937025 Pressure is a macroscopic property. The smaller the system, the larger the fluctuations will be. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.warren at monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 13 Mar 2020 at 02:03, Afsane Farhadi wrote: > hiI want to simulate a box of methyldiethanol amine and see the actual > density . I set 100 amine molecules in a cubic box 4?4?4 (nm^3)I first used > energy minimization for 400ps . then I used npt for 2ns. I saw a lot > fluctuation in pressure .pressure is 1bar.I used Rahman ....barostat. is my > procedure correct? what is the suitable fluctuation around pressure?what is > the number of compressibility isotherm of MDEA? > Sent from Yahoo Mail on Android > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From b.mijiddorj at gmail.com Fri Mar 13 02:11:20 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Fri, 13 Mar 2020 01:11:20 -0000 Subject: [gmx-users] Setting a electric field in a simulation In-Reply-To: References: Message-ID: Dear Prof. David van der Spoel, Thank you very much for your helpful response. I am sorry for further asking. I tried to field information during the MD using -field option. It gave me ***************************** @ title "Applied electric field" @ xaxis label "Time (ps)" @ yaxis label "E (V/nm)" @TYPE xy 0 0.5 0 0 0.001 0.412668 0 0 ******************************** Then, gmx potential gave the field.xvg file? This filed.xvg contains box and field. ********************************* @ title "Electric Field" @ xaxis label "Box (nm)" @ yaxis label "Field (V/nm)" 0 0 1.065423250198364 0.199576498258186 2.130846500396729 0.2431408787146726 3.196269750595093 0.1159880973735597 ************************************* Do you mean this field.xvg output? I am sorry again. Best regards, Mijiddorj ------------------------------ Message: 4 Date: Tue, 10 Mar 2020 09:09:50 +0100 From: David van der Spoel To: gmx-users at gromacs.org Subject: Re: [gmx-users] Setting a electric field in a simulation Message-ID: <92e46fbb-adf6-de46-5391-c8dc509bb4f5 at xray.bmc.uu.se> Content-Type: text/plain; charset=windows-1252; format=flowed Den 2020-03-10 kl. 03:17, skrev Mijiddorj B: > Dear GMX users, > > I would like to perform MD simulations of solutions applying electric > fields such as the microwave heating process. Is it possible to perform in > gromacs? > > 1. How can I set the external electric field in the simulations? > (from the user guide, I understood that I need to set 4 values > > electric-field-x = 2.0 150 5 0 > > How can I adjust the 2.45 GHz frequency? > > If you do not mind, please guide me. > > Best regards, > > Mijiddorj > Why don't you try to play around and check the output file field.xvg to see what frequency you get? -- 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 cy16f01.dilip at nitk.edu.in Fri Mar 13 08:20:24 2020 From: cy16f01.dilip at nitk.edu.in (Dilip.H.N) Date: Fri, 13 Mar 2020 07:20:24 -0000 Subject: [gmx-users] Regarding parameters for Bromine ion in Charmm36 FF Message-ID: Hello all, In charmm36 FF of gromacs among the halogens only chlorine ion (Cl-) parameter is defined but parameters for Fluorine (F-), Bromine (Br-), Iodine (I-) anions are not defined. So, can anybody kindly help regarding getting the parameters of Fluorine (F-), Bromine (Br-), Iodine (I-) anions in charmm36 FF...? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] Sender notified by Mailtrack 13/03/20, 12:46:30 From omkantnirala92 at gmail.com Fri Mar 13 12:36:05 2020 From: omkantnirala92 at gmail.com (Omkar Singh) Date: Fri, 13 Mar 2020 11:36:05 -0000 Subject: [gmx-users] Regarding sg parameter Message-ID: Hello all, 1. Can anyone help me for making a ndx file for calculating the sg parameter for water? 2. How can i select water between first and second minima of Solvation shells? Thank you From zhangxuan7788 at gmail.com Fri Mar 13 18:53:43 2020 From: zhangxuan7788 at gmail.com (xuan Zhang) Date: Fri, 13 Mar 2020 17:53:43 -0000 Subject: [gmx-users] Gromacs Install problem Message-ID: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **********/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 at gmail.com From dburns at iastate.edu Fri Mar 13 22:16:21 2020 From: dburns at iastate.edu (Daniel Burns) Date: Fri, 13 Mar 2020 21:16:21 -0000 Subject: [gmx-users] checkpoint files with replica exchange/ -multidir In-Reply-To: References: Message-ID: I started another run to check exchanges after letting the systems equilibrate more. I made the input by using grompp with the .cpt file - now they are exchanging 100% of the time. Each file was grompped with it's own original tpr and cpt file - I can't figure out what's happening. Dan On Thu, Mar 12, 2020 at 2:49 PM Daniel Burns wrote: > Thanks Mark, > > From my experience so far if I stayed at 4ps, I would continue to get > lower exchange rates. > > As for starting at 1ps, my system must not have been equilibrated because > it was blowing up on the first exchange attempt which Is why I decided to > restart with the checkpoint file. > > Dan > > On Thu, Mar 12, 2020 at 2:44 PM Mark Abraham > wrote: > >> Hi, >> >> On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: >> >> > Hello, >> > >> > I'm using 2 replicas to test exchange conditions. I restarted a run and >> > included the checkpoint file name (which is identical in each directory >> > provided under the -multidir option). After the restart, I'm getting >> 100% >> > exchange when before it was 50%. >> > >> > Does the -cpi option work properly for replica exchange/ multidir runs? >> > >> >> As far as we know :-) >> >> The only thing I changed was the exchange attempt frequency from every 4ps >> > to 1ps. >> > >> >> What happens if you start at 4 and stay there? Start at 1 and stay there? >> >> Mark >> >> >> > 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 zhangxuan7788 at gmail.com Fri Mar 13 23:06:49 2020 From: zhangxuan7788 at gmail.com (xuan Zhang) Date: Fri, 13 Mar 2020 22:06:49 -0000 Subject: [gmx-users] Gromacs Install problem In-Reply-To: References: Message-ID: Hi? For now, I have added the compiler to cmake and it works. But in the *make *step, the errors were shown as below. Thank you very much. Best regards, Xuan src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make:79: recipe for target 'src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o' failed make[2]: *** [src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o] Error 1 CMakeFiles/Makefile2:4229: recipe for target 'src/gromacs/CMakeFiles/lmfit_objlib.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/lmfit_objlib.dir/all] Error 2 Makefile:179: recipe for target 'all' failed make: *** [all] Error 2 liy0i at kw60520:/data16/XUAN/gromacs-2020.1/build$ ./configure -bash: ./configure: No such file or directory On Sat, Mar 14, 2020 at 1:53 AM xuan Zhang wrote: > Hi, > > When I install the Gromacs on Linux, the cmake occurs error like below. I > am a newer on this software. I appreciate very much that you can help me. > > Best regards, > Xuan > > **********/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > CMake Error at cmake/FindLibStdCpp.cmake:162 (message): > GROMACS requires C++14, but a test of such functionality in the C++ > standard library failed to compile. The g++ found at /usr/bin/g++ had a > suitable version, so ;something else must be the problem > Call Stack (most recent call first): > CMakeLists.txt:69 (find_package) > > > -- Configuring incomplete, errors occurred! > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". > > > *#cmakeerror.log as below:* > > Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following > output: > Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp > > Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f > CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build > make[1]: Entering directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o > /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ > -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o > CMakeFiles/cmTC_203a2.dir/src.cxx.o -c > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: > namespace "std" has no member "cbegin" > int main() { int a[2]; std::cbegin(a); } > ^ > > compilation aborted for > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) > CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target > 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed > make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 > make[1]: Leaving directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Makefile:138: recipe for target 'cmTC_203a2/fast' failed > make: *** [cmTC_203a2/fast] Error 2 > > > Source file was: > #include > int main() { int a[2]; std::cbegin(a); } > > -- > *Xuan Zhang* > > PhD Candidate > China University of Petroleum(East China) > School of Petroleum Engineering > No.66 Changjiang West Road, Qingdao > > > Visiting scholar (2017.12-2018.12) > The University of Texas at Austin > Cockrell School of Engineering > McKetta Department of Chemical Engineering > 200 E Dean Keeton St. Stop C0400 > CPE 5.428 > > *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 at gmail.com > -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 at gmail.com From Alexander.Tzanov at csi.cuny.edu Sat Mar 14 01:10:27 2020 From: Alexander.Tzanov at csi.cuny.edu (Alexander Tzanov) Date: Sat, 14 Mar 2020 00:10:27 -0000 Subject: [gmx-users] Gromacs Install problem In-Reply-To: References: Message-ID: <7fc5b86e-8a08-4a3e-bc4b-8a176a818a9f@email.android.com> For that error you may use normal and better Intel compiler or gcc above 6.3. The 2020.1 compiles well after correcting stupid bug in multidimensional array routine and with use of Intel 19 and gcc above 6. I use 7.3 Your compiler is too old to support C++14 but there other problem as well Alex On Mar 13, 2020 1:54 PM, xuan Zhang wrote: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **********/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 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 Alexander.Tzanov at csi.cuny.edu Sat Mar 14 01:10:27 2020 From: Alexander.Tzanov at csi.cuny.edu (Alexander Tzanov) Date: Sat, 14 Mar 2020 00:10:27 -0000 Subject: [gmx-users] Gromacs Install problem In-Reply-To: References: Message-ID: <09011eb3-3d29-435b-bcde-4a26325eb3ab@email.android.com> The new version from March 2020.1 is buggy. Try version 2020. There is another bug in multidimensional array ... Alex On Mar 13, 2020 1:54 PM, xuan Zhang wrote: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **********/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 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 kushalrajroyfc at gmail.com Sat Mar 14 06:58:41 2020 From: kushalrajroyfc at gmail.com (Kushal Roy) Date: Sat, 14 Mar 2020 05:58:41 -0000 Subject: [gmx-users] Can you help regarding this Message-ID: 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: /mnt/c/Users/kushal/Desktop/New folder (10) 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 -694988524 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file topol.top, line 11469]: System has non-zero total charge: 10.000000 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. ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) Fatal error: number of coordinates in coordinate file (solv.gro, 45034) does not match topology (topol.top, 44947) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- kushalrajroy at DESKTOP-RVURRJU:/mnt/c/Users/kushal/Desktop/New folder (10)$ 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: /mnt/c/Users/kushal/Desktop/New folder (10) 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 1547355040 ERROR 1 [file ligand.prm, line 4]: Unknown bond_atomtype CG2O2 There was 1 note ------------------------------------------------------- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 777) Fatal error: There was 1 error in input file(s) From billy.williams-noonan at monash.edu Sat Mar 14 06:59:54 2020 From: billy.williams-noonan at monash.edu (Billy Williams-Noonan) Date: Sat, 14 Mar 2020 05:59:54 -0000 Subject: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx Message-ID: Hi Experts, This is a long-ish e-mail so thank you very much for your time I am using the GROMACS compatible charmm36 forcefield for betapeptides described here: https://gitlab.com/awacha/charmm-beta.ff In merged.rtp I have redefined the MYR residue hoping I could link it to the N-terminus of my b-peptide [ MYR ] [ atoms ] O1 OCL -0.546 1 C1 CL 0.542 2 C2 CA -0.280 3 H2R HAL2 0.090 4 H2S HAL2 0.090 5 C3 CTL2 -0.180 6 H3R HAL2 0.090 7 H3S HAL2 0.090 8 C4 CTL2 -0.180 9 H4R HAL2 0.090 10 H4S HAL2 0.090 11 C5 CTL2 -0.180 12 H5R HAL2 0.090 13 H5S HAL2 0.090 14 C6 CTL2 -0.180 15 H6R HAL2 0.090 16 H6S HAL2 0.090 17 C7 CTL2 -0.180 18 H7R HAL2 0.090 19 H7S HAL2 0.090 20 C8 CTL2 -0.180 21 H8R HAL2 0.090 22 H8S HAL2 0.090 23 C9 CTL2 -0.180 24 H9R HAL2 0.090 25 H9S HAL2 0.090 26 C10 CTL2 -0.180 27 H10R HAL2 0.090 28 H10S HAL2 0.090 29 C11 CTL2 -0.180 30 H11R HAL2 0.090 31 H11S HAL2 0.090 32 C12 CTL2 -0.180 33 H12R HAL2 0.090 34 H12S HAL2 0.090 35 C13 CTL2 -0.180 36 H13R HAL2 0.090 37 H13S HAL2 0.090 38 C14 CTL3 -0.270 39 H14R HAL3 0.090 40 H14S HAL3 0.090 41 H14T HAL3 0.090 42 [ bonds ] O1 C1 C1 C2 C1 +N C2 H2R C2 H2S C2 C3 C3 H3R C3 H3S C3 C4 C4 H4R C4 H4S C4 C5 C5 H5R C5 H5S C5 C6 C6 H6R C6 H6S C6 C7 C7 H7R C7 H7S C7 C8 C8 H8R C8 H8S C8 C9 C9 H9R C9 H9S C9 C10 C10 H10R C10 H10S C10 C11 C11 H11R C11 H11S C11 C12 C12 H12R C12 H12S C12 C13 C13 H13R C13 H13S C13 C14 C14 H14R C14 H14S C14 H14T [ impropers ] C1 C2 +N O1 In ffnonbonded.itp I have added the following dihedral types: C2 C1 +N C 9 0.000000 7.531200 1 C2 C1 +N HN 9 0.000000 7.531200 1 Running pdb2gmx I get the following error: *gmx pdb2gmx -f outpdb.pdb -o pep.pdb -p pep.top -ter* Processing chain 1 'A' (105 atoms, 4 residues) Identified residue MYR1 as a starting terminus. Identified residue B3K4 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for MYR-1 0: Beta3NH3+ 1: Beta2NH3+ 2: Beta23NH3+ 3: B3_NH2 4: B2_NH2 5: B23_NH2 6: 5TER 7: None 7 Start terminus MYR-1: None Select end terminus type for B3K-4 0: BetaCOO- 1: BetaCOOH 2: BetaCT2 3: 3TER 4: None 0 End terminus B3K-4: BetaCOO- Opening force field file ./charmm36_betapep.ff/betaaminoacids.arn Opening force field file ./charmm36_betapep.ff/cyclicbeta.arn Opening force field file ./charmm36_betapep.ff/merged.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 4 residues with 106 atoms Making bonds... Number of bonds was 105, now 105 Generating angles, dihedrals and pairs... Before cleaning: 288 pairs ------------------------------------------------------- Program: gmx pdb2gmx, version 2018.2 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148) Fatal error: Residue 2 named MYR of a molecule in the input file was mapped to an entry in the topology database, but the atom C used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems to be having a problem recognising the link between C1 of Myr and the N-terminus of the next residue (B3K) - is there a file where I can explicitly mention this? Any help would be appreciated - how do I fix this? Cheers, Billy -- Billy Noonan* | *Postdoctoral Research Fellow *|* Bsci ( *Adv* ), IA Hon *LinkedIn Profile **|* +61420 382 557 Monash Institute for Pharmaceutical Sciences ( *MIPS* ) Royal Parade, Parkville, 3052 From paul.bauer.q at gmail.com Sat Mar 14 09:09:10 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Sat, 14 Mar 2020 08:09:10 -0000 Subject: [gmx-users] Gromacs Install problem In-Reply-To: <09011eb3-3d29-435b-bcde-4a26325eb3ab@email.android.com> References: <09011eb3-3d29-435b-bcde-4a26325eb3ab@email.android.com> Message-ID: <0aac63fa-b889-98b5-ee9e-0516126026ca@gmail.com> Hello, if you have found a bug in the multi-dimensional array please report it on redmine.gromacs.org so we can fix it, together with the build configuration that causes it. Cheers Paul On 14/03/2020 00:51, Alexander Tzanov wrote: > The new version from March 2020.1 is buggy. Try version 2020. There is another bug in multidimensional array ... > > Alex > > On Mar 13, 2020 1:54 PM, xuan Zhang wrote: > Hi, > > When I install the Gromacs on Linux, the cmake occurs error like below. I > am a newer on this software. I appreciate very much that you can help me. > > Best regards, > Xuan > > **********/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > CMake Error at cmake/FindLibStdCpp.cmake:162 (message): > GROMACS requires C++14, but a test of such functionality in the C++ > standard library failed to compile. The g++ found at /usr/bin/g++ had a > suitable version, so ;something else must be the problem > Call Stack (most recent call first): > CMakeLists.txt:69 (find_package) > > > -- Configuring incomplete, errors occurred! > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". > > > *#cmakeerror.log as below:* > > Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following > output: > Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp > > Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f > CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build > make[1]: Entering directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o > /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ > -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o > CMakeFiles/cmTC_203a2.dir/src.cxx.o -c > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: > namespace "std" has no member "cbegin" > int main() { int a[2]; std::cbegin(a); } > ^ > > compilation aborted for > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) > CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target > 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed > make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 > make[1]: Leaving directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Makefile:138: recipe for target 'cmTC_203a2/fast' failed > make: *** [cmTC_203a2/fast] Error 2 > > > Source file was: > #include > int main() { int a[2]; std::cbegin(a); } > > -- > *Xuan Zhang* > > PhD Candidate > China University of Petroleum(East China) > School of Petroleum Engineering > No.66 Changjiang West Road, Qingdao > > > Visiting scholar (2017.12-2018.12) > The University of Texas at Austin > Cockrell School of Engineering > McKetta Department of Chemical Engineering > 200 E Dean Keeton St. Stop C0400 > CPE 5.428 > > *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7788 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. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From dodia at mpip-mainz.mpg.de Sat Mar 14 09:23:19 2020 From: dodia at mpip-mainz.mpg.de (dodia) Date: Sat, 14 Mar 2020 08:23:19 -0000 Subject: [gmx-users] Creating a simple water box Message-ID: <716d7349815908eba9ce78c0bb4b3617@mpip-mainz.mpg.de> Dear gromacs users, I was trying a simple gmx solvate test on a water box of size 25*20*20 angstrom, creating a water box of density 1 g/cm^3. By my calculations the no. of water molecules in the box should by 332 (each water molecule has a volume of (3.11 angstrom)^3). When I use the solvate command: gmx solvate -cs spc216 -box 2.5 2 2 -o test2.pdb -maxsol 332 with gromacs 5.0.7, I get 291 water molecules in the box, and the density as 0.87 g/cm^3 with gromacs 2016.1, I get 295 water molecules in the box, and the density as 0.88 g/cm^3 When I try using the -scale option: gmx solvate -cs spc216 -scale 0.40 -box 2.5 2 2 -o test.pdb -maxsol 332 I can get a density of 0.993 g/cm3, however when I visualize the structure, I can notice a lot of close contact between O-O atoms (the distance between O-O atoms becomes lower than 1.49 angstroms, the O-O bond length). So is there any other way to fine tune the gmx solvate command so as to generate the water box with density close to 1 g/cm^3, without the close contact problem? Best Regards, Mayank Dodia From fnabi at myamu.ac.in Sat Mar 14 09:32:36 2020 From: fnabi at myamu.ac.in (FAISAL NABI) Date: Sat, 14 Mar 2020 08:32:36 -0000 Subject: [gmx-users] (no subject) Message-ID: Hi, I have been a new user and i was following the protein-ligand complex tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology i have used ATB webserver. I did download the .itp and .pdb file from there and converted that to .gro file. The problem i am facing is it shows an error while i add ions that "Atomtype CAro not found", although i have added the atomtypes in the gromacs topology file still it's showing the same error. I request if somebody could provie me a stepwise protocol i could follow. Thank you -- Faisal Nabi *Pre-Doctoral Fellow (CSIR-JRF)* C/o Professor Rizwan Hassan Khan Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, INDIA. Email- *fnabi at myamy.ac.in * * faisalbiochem at gmail.com * Contact no. - *+91-8923713214* From prasanthghanta at sssihl.edu.in Sat Mar 14 10:11:04 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Sat, 14 Mar 2020 09:11:04 -0000 Subject: [gmx-users] Can you help regarding this Message-ID: Dear Kushal, Regarding the first error, I feel that you have done a few mistakes while updating your topology section as your system has more atoms than what is in the topology. Kindly go through the tutorials on this site - http://www.mdtutorials.com/gmx/index.html, to get a picture on how to do it. Regarding second error, I think your system has a ligand that the forcefield is not able to define. I am guessing you have already parametrized this. If you have submitted this ligand to a server, maybe you are using a different file than what you were supposed to? Kindly recheck. -- Regards, Prasanth. From peter.mawanga.lagos at gmail.com Sun Mar 15 00:24:39 2020 From: peter.mawanga.lagos at gmail.com (Peter Mawanga) Date: Sat, 14 Mar 2020 23:24:39 -0000 Subject: [gmx-users] Request for Plumed sample scripts Message-ID: Hello everyone I am looking for a sample Gromacs script and a Plumed file with Distance Colvar. Please send me one if feasible. -- Cheers Peter From afsane_farhadi at yahoo.com Sun Mar 15 00:25:57 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Sat, 14 Mar 2020 23:25:57 -0000 Subject: [gmx-users] potential energy doesn't have negative value References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> Message-ID: <38781414.3298421.1584227748267@mail.yahoo.com> I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. ?the mdp file is attached. Sent from Yahoo Mail on Android From neena.susaneappen at mail.utoronto.ca Sun Mar 15 00:54:02 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Sat, 14 Mar 2020 23:54:02 -0000 Subject: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx In-Reply-To: References: Message-ID: Hi Billy, 1. Firstly, why is that gromacs reads MYR as residue 2 and not 1? What does it say in your PDB file? 2. There is no atom labelled C in your MYR atom list. Looks like you have listed atom C in the dihedral type (ffnonbonded.itp), change that. 3. If you think it is not recognizing the link between MYR and B3K, then in the aminoacids.rtp file, for B3K, check if in the improper dihedral (involving terminal N) if there is atom C listed instead of C1. If yes, change it to C1. Hope this helps, Neena From jalemkul at vt.edu Sun Mar 15 00:58:06 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 14 Mar 2020 23:58:06 -0000 Subject: [gmx-users] Linking MYR residue to N-terminus using pdb2gmx In-Reply-To: References: Message-ID: <468a653b-3b78-8947-cd6c-85727611d42e@vt.edu> On 3/14/20 1:59 AM, Billy Williams-Noonan wrote: > Hi Experts, > > This is a long-ish e-mail so thank you very much for your time > > I am using the GROMACS compatible charmm36 forcefield for > betapeptides described here: > https://gitlab.com/awacha/charmm-beta.ff > > In merged.rtp I have redefined the MYR residue hoping I could link it to > the N-terminus of my b-peptide > > > [ MYR ] > [ atoms ] > O1 OCL -0.546 1 > C1 CL 0.542 2 > C2 CA -0.280 3 > H2R HAL2 0.090 4 > H2S HAL2 0.090 5 > C3 CTL2 -0.180 6 > H3R HAL2 0.090 7 > H3S HAL2 0.090 8 > C4 CTL2 -0.180 9 > H4R HAL2 0.090 10 > H4S HAL2 0.090 11 > C5 CTL2 -0.180 12 > H5R HAL2 0.090 13 > H5S HAL2 0.090 14 > C6 CTL2 -0.180 15 > H6R HAL2 0.090 16 > H6S HAL2 0.090 17 > C7 CTL2 -0.180 18 > H7R HAL2 0.090 19 > H7S HAL2 0.090 20 > C8 CTL2 -0.180 21 > H8R HAL2 0.090 22 > H8S HAL2 0.090 23 > C9 CTL2 -0.180 24 > H9R HAL2 0.090 25 > H9S HAL2 0.090 26 > C10 CTL2 -0.180 27 > H10R HAL2 0.090 28 > H10S HAL2 0.090 29 > C11 CTL2 -0.180 30 > H11R HAL2 0.090 31 > H11S HAL2 0.090 32 > C12 CTL2 -0.180 33 > H12R HAL2 0.090 34 > H12S HAL2 0.090 35 > C13 CTL2 -0.180 36 > H13R HAL2 0.090 37 > H13S HAL2 0.090 38 > C14 CTL3 -0.270 39 > H14R HAL3 0.090 40 > H14S HAL3 0.090 41 > H14T HAL3 0.090 42 > [ bonds ] > O1 C1 > C1 C2 > C1 +N > C2 H2R > C2 H2S > C2 C3 > C3 H3R > C3 H3S > C3 C4 > C4 H4R > C4 H4S > C4 C5 > C5 H5R > C5 H5S > C5 C6 > C6 H6R > C6 H6S > C6 C7 > C7 H7R > C7 H7S > C7 C8 > C8 H8R > C8 H8S > C8 C9 > C9 H9R > C9 H9S > C9 C10 > C10 H10R > C10 H10S > C10 C11 > C11 H11R > C11 H11S > C11 C12 > C12 H12R > C12 H12S > C12 C13 > C13 H13R > C13 H13S > C13 C14 > C14 H14R > C14 H14S > C14 H14T > [ impropers ] > C1 C2 +N O1 > > > In ffnonbonded.itp I have added the following dihedral types: > > C2 C1 +N C 9 0.000000 7.531200 1 > C2 C1 +N HN 9 0.000000 7.531200 1 > > > > > Running pdb2gmx I get the following error: > > *gmx pdb2gmx -f outpdb.pdb -o pep.pdb -p pep.top -ter* > > Processing chain 1 'A' (105 atoms, 4 residues) > Identified residue MYR1 as a starting terminus. > Identified residue B3K4 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Select start terminus type for MYR-1 > 0: Beta3NH3+ > 1: Beta2NH3+ > 2: Beta23NH3+ > 3: B3_NH2 > 4: B2_NH2 > 5: B23_NH2 > 6: 5TER > 7: None > 7 > Start terminus MYR-1: None > Select end terminus type for B3K-4 > 0: BetaCOO- > 1: BetaCOOH > 2: BetaCT2 > 3: 3TER > 4: None > 0 > End terminus B3K-4: BetaCOO- > Opening force field file ./charmm36_betapep.ff/betaaminoacids.arn > Opening force field file ./charmm36_betapep.ff/cyclicbeta.arn > Opening force field file ./charmm36_betapep.ff/merged.arn > Checking for duplicate atoms.... > Generating any missing hydrogen atoms and/or adding termini. > Now there are 4 residues with 106 atoms > Making bonds... > Number of bonds was 105, now 105 > Generating angles, dihedrals and pairs... > Before cleaning: 288 pairs > > ------------------------------------------------------- > Program: gmx pdb2gmx, version 2018.2 > Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148) > > Fatal error: > Residue 2 named MYR of a molecule in the input file was mapped > to an entry in the topology database, but the atom C used in > an interaction of type improper in that entry is not found in the > input file. Perhaps your atom and/or residue naming needs to be > fixed. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > It seems to be having a problem recognising the link between C1 of Myr and > the N-terminus of the next residue (B3K) - is there a file where I can > explicitly mention this? > > Any help would be appreciated - how do I fix this? The issue comes from whatever the amino acid is; the [impropers] and [cmap] entries specify that -C is needed to impose these bonded interactions. Your MYR residue does not have an atom named C, so you get an error. The cleanest solution is probably to create a complete residue for a custom residue already linked to MYR (merge MYR with the amino acid). You likely don't want a CMAP on that residue, anyway. -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 Mar 15 00:59:15 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sat, 14 Mar 2020 23:59:15 -0000 Subject: [gmx-users] potential energy doesn't have negative value In-Reply-To: <38781414.3298421.1584227748267@mail.yahoo.com> References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> <38781414.3298421.1584227748267@mail.yahoo.com> Message-ID: On 3/14/20 7:15 PM, Afsane Farhadi wrote: > I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. ?the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From afsane_farhadi at yahoo.com Sun Mar 15 01:05:51 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Sun, 15 Mar 2020 00:05:51 -0000 Subject: [gmx-users] potential energy doesn't have negative value In-Reply-To: References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> <38781414.3298421.1584227748267@mail.yahoo.com> Message-ID: <1671917561.3281767.1584230739272@mail.yahoo.com> what do I have to do for solving this mater??I want to use a opls as forcefield. ?how can I find that forcefield for methyldiethanolamine? Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: On 3/14/20 7:15 PM, Afsane Farhadi wrote: > I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. ?the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From jalemkul at vt.edu Sun Mar 15 01:06:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Sun, 15 Mar 2020 00:06:57 -0000 Subject: [gmx-users] potential energy doesn't have negative value In-Reply-To: <1671917561.3281767.1584230739272@mail.yahoo.com> References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> <38781414.3298421.1584227748267@mail.yahoo.com> <1671917561.3281767.1584230739272@mail.yahoo.com> Message-ID: <2b076ed1-caed-3917-1f50-d550ccf99612@vt.edu> On 3/14/20 8:05 PM, Afsane Farhadi wrote: > what do I have to do for solving this mater??I want to use a opls as forcefield. ?how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin > Sent from Yahoo Mail on Android > > On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: > > On 3/14/20 7:15 PM, Afsane Farhadi wrote: >> I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. ?the mdp file is attached. > The mailing list does not accept attachments. > > ATB does produce GROMOS-compatible force fields, but it is always up to > the user to determine if the parameters are suitable. A positive > potential energy means that the intermolecular interactions are weak > compared to the intramolecular (bonded) interactions. You can use gmx > energy or look in the .log file to see the various contributions to the > total potential energy. > > -Justin > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From afsane_farhadi at yahoo.com Sun Mar 15 01:14:05 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Sun, 15 Mar 2020 00:14:05 -0000 Subject: [gmx-users] potential energy doesn't have negative value In-Reply-To: <2b076ed1-caed-3917-1f50-d550ccf99612@vt.edu> References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> <38781414.3298421.1584227748267@mail.yahoo.com> <1671917561.3281767.1584230739272@mail.yahoo.com> <2b076ed1-caed-3917-1f50-d550ccf99612@vt.edu> Message-ID: <1089710201.3302832.1584231239765@mail.yahoo.com> thank you so much Mr.justin? Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:38, Justin Lemkul wrote: On 3/14/20 8:05 PM, Afsane Farhadi wrote: > what do I have to do for solving this mater??I want to use a opls as forcefield. ?how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin > Sent from Yahoo Mail on Android >? >? ? On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: > > On 3/14/20 7:15 PM, Afsane Farhadi wrote: >> I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. ?the mdp file is attached. > The mailing list does not accept attachments. > > ATB does produce GROMOS-compatible force fields, but it is always up to > the user to determine if the parameters are suitable. A positive > potential energy means that the intermolecular interactions are weak > compared to the intramolecular (bonded) interactions. You can use gmx > energy or look in the .log file to see the various contributions to the > total potential energy. > > -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 spoel at xray.bmc.uu.se Sun Mar 15 07:11:36 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 15 Mar 2020 06:11:36 -0000 Subject: [gmx-users] potential energy doesn't have negative value In-Reply-To: References: <38781414.3298421.1584227748267.ref@mail.yahoo.com> <38781414.3298421.1584227748267@mail.yahoo.com> Message-ID: <1de68560-227d-fee1-6f33-476725f73da6@xray.bmc.uu.se> Den 2020-03-15 kl. 00:59, skrev Justin Lemkul: > > > On 3/14/20 7:15 PM, Afsane Farhadi wrote: >> I generate a box of 100 molecules of methyldiethanolamine with >> insert-molecules command .I downloaded its itp file from ATB server. I >> think that forcefield is gromos . after an energy minimization the >> potential energy is positive. ?the mdp file is attached. > > The mailing list does not accept attachments. > > ATB does produce GROMOS-compatible force fields, but it is always up to > the user to determine if the parameters are suitable. A positive > potential energy means that the intermolecular interactions are weak > compared to the intramolecular (bonded) interactions. You can use gmx > energy or look in the .log file to see the various contributions to the > total potential energy. > > -Justin > The baseline oof the potential energy is not a meaningful number in classical force fields. You have to subtract 100 times the energy of the monomer, then you will have the enthalpy of vaporization (+/- kT) which you can compare to experiment. -- 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 mohammad.madani at uconn.edu Sun Mar 15 10:39:57 2020 From: mohammad.madani at uconn.edu (Mohammad Madani) Date: Sun, 15 Mar 2020 09:39:57 -0000 Subject: [gmx-users] Regarding REMD using gromacs4.5.5 In-Reply-To: References: Message-ID: Hi Amit Could you please send me your mdp file for implicit solvent remd? Many thanks On Thu, Mar 5, 2020 at 5:07 AM Amit Kumar wrote: > *Message sent from a system outside of UConn.* > > > Thank You Daniel Burns, > Actually, right now I am looking at the installation and trying to install > fresh as I found some error and created mess again while rectifying each > one. At the time of installation "mdrun_mpi -h" worked perfectly so I > thought installation is fine. But really thank you for your valuable > inputs. > > Amit Kumar > > On Wed, Mar 4, 2020 at 7:39 PM Daniel Burns wrote: > > > Hi Amit, > > > > I?m not the best resource for solutions but I?ve been having this issue > > with gromacs 2018. It seems to be related to the process manager or our > > open mpi module we are using. The job would hang on some open mpi > > communication step. > > > > I found it would work if each replica was assigned its own entire node > but > > that becomes prohibitively resource expensive with more than a few > > replicas. > > > > I was finally able to get it to work on our least used cluster where > things > > must have been installed correctly. > > > > You might have your IT look at what?s happening with the process manager > > and open mpi or whatever dependencies you have loaded. You might try a > > small job where you can assign each replica to its own node and see if > you > > get the full output. Our IT dept has been working for two weeks and still > > haven?t gotten it to work on the other clusters. > > > > > > Dan > > > > > > On Tuesday, March 3, 2020, Amit Kumar wrote: > > > > > Dear Gromacs users, > > > > > > I am trying to run a REMD simulation in gromacs 4.5.5 in implicit > solvent > > > but I am unable to get any output file containing significant data > > (logfile > > > is obtained with only developers' details) or any error file. > > > I am unable to understand why this is happening and how can I tackle > the > > > situation? > > > Kindly, help me out of this situation. > > > > > > ThankYou > > > Amit Kumar > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 ebl30 at cam.ac.uk Sun Mar 15 16:28:52 2020 From: ebl30 at cam.ac.uk (Eric Legresley) Date: Sun, 15 Mar 2020 15:28:52 -0000 Subject: [gmx-users] "No atom pairs for dispersion correction" Warning from GROMACS 2020 mdrun Message-ID: Hello All, I am performing a gpu accelerated simulation on a 292683 atom system (a solvated multimeric protein) using the amber99sb-ildn forcefield. Grompp does not throw any errors or warnings. However, mdrun throws the following warning prior to simulation: WARNING: There are no atom pairs for dispersion correction The machine has an i7-8750H CPU with a GTX 1050Ti GPU, and is running GROMACS 2019.3. However, when I run the exact same system on another machine with a Ryzen 5 3600 CPU with a GTX 1650 Super GPU running GROMACS 2020, I do not get this warning. What could be causing this warning? Is it due to the difference in GROMACS versions? Has anything changed between versions that would cause a warning like this? Thanks, Eric My production .mdp is as follows: integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 * 5,000,000 = 10 ns dt = 0.002 ; 2 fs comm-mode = Linear ; remove center of mass translation nstxout = 25000 ; save coordinates to .trr every 50ps nstvout = 25000 ; save velocities to .trr every 50ps nstfout = 0 ; don't save forces to .trr nstxout-compressed = 25000 ; xtc compressed trajectory output every 50ps compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 25000 ; log every 50 ps nstenergy = 2500 ; save energies every 5 ps nstcalcenergy = 100 ; calculate energies every 100 steps constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; h bonds are constrained continuation = yes ; not first run cutoff-scheme = Verlet ns-type = grid ; search neighboring grid cells nstlist = 20 ; irrelevent with Verlet pbc = xyz ; 3D PBC coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) ewald_geometry = 3d ; Ewald sum is performed in all three dimensions pme-order = 4 ; interpolation order for PME (default is 4) fourierspacing = 0.12 ; grid spacing for FFT (default is 0.12) ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 0.005 ; replaces/defines rlist (default 0.005) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure tcoupl = nose-hoover tc_grps = protein non-protein tau_t = 1.0 1.0 ref_t = 310 310 pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 5.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) refcoord-scaling = all gen_vel = no ; Velocity generation is off From adarsh_p130085bt at nitc.ac.in Sun Mar 15 18:10:19 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Sun, 15 Mar 2020 17:10:19 -0000 Subject: [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings? Message-ID: Dear all, How to overcome this error ? How to overcome this error. Simply delete the lines which give warnings? *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* The above command returns following 'error message' while using with " ions.mdp " This run will generate roughly 13 Mb of data There were 3 notes There were 3 warnings ----------------------------------------------------- Fatal error: Too many warnings (3). WARNING 1 [file lig.prm, line 11]: Overriding U-B parameters. WARNING 2 [file lig.prm, line 14]: Overriding U-B parameters. WARNING 3 [file lig.prm, line 17]: Overriding U-B parameters. ----------------------------------------------------- From adarsh_p130085bt at nitc.ac.in Sun Mar 15 18:31:40 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Sun, 15 Mar 2020 17:31:40 -0000 Subject: [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings? Message-ID: Dear all, How to overcome this error ? How to overcome this error. Simply delete the lines which give warnings? *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* The above command returns following 'error message' while using with " ions.mdp " This run will generate roughly 13 Mb of data There were 3 notes There were 3 warnings ----------------------------------------------------- Fatal error: Too many warnings (3). WARNING 1 [file lig.prm, line 11]: Overriding U-B parameters. WARNING 2 [file lig.prm, line 14]: Overriding U-B parameters. WARNING 3 [file lig.prm, line 17]: Overriding U-B parameters. ----------------------------------------------------- From afsane_farhadi at yahoo.com Sun Mar 15 20:53:28 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Sun, 15 Mar 2020 19:53:28 -0000 Subject: [gmx-users] positive potential energy References: <1382898359.3513997.1584302000784.ref@mail.yahoo.com> Message-ID: <1382898359.3513997.1584302000784@mail.yahoo.com> hi all?I generated a box 4?4?4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased ?but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android From spoel at xray.bmc.uu.se Sun Mar 15 21:38:50 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 15 Mar 2020 20:38:50 -0000 Subject: [gmx-users] positive potential energy In-Reply-To: <1382898359.3513997.1584302000784@mail.yahoo.com> References: <1382898359.3513997.1584302000784.ref@mail.yahoo.com> <1382898359.3513997.1584302000784@mail.yahoo.com> Message-ID: <718bcd74-7ee4-f924-2c8e-ba5082425a64@xray.bmc.uu.se> Den 2020-03-15 kl. 20:53, skrev Afsane Farhadi: > hi all?I generated a box 4?4?4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased ?but had a positive value . is my simulation wrong ? help me please > > Sent from Yahoo Mail on Android > No. I just answered a similar question. -- 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 alexanderwien2k at gmail.com Mon Mar 16 01:17:34 2020 From: alexanderwien2k at gmail.com (Alex) Date: Mon, 16 Mar 2020 00:17:34 -0000 Subject: [gmx-users] Reproducibility of a PMF plot Message-ID: Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas of a simulation and then average over the quantity of interest, specially for a publishable result. I wonder if that also is necessary for a potential of mean force (PMF) calculation using umbrella sampling in which the bootstrap analysis is performed to calculate the standard deviation? Or for an alchemical free energy calculation where the e.g. the block averaging is used? Regards, Alex From prasanthghanta at sssihl.edu.in Mon Mar 16 07:29:03 2020 From: prasanthghanta at sssihl.edu.in (Prasanth G, Research Scholar) Date: Mon, 16 Mar 2020 06:29:03 -0000 Subject: [gmx-users] no subject Message-ID: Hello Faisal, Easiest way to do this is by navigating to the MD files tab and download the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield..." The folder contains the procedure to modify the 54a7 forcefield to include the non-standard atomtypes. However the easiest way to just include the whole folder in your working directory (wd) and when you prepare gro from pdb in the first step, you can choose the option 1 (you will see that you receive a prompt saying this ff is from the wd). Hope it helps. If you are interested in Ligand- protein interaction studies. I would suggest you to use Amber or Charmm ff. This is because GROMOS is a united atom ff and an all atom ff might be better in helping you understand these interactions. Please go through the last part of this thread - https://www.researchgate.net/post/How_can_I_use_a_Topology_file_generated_by_an_ATB_server If you want to use Amber ff. you can use ACPYPE which works in conjunction with AMBER to prepare files necessary in gromacs compatible format. As antechamber (part of AMBER) is a semi qm/mm technique the parametrization happens faster , plus it can be done directly on your system. All the best -- Regards, Prasanth. From jun.zhou at monash.edu Mon Mar 16 08:25:24 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Mon, 16 Mar 2020 07:25:24 -0000 Subject: [gmx-users] Fwd: Problems with Non-equilibrium MD In-Reply-To: References: Message-ID: Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image. I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From benson_muite at emailplus.org Mon Mar 16 08:29:37 2020 From: benson_muite at emailplus.org (Benson Muite) Date: Mon, 16 Mar 2020 07:29:37 -0000 Subject: [gmx-users] Fwd: Problems with Non-equilibrium MD In-Reply-To: References: Message-ID: Hi Jun, Can you add a link to your image online rather than attaching it? Benson On Mon, Mar 16, 2020, at 10:25 AM, Jun Zhou wrote: > Hi all, > > I am using non-equilibrium MD to calculate the viscosity of the liquid by > applying a shear on xy direction. My problem is that when I observe the > trajectory of the simulation, I find only the box deformed and particles > did not change correspondingly, as shown in the attached image. > > I also attached my mdp file, can anyone give me some suggestions? Thanks. > > Regards > > -- > *Jun ZHOU* > Postgraduate Student , > Room 117, Building 36 > Department of Civil Engineering, > Monash University, > Victoria 3800, Australia. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mon Mar 16 14:15:47 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 16 Mar 2020 13:15:47 -0000 Subject: [gmx-users] Creating a simple water box In-Reply-To: <716d7349815908eba9ce78c0bb4b3617@mpip-mainz.mpg.de> References: <716d7349815908eba9ce78c0bb4b3617@mpip-mainz.mpg.de> Message-ID: Is the "close contact" really an issue? As soon as you start any sort of MD that will quickly adjust itself. On Sat, 14 Mar. 2020, 7:23 pm dodia, wrote: > Dear gromacs users, > > I was trying a simple gmx solvate test on a water box of size 25*20*20 > angstrom, creating a water box of density 1 g/cm^3. By my calculations > the no. of water molecules in the box should by 332 (each water molecule > has a volume of (3.11 angstrom)^3). When I use the solvate command: > > gmx solvate -cs spc216 -box 2.5 2 2 -o test2.pdb -maxsol 332 > > with gromacs 5.0.7, I get 291 water molecules in the box, and the > density as 0.87 g/cm^3 > > with gromacs 2016.1, I get 295 water molecules in the box, and the > density as 0.88 g/cm^3 > > When I try using the -scale option: > > gmx solvate -cs spc216 -scale 0.40 -box 2.5 2 2 -o test.pdb -maxsol 332 > > I can get a density of 0.993 g/cm3, however when I visualize the > structure, I can notice a lot of close contact between O-O atoms (the > distance between O-O atoms becomes lower than 1.49 angstroms, the O-O > bond length). So is there any other way to fine tune the gmx solvate > command so as to generate the water box with density close to 1 g/cm^3, > without the close contact problem? > > Best Regards, > Mayank Dodia > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mon Mar 16 14:19:42 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 16 Mar 2020 13:19:42 -0000 Subject: [gmx-users] Can you help regarding this In-Reply-To: References: Message-ID: What specifically do you need help with? Both the error messages there are explicit about what the issues are, first you have failed to correctly adjust the number of molecules of the topology (.top) to match the coordinate file. You also have a +10 net charge, which is unlikely to be a good idea. On Sat, 14 Mar. 2020, 4:58 pm Kushal Roy, wrote: > 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: /mnt/c/Users/kushal/Desktop/New folder (10) > 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 -694988524 > Generated 165 of the 1596 non-bonded parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_X' > Excluding 2 bonded neighbours molecule type 'SOL' > > NOTE 2 [file topol.top, line 11469]: > System has non-zero total charge: 10.000000 > 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. > > > > > ------------------------------------------------------- > Program: gmx grompp, version 2018.1 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) > > Fatal error: > number of coordinates in coordinate file (solv.gro, 45034) > does not match topology (topol.top, 44947) > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > kushalrajroy at DESKTOP-RVURRJU:/mnt/c/Users/kushal/Desktop/New folder (10)$ > 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: /mnt/c/Users/kushal/Desktop/New folder (10) > 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 1547355040 > > ERROR 1 [file ligand.prm, line 4]: > Unknown bond_atomtype CG2O2 > > > > There was 1 note > > ------------------------------------------------------- > Program: gmx grompp, version 2018.1 > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 777) > > Fatal error: > There was 1 error in input file(s) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mon Mar 16 14:21:30 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Mon, 16 Mar 2020 13:21:30 -0000 Subject: [gmx-users] (no subject) In-Reply-To: References: Message-ID: Download and use the forcefield files from the ATB server website, and then make that you correctly point to it in your top file. On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI, wrote: > Hi, > I have been a new user and i was following the protein-ligand complex > tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology > i have used ATB webserver. I did download the .itp and .pdb file from there > and converted that to .gro file. The problem i am facing is it shows an > error while i add ions that "Atomtype CAro not found", although i have > added the atomtypes in the gromacs topology file still it's showing the > same error. I request if somebody could provie me a stepwise protocol i > could follow. > > Thank you > > -- > > Faisal Nabi > > *Pre-Doctoral Fellow (CSIR-JRF)* > C/o Professor Rizwan Hassan Khan > Interdisciplinary Biotechnology Unit, > Aligarh Muslim University, Aligarh, UP, INDIA. > Email- *fnabi at myamy.ac.in * > * faisalbiochem at gmail.com * > Contact no. - *+91-8923713214* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From jpt33 at bath.ac.uk Mon Mar 16 15:07:29 2020 From: jpt33 at bath.ac.uk (Joe Paul-Taylor) Date: Mon, 16 Mar 2020 14:07:29 -0000 Subject: [gmx-users] gmx msd unusual unit Message-ID: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. # Created by: # :-) GROMACS - gmx msd, 2019.2 (-: # Command line: # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg # gmx msd is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @ title "Mean Square Displacement" @ xaxis label "Time (ps)" @ yaxis label "MSD (nm\S2\N)" @TYPE xy # MSD gathered over 10000 ps with 1001 restarts # Diffusion constants fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe From jalemkul at vt.edu Mon Mar 16 15:09:37 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 16 Mar 2020 14:09:37 -0000 Subject: [gmx-users] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings? In-Reply-To: References: Message-ID: <80ad2c87-0f3a-b59a-43a3-362410aafb65@vt.edu> On 3/15/20 6:39 PM, Adarsh V. K. wrote: > Dear all, > > How to overcome this error ? > How to overcome this error. Simply delete the lines which give warnings? > > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* > The above command returns following 'error message' while using with " > ions.mdp " > > This run will generate roughly 13 Mb of data > There were 3 notes > There were 3 warnings > ----------------------------------------------------- > > Fatal error: > Too many warnings (3). > > WARNING 1 [file lig.prm, line 11]: > Overriding U-B parameters. > > WARNING 2 [file lig.prm, line 14]: > Overriding U-B parameters. > > WARNING 3 [file lig.prm, line 17]: > Overriding U-B parameters. > ----------------------------------------------------- You have parameters in your .prm file that are already present in ffbonded.itp, which happens due to the CGenFF server version (4.0) being behind that of the CHARMM36 port (CGenFF 4.1). Remove the offending parameters from the .prm 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 Mon Mar 16 15:10:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 16 Mar 2020 14:10:21 -0000 Subject: [gmx-users] gmx msd unusual unit In-Reply-To: References: Message-ID: <4c85d388-e819-df5a-280c-866c421d1e11@vt.edu> On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: > Hello > > With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. The unit is correct. GROMACS does all distance calculations in terms of nm. You get an interpreted output of the MSD in traditional units for the diffusion constant. -Justin > # Created by: > # :-) GROMACS - gmx msd, 2019.2 (-: > # Command line: > # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg > # gmx msd is part of G R O M A C S: > # > # Gromacs Runs One Microsecond At Cannonball Speeds > # > @ title "Mean Square Displacement" > @ xaxis label "Time (ps)" > @ yaxis label "MSD (nm\S2\N)" > @TYPE xy > # MSD gathered over 10000 ps with 1001 restarts > # Diffusion constants fitted from time 1000 to 9000 ps > # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) > > Thank you > > Joe > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 tdeepanshi248 at gmail.com Mon Mar 16 16:07:04 2020 From: tdeepanshi248 at gmail.com (Deepanshi .) Date: Mon, 16 Mar 2020 15:07:04 -0000 Subject: [gmx-users] energy minimization in vacuum Message-ID: Dear all, I am trying to simulate an all atom protein in water. I wanted to ask that what is the importance of minimizing the protein in a vacuum. It is not mentioned in the lysozyme tutorial. Thanks. Regards, Deepanshi From 177cy500.bratin at nitk.edu.in Mon Mar 16 17:45:20 2020 From: 177cy500.bratin at nitk.edu.in (Bratin Kumar Das) Date: Mon, 16 Mar 2020 16:45:20 -0000 Subject: [gmx-users] energy minimization in vacuum In-Reply-To: References: Message-ID: Hi, If u minimise the protein in vaccum...the bad contact within the protein atoms will be removed After solvation if u do...then both the bad water contact and steric clashes within the protein will be removed. On Mon 16 Mar, 2020, 8:37 PM Deepanshi ., wrote: > Dear all, > > I am trying to simulate an all atom protein in water. I wanted to ask that > what is the importance of minimizing the protein in a vacuum. It is not > mentioned in the lysozyme tutorial. > > Thanks. > > Regards, > Deepanshi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Mon Mar 16 18:13:10 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 16 Mar 2020 17:13:10 -0000 Subject: [gmx-users] gmx msd unusual unit In-Reply-To: <4c85d388-e819-df5a-280c-866c421d1e11@vt.edu> References: <4c85d388-e819-df5a-280c-866c421d1e11@vt.edu> Message-ID: <4f5590c2-fbd3-3237-f00c-124a77bd3415@xray.bmc.uu.se> Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: > > > On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: >> Hello >> >> With running gmx msd I am told in the output the y axis unit is nm/ >> S2/ N, which is unexpected. Is this simply an print error or is there >> an error within the calculation? I have provided a copy of the output >> below, noting the units of the self-diffusion coefficient are >> sensible. Any insight would be much appreciated. > > The unit is correct. GROMACS does all distance calculations in terms of > nm. You get an interpreted output of the MSD in traditional units for > the diffusion constant. The confusion maybe about the xmgrace formatting :) nm^2 if you use the right software... > > -Justin > >> # Created by: >> #?????????????????????? :-) GROMACS - gmx msd, 2019.2 (-: >> # Command line: >> #?? gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o >> msd_IRMOF-NHPr_3OCT_8_run_1.xvg >> # gmx msd is part of G R O M A C S: >> # >> # Gromacs Runs One Microsecond At Cannonball Speeds >> # >> @??? title "Mean Square Displacement" >> @??? xaxis? label "Time (ps)" >> @??? yaxis? label "MSD (nm\S2\N)" >> @TYPE xy >> # MSD gathered over 10000 ps with 1001 restarts >> # Diffusion constants fitted from time 1000 to 9000 ps >> # D[?????? UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) >> >> Thank you >> >> Joe >> >> > -- 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 sadafrani6 at gmail.com Mon Mar 16 19:05:18 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 16 Mar 2020 18:05:18 -0000 Subject: [gmx-users] makes sense for Ryckaert Bellemans dihs. only. Message-ID: Dear Gromacs users I am calculating a dihedral angle between certain atoms by following command:- gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg Group 0 ( dihedral1) has 4 elements Group 1 ( dihedral2) has 4 elements Group 2 ( dihedral3) has 4 elements Select a group: 2 Selected 2: 'dihedral3' I get a warning as below:- Warning: calculating fractions as defined in this program makes sense for Ryckaert Bellemans dihs. only. Ignoring -of What does it mean? Can anyone please help me to understand? I am using gromacs 2020 Thanks. Sadaf From jpt33 at bath.ac.uk Mon Mar 16 19:19:33 2020 From: jpt33 at bath.ac.uk (Joe Paul-Taylor) Date: Mon, 16 Mar 2020 18:19:33 -0000 Subject: [gmx-users] gmx msd unusual unit In-Reply-To: <4f5590c2-fbd3-3237-f00c-124a77bd3415@xray.bmc.uu.se> References: <4c85d388-e819-df5a-280c-866c421d1e11@vt.edu> <4f5590c2-fbd3-3237-f00c-124a77bd3415@xray.bmc.uu.se> Message-ID: Thank you Justin and David, that's very helpful ? -----Original Message----- From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se On Behalf Of David van der Spoel Sent: 16 March 2020 17:13 To: gmx-users at gromacs.org Subject: Re: [gmx-users] gmx msd unusual unit CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: > > > On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: >> Hello >> >> With running gmx msd I am told in the output the y axis unit is nm/ >> S2/ N, which is unexpected. Is this simply an print error or is there >> an error within the calculation? I have provided a copy of the output >> below, noting the units of the self-diffusion coefficient are >> sensible. Any insight would be much appreciated. > > The unit is correct. GROMACS does all distance calculations in terms > of nm. You get an interpreted output of the MSD in traditional units > for the diffusion constant. The confusion maybe about the xmgrace formatting :) nm^2 if you use the right software... > > -Justin > >> # Created by: >> # :-) GROMACS - gmx msd, 2019.2 (-: >> # Command line: >> # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o >> msd_IRMOF-NHPr_3OCT_8_run_1.xvg >> # gmx msd is part of G R O M A C S: >> # >> # Gromacs Runs One Microsecond At Cannonball Speeds # >> @ title "Mean Square Displacement" >> @ xaxis label "Time (ps)" >> @ yaxis label "MSD (nm\S2\N)" >> @TYPE xy >> # MSD gathered over 10000 ps with 1001 restarts # Diffusion constants >> fitted from time 1000 to 9000 ps # D[?????? UNK] = 0.0031 (+/- >> 0.0004) (1e-5 cm^2/s) >> >> Thank you >> >> Joe >> >> > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From b.mijiddorj at gmail.com Tue Mar 17 02:17:06 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Tue, 17 Mar 2020 01:17:06 -0000 Subject: [gmx-users] Electric field Message-ID: Dear GMX users, I would like to perform MD simulations with external electric field. I would like to control the frequency. In the manual, I found that we should use ? 2.45 GHz, like microwave, and it was defined as ?=2?c/?. I think that ? is equal to 0.1224 m. Finally, I think that ? = 2*3.14*3e10^8 / 0.1224 = 0.0154 /ps Is it right? Thank you very much for any advice. Best regards, Mijiddorj From vhariha5 at jhu.edu Tue Mar 17 03:36:02 2020 From: vhariha5 at jhu.edu (Vinu Harihar) Date: Tue, 17 Mar 2020 02:36:02 -0000 Subject: [gmx-users] Quick and Dirty Installation Error Message-ID: Hello, I am trying to install GROMACS 2020 on my Windows laptop using Cygwin 3.1.4. I have run the steps outlined in the installation guide (http://manual.gromacs.org/documentation/2020/install-guide/index.html) before the command "make", version 4.3,. The command cmake in the build folder executed properly. When I try to execute "make", it returns the following error: /gromacs-2020/src/external/thread_mpi/src/tmpi_init.cpp:476:42: error: 'strdup' was not declared in this scope; did you mean 'strcmp'? 476 | threads[i].argv[j] = strdup( (*argv)[j] ); | ^~~~~~ | strcmp The error has to do with the C++ compiler I installed (g++ from gcc version 9.2.0) not recognizing the object 'strdup'. Is there a way to fix this error? Best, Vinu Harihar From jun.zhou at monash.edu Tue Mar 17 08:42:46 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Tue, 17 Mar 2020 07:42:46 -0000 Subject: [gmx-users] Problems with Non-equilibrium MD Message-ID: Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image ( https://drive.google.com/file/d/11GJntUJU7-phc-Bz-hWBICvQWFIGUJDI/view?usp=sharing ). Another question is that when I try to increase the deform rate, there is a warning: triclinic box is to skewed ... cannot fix pbc. And the simulation will stop after 1000 steps. How to prevent this? I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From alessandra.villa.biosim at gmail.com Tue Mar 17 08:53:16 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 17 Mar 2020 07:53:16 -0000 Subject: [gmx-users] makes sense for Ryckaert Bellemans dihs. only. In-Reply-To: References: Message-ID: Hi, This may be the answer to your question https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2004-February/009490.html Best regards Alessandra On Mon, Mar 16, 2020 at 7:05 PM Sadaf Rani wrote: > Dear Gromacs users > > I am calculating a dihedral angle between certain atoms by following > command:- > > gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of > trans.xvg > > Group 0 ( dihedral1) has 4 elements > Group 1 ( dihedral2) has 4 elements > Group 2 ( dihedral3) has 4 elements > Select a group: 2 > Selected 2: 'dihedral3' > I get a warning as below:- > Warning: calculating fractions as defined in this program > makes sense for Ryckaert Bellemans dihs. only. Ignoring -of > > What does it mean? Can anyone please help me to understand? I am using > gromacs 2020 > > 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 Tue Mar 17 08:53:17 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Tue, 17 Mar 2020 07:53:17 -0000 Subject: [gmx-users] makes sense for Ryckaert Bellemans dihs. only. In-Reply-To: References: Message-ID: Hi, This may be the answer to your question https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2004-February/009490.html Best regards Alessandra On Mon, Mar 16, 2020 at 7:05 PM Sadaf Rani wrote: > Dear Gromacs users > > I am calculating a dihedral angle between certain atoms by following > command:- > > gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of > trans.xvg > > Group 0 ( dihedral1) has 4 elements > Group 1 ( dihedral2) has 4 elements > Group 2 ( dihedral3) has 4 elements > Select a group: 2 > Selected 2: 'dihedral3' > I get a warning as below:- > Warning: calculating fractions as defined in this program > makes sense for Ryckaert Bellemans dihs. only. Ignoring -of > > What does it mean? Can anyone please help me to understand? I am using > gromacs 2020 > > 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 thomas.mcdonnell.11 at ucl.ac.uk Tue Mar 17 17:57:16 2020 From: thomas.mcdonnell.11 at ucl.ac.uk (McDonnell, Thomas) Date: Tue, 17 Mar 2020 16:57:16 -0000 Subject: [gmx-users] Gromax NDG/BGLC Force field Error In-Reply-To: References: Message-ID: Hey I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is: N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2 How do I modify the input files to overcome this, or is there a different forcefield I should be using? Thanks Thomas. From mwinokan at me.com Tue Mar 17 18:00:37 2020 From: mwinokan at me.com (Max Winokan) Date: Tue, 17 Mar 2020 17:00:37 -0000 Subject: [gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR) Message-ID: <1C316B87-7F45-47E3-AC7C-696EE40E97CB@me.com> Dear GMX-Users, Firstly, in light of the current situation with CoVID-19 I would like to wish everyone the best of luck with staying healthy and safe during these uncertain times. Now on to my Gromacs issue: I am relatively new to Gromacs and molecular dynamics. For my research I am studying enzymes, and so far have successfully simulated solvated Lysozyme and Helicase enzymes (using CHARMM36). Of course the more interesting properties of enzymes involve interactions with ligands. One case study I have been attempting to simulate is DNA helicase separating a DNA fragment. The PDB I am having trouble simulating is 3PJR (https://www.rcsb.org/structure/3PJR). I am using Gromacs 2018 on my faculty?s HPC cluster. I have made attempts with the CHARMM-36 force field, namely the March 2019 release (http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs). I chose this FF because it includes amino acid, DNA nucleotide, and ATP residues, but am not otherwise partial to CHARMM ? so I am open to suggestions for alternatives. I have also attempted generating the topology with charmm36-jul2017 to no avail. The specific error that I run into is: ? Program:???? gmx pdb2gmx, version 2018 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132) Fatal error: atom N not found in buiding block 1DG while combining tdb and rtp ? (log file result of $ gmx_mpi pdb2gmx -f 3pjr.pdb -o 3pjr_processed.gro -ff charmm36-mar2019 -water spce) It seems that similar error messages were produced when creating DNA topologies with CHARMM in the 4.0.99 version of Gromacs and were subsequently fixed (https://redmine.gromacs.org/issues/465). I have tried generating the topology for their DNA structure but with my methodology and get the same error, suggesting that the fix is not included in the FFs I have tried or there is an error in my method. Please could someone let me know how I can fix the problem if it is an error in my methodology, or how I can report this issue if it is due to a bug? Thank you for your time and best regards, Max Winokan PhD Candidate in Theoretical Physics Leverhulme Quantum Biology Doctoral Training Centre University of Surrey From jalemkul at vt.edu Tue Mar 17 18:03:14 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 17 Mar 2020 17:03:14 -0000 Subject: [gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR) In-Reply-To: <1C316B87-7F45-47E3-AC7C-696EE40E97CB@me.com> References: <1C316B87-7F45-47E3-AC7C-696EE40E97CB@me.com> Message-ID: <83dc310f-713b-f0e1-a5bb-605ee617fd00@vt.edu> On 3/17/20 1:00 PM, Max Winokan wrote: > Dear GMX-Users, > > > > Firstly, in light of the current situation with CoVID-19 I would like to wish everyone the best of luck with staying healthy and safe during these uncertain times. Now on to my Gromacs issue: > > > > I am relatively new to Gromacs and molecular dynamics. For my research I am studying enzymes, and so far have successfully simulated solvated Lysozyme and Helicase enzymes (using CHARMM36). Of course the more interesting properties of enzymes involve interactions with ligands. One case study I have been attempting to simulate is DNA helicase separating a DNA fragment. > > > > The PDB I am having trouble simulating is 3PJR (https://www.rcsb.org/structure/3PJR). I am using Gromacs 2018 on my faculty?s HPC cluster. I have made attempts with the CHARMM-36 force field, namely the March 2019 release (http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs). I chose this FF because it includes amino acid, DNA nucleotide, and ATP residues, but am not otherwise partial to CHARMM ? so I am open to suggestions for alternatives. I have also attempted generating the topology with charmm36-jul2017 to no avail. > > > > The specific error that I run into is: > > > > ? > > Program:???? gmx pdb2gmx, version 2018 > > Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132) > > > > Fatal error: > > atom N not found in buiding block 1DG while combining tdb and rtp > > ? > > > > (log file result of $ gmx_mpi pdb2gmx -f 3pjr.pdb -o 3pjr_processed.gro -ff charmm36-mar2019 -water spce) You need to manually choose termini types. Due to some technical reasons for the way we convert CHARMM files to GROMACS format, we can't produce separate .rtp file for amino acids, RNA, DNA, etc. so unfortunately that means that .tdb files have to contain both protein and nucleic acid termini types. The default choices (based on order in the files) is protein. -Justin > > > It seems that similar error messages were produced when creating DNA topologies with CHARMM in the 4.0.99 version of Gromacs and were subsequently fixed (https://redmine.gromacs.org/issues/465). I have tried generating the topology for their DNA structure but with my methodology and get the same error, suggesting that the fix is not included in the FFs I have tried or there is an error in my method. Please could someone let me know how I can fix the problem if it is an error in my methodology, or how I can report this issue if it is due to a bug? > > > > Thank you for your time and best regards, > > > > Max Winokan > > > > PhD Candidate in Theoretical Physics > > Leverhulme Quantum Biology Doctoral Training Centre University of Surrey > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From jalemkul at vt.edu Tue Mar 17 18:04:39 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 17 Mar 2020 17:04:39 -0000 Subject: [gmx-users] Gromax NDG/BGLC Force field Error In-Reply-To: References: Message-ID: On 3/17/20 12:57 PM, McDonnell, Thomas wrote: > Hey > > I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is: > > N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2 > > How do I modify the input files to overcome this, or is there a different forcefield I should be using? What is NDG? There is no such residue or patch in the CHARMM force field so I don't know why CHARMM-GUI produced any file with such a residue name. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From alexanderwien2k at gmail.com Tue Mar 17 18:15:08 2020 From: alexanderwien2k at gmail.com (Alex) Date: Tue, 17 Mar 2020 17:15:08 -0000 Subject: [gmx-users] Fwd: Reproducibility of a PMF plot In-Reply-To: References: Message-ID: Any comment, please? Thank you, Alex ---------- Forwarded message --------- From: Alex Date: Sun, Mar 15, 2020 at 8:16 PM Subject: Reproducibility of a PMF plot To: Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas of a simulation and then average over the quantity of interest, specially for a publishable result. I wonder if that also is necessary for a potential of mean force (PMF) calculation using umbrella sampling in which the bootstrap analysis is performed to calculate the standard deviation? Or for an alchemical free energy calculation where the e.g. the block averaging is used? Regards, Alex From faridaaziz90 at yahoo.com Tue Mar 17 19:39:18 2020 From: faridaaziz90 at yahoo.com (Farida Aziz) Date: Tue, 17 Mar 2020 18:39:18 -0000 Subject: [gmx-users] Extraction of frames at different interval References: <106680237.4263419.1584470351171.ref@mail.yahoo.com> Message-ID: <106680237.4263419.1584470351171@mail.yahoo.com> ?Hey,?To extract the first frame (t = 0 ns) of the trajectory i have used the below command? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0 ?to extract the frames at 6000 ps, 8600 ps and 9500 ps the following command i adjust like below, are these ok? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start1.pdb -dump 6000 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.2pdb -dump 8600 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start3.pdb -dump 9500 From moura at ufscar.br Tue Mar 17 19:40:48 2020 From: moura at ufscar.br (=?UTF-8?Q?Andr=C3=A9_Farias_de_Moura?=) Date: Tue, 17 Mar 2020 18:40:48 -0000 Subject: [gmx-users] Fwd: Reproducibility of a PMF plot In-Reply-To: References: Message-ID: Dear Alex, in a nutshell: yes, convergence might not have been achieved even if the estimated error bars seem small. maybe this reference might be helpful: https://doi.org/10.1016/j.bbamem.2016.03.006 best, Andre On Tue, Mar 17, 2020 at 2:14 PM Alex wrote: > Any comment, please? > > Thank you, > Alex > > ---------- Forwarded message --------- > From: Alex > Date: Sun, Mar 15, 2020 at 8:16 PM > Subject: Reproducibility of a PMF plot > To: > > > Dear all, > > Of course it is always good to prove that a MD simulation is reproducible > by repeating several replicas of a simulation and then average over the > quantity of interest, specially for a publishable result. > I wonder if that also is necessary for a potential of mean force (PMF) > calculation using umbrella sampling in which the bootstrap analysis is > performed to calculate the standard deviation? > Or for an alchemical free energy calculation where the e.g. the block > averaging is used? > > Regards, > Alex > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 From poncho_8629 at hotmail.com Tue Mar 17 20:49:36 2020 From: poncho_8629 at hotmail.com (Poncho Arvayo Zatarain) Date: Tue, 17 Mar 2020 19:49:36 -0000 Subject: [gmx-users] About membrane leaflets and msd Message-ID: Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks From poncho_8629 at hotmail.com Tue Mar 17 23:14:52 2020 From: poncho_8629 at hotmail.com (Poncho Arvayo Zatarain) Date: Tue, 17 Mar 2020 22:14:52 -0000 Subject: [gmx-users] About gmx msd and membrane leaflets In-Reply-To: References: Message-ID: Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks From antoszewski at uchicago.edu Tue Mar 17 23:15:41 2020 From: antoszewski at uchicago.edu (Adam Antoszewski) Date: Tue, 17 Mar 2020 22:15:41 -0000 Subject: [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4) Message-ID: Hey all, I am trying to install GROMACS 2019.4 (patched with plumed 2.5.3) on the Bridges cluster, which uses Intel Haswell CPUS. When compiling/installing with GNU compiler (GCC 4.8.4) and OpenMPI, the compile runs well. The cmake command I used was : cmake .. \ -DCMAKE_C_COMPILER=mpicc \ -DCMAKE_CXX_COMPILER=mpicxx \ -DGMX_MPI=ON \ -DCMAKE_INSTALL_PREFIX="${INSTALL_ROOT}" \ -DGMX_BUILD_OWN_FFTW=OFF \ -DGMX_FFT_LIBRARY=fftw3 \ -DREGRESSIONTEST_PATH="${BUILD_ROOT}/regressiontests-2019.4" \ -DGMX_SIMD=AVX2_256 Upon running 'make check', I pass 47/48 tests. The only test I fail is the HardwareUnitTests, specifically the HardwareTopologyTest. The error message I receive is reproduced below. ------- 11/46 Test #11: HardwareUnitTests ...................***Failed 0.65 sec [==========] Running 5 tests from 2 test cases. [----------] Global test environment set-up. [----------] 1 test from CpuInfoTest [ RUN ] CpuInfoTest.SupportLevel [ OK ] CpuInfoTest.SupportLevel (1 ms) [----------] 1 test from CpuInfoTest (1 ms total) [----------] 4 tests from HardwareTopologyTest [ RUN ] HardwareTopologyTest.Execute [ OK ] HardwareTopologyTest.Execute (57 ms) [ RUN ] HardwareTopologyTest.HwlocExecute /pylon5/mc5fphp/anto/gromacs_src/gromacs-2019.4/src/gromacs/hardware/tests/hardwaretopology.cpp:88: Failure Expected: (hwTop.supportLevel()) >= (gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00 00-00> vs 4-byte object <02-00 00-00> Cannot determine basic hardware topology from hwloc. GROMACS will still work, but it might affect your performance for large nodes. Please mail gmx-developers at gromacs.org so we can try to fix it. [ FAILED ] HardwareTopologyTest.HwlocExecute (51 ms) [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms) [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (48 ms) [----------] 4 tests from HardwareTopologyTest (206 ms total) [----------] Global test environment tear-down [==========] 5 tests from 2 test cases ran. (207 ms total) [ PASSED ] 4 tests. [ FAILED ] 1 test, listed below: [ FAILED ] HardwareTopologyTest.HwlocExecute 1 FAILED TEST . . . 98% tests passed, 1 tests failed out of 46 Label Time Summary: GTest = 137.68 sec (40 tests) IntegrationTest = 103.21 sec (5 tests) MpiTest = 1.36 sec (3 tests) SlowTest = 15.28 sec (1 test) UnitTest = 19.18 sec (34 tests) Total Test time (real) = 1461.58 sec The following tests FAILED: 11 - HardwareUnitTests (Failed) Errors while running CTest make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[1]: *** [CMakeFiles/check -------- The rest of the tests pass without issue, so . Any ideas? Is this some issue with hwloc, and is there anything I can do to fix it, or do I need to contact the sys admins? Is this a big issue, even with the failed test? The nodes only ever have 24 CPUs, so I'm not sure if that counts as a 'large node' (or if the number of nodes used per simulation would matter). Thanks in advance for the help! By the way, I am emailing this list because the error message told me to email gmx-developers, but I don't have permissions to post there - I apologize if this is the wrong forum. Thanks so much! -- Adam Antoszewski, PhD Candidate Dept. of Chemistry, The University of Chicago antoszewski at uchicago.edu From roland.schulz at intel.com Tue Mar 17 23:35:42 2020 From: roland.schulz at intel.com (Schulz, Roland) Date: Tue, 17 Mar 2020 22:35:42 -0000 Subject: [gmx-users] GROMACS Quick and Dirty Installation Error In-Reply-To: References: Message-ID: Hi, You should not send any GROMACS developer personal emails but use gmx-users mailinglist. You get the 404 because the comma at the end of the URL. Without it the link should work. As context the old archived email is: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090827.html The correct link is https://gerrit.gromacs.org/c/3764 The fix has been included since GROMACS 5. So any somewhat recent version shouldn't have that specific problem. But we don't regularly test GROMACS on CYGWIN. You might have more success if you use WSL (Windows subsystem for Linux) as a solution on Windows. Roland > -----Original Message----- > From: Vinu Harihar > Sent: Tuesday, March 17, 2020 2:46 PM > To: Schulz, Roland > Subject: GROMACS Quick and Dirty Installation Error > > Dear Mr. Schulz, > > > > I am a student trying to install GROMACS on my Windows laptop through > Cygwin. When I try to use the "quick and dirty installation guide" on the > GROMACS webpage, I run into an error when executing the "make" > command: > > /gromacs-2020/src/external/thread_mpi/src/tmpi_init.cpp:476:42: error: > 'strdup' was not declared in this scope; did you mean 'strcmp'? > > 476 | threads[i].argv[j] = strdup( (*argv)[j] ); > > | ^~~~~~ > > | strcmp > > I found an old post of yours on the gmx-users forum where you describe a > patch you developed for a similar issue. When I tried to access the patch on > Gerrit, I got a 404 error. I have tried to follow the instructions posted by other > users in the gmx-users thread but I still get this error. I was wondering if you > have any suggestions on how to fix the error or a newer version of the patch? > > > > With Gratitude, > > Vinu Harihar > > From thomas.mcdonnell.11 at ucl.ac.uk Wed Mar 18 00:33:19 2020 From: thomas.mcdonnell.11 at ucl.ac.uk (McDonnell, Thomas) Date: Tue, 17 Mar 2020 23:33:19 -0000 Subject: [gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 42 In-Reply-To: References: Message-ID: Re Gromacs NDG BGLC error. Dear Justin Apologies for not being clearer. NDG was from the crystal structure, CHARM GUI has replaced it with BGLC which is also not recognized. Could you advise me which forcefield would be best for this or how to modify my inputs? Thanks Thomas Get Outlook for Android ________________________________ 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: Tuesday, March 17, 2020 10:14:53 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: gromacs.org_gmx-users Digest, Vol 191, Issue 42 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=cZCWC%2F257tci0QXNCUKwqlQAJenRX0i8Dp2AQgCKiAw%3D&reserved=0 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: Gromax NDG/BGLC Force field Error (Justin Lemkul) 2. Fwd: Reproducibility of a PMF plot (Alex) 3. Extraction of frames at different interval (Farida Aziz) 4. Re: Fwd: Reproducibility of a PMF plot (Andr? Farias de Moura) 5. About membrane leaflets and msd (Poncho Arvayo Zatarain) 6. About gmx msd and membrane leaflets (Poncho Arvayo Zatarain) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Mar 2020 13:04:08 -0400 From: Justin Lemkul To: gmx-users at gromacs.org Subject: Re: [gmx-users] Gromax NDG/BGLC Force field Error Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed On 3/17/20 12:57 PM, McDonnell, Thomas wrote: > Hey > > I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is: > > N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2 > > How do I modify the input files to overcome this, or is there a different forcefield I should be using? What is NDG? There is no such residue or patch in the CHARMM force field so I don't know why CHARMM-GUI produced any file with such a residue name. -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 https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=zMm9lu%2BkBcOf1MR%2FTKd6BqSZHWRYuXSHxin%2Fgz7d8l8%3D&reserved=0 ================================================== ------------------------------ Message: 2 Date: Tue, 17 Mar 2020 13:14:29 -0400 From: Alex To: gmx-users at gromacs.org Subject: [gmx-users] Fwd: Reproducibility of a PMF plot Message-ID: Content-Type: text/plain; charset="UTF-8" Any comment, please? Thank you, Alex ---------- Forwarded message --------- From: Alex Date: Sun, Mar 15, 2020 at 8:16 PM Subject: Reproducibility of a PMF plot To: Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas of a simulation and then average over the quantity of interest, specially for a publishable result. I wonder if that also is necessary for a potential of mean force (PMF) calculation using umbrella sampling in which the bootstrap analysis is performed to calculate the standard deviation? Or for an alchemical free energy calculation where the e.g. the block averaging is used? Regards, Alex ------------------------------ Message: 3 Date: Tue, 17 Mar 2020 18:39:11 +0000 (UTC) From: Farida Aziz To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] Extraction of frames at different interval Message-ID: <106680237.4263419.1584470351171 at mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 ?Hey,?To extract the first frame (t = 0 ns) of the trajectory i have used the below command? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0 ?to extract the frames at 6000 ps, 8600 ps and 9500 ps the following command i adjust like below, are these ok? gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start1.pdb -dump 6000 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.2pdb -dump 8600 gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start3.pdb -dump 9500 ------------------------------ Message: 4 Date: Tue, 17 Mar 2020 15:10:38 -0300 From: Andr? Farias de Moura To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: Reproducibility of a PMF plot Message-ID: Content-Type: text/plain; charset="UTF-8" Dear Alex, in a nutshell: yes, convergence might not have been achieved even if the estimated error bars seem small. maybe this reference might be helpful: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.bbamem.2016.03.006&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=EW1W6sxEg5ZkOxJ67KrQpBoI%2F7JYGTdTkrSZiboQbmA%3D&reserved=0 best, Andre On Tue, Mar 17, 2020 at 2:14 PM Alex wrote: > Any comment, please? > > Thank you, > Alex > > ---------- Forwarded message --------- > From: Alex > Date: Sun, Mar 15, 2020 at 8:16 PM > Subject: Reproducibility of a PMF plot > To: > > > Dear all, > > Of course it is always good to prove that a MD simulation is reproducible > by repeating several replicas of a simulation and then average over the > quantity of interest, specially for a publishable result. > I wonder if that also is necessary for a potential of mean force (PMF) > calculation using umbrella sampling in which the bootstrap analysis is > performed to calculate the standard deviation? > Or for an alchemical free energy calculation where the e.g. the block > averaging is used? > > Regards, > Alex > -- > Gromacs Users mailing list > > * Please search the archive at > https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=sgz6a1xlZoQ47DF40KMRMkkwvlXwFkw6HM%2BylpaSjss%3D&reserved=0 before > posting! > > * Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=DD%2FRLj4MKlGZ%2BA5uMITT7C6OIoIvBAheONuKckas8pU%3D&reserved=0 > > * For (un)subscribe requests visit > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=cZCWC%2F257tci0QXNCUKwqlQAJenRX0i8Dp2AQgCKiAw%3D&reserved=0 or > send a mail to gmx-users-request at gromacs.org. > -- _____________ Prof. Dr. Andr? Farias de Moura Department of Chemistry Federal University of S?o Carlos S?o Carlos - Brazil phone: +55-16-3351-8090 ------------------------------ Message: 5 Date: Tue, 17 Mar 2020 19:49:31 +0000 From: Poncho Arvayo Zatarain To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: [gmx-users] About membrane leaflets and msd Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks ------------------------------ Message: 6 Date: Tue, 17 Mar 2020 22:14:48 +0000 From: Poncho Arvayo Zatarain To: "gromacs.org_gmx-users at maillist.sys.kth.se" Subject: [gmx-users] About gmx msd and membrane leaflets Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd? Thanks ------------------------------ -- Gromacs Users mailing list * Please search the archive at https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=sgz6a1xlZoQ47DF40KMRMkkwvlXwFkw6HM%2BylpaSjss%3D&reserved=0 before posting! * Can't post? Read https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=DD%2FRLj4MKlGZ%2BA5uMITT7C6OIoIvBAheONuKckas8pU%3D&reserved=0 * For (un)subscribe requests visit https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=cZCWC%2F257tci0QXNCUKwqlQAJenRX0i8Dp2AQgCKiAw%3D&reserved=0 or send a mail to gmx-users-request at gromacs.org. End of gromacs.org_gmx-users Digest, Vol 191, Issue 42 ****************************************************** From jun.zhou at monash.edu Wed Mar 18 03:39:58 2020 From: jun.zhou at monash.edu (Jun Zhou) Date: Wed, 18 Mar 2020 02:39:58 -0000 Subject: [gmx-users] Viscosity of non-newtonian fluid Message-ID: Hi all, Can I use GROMACS to simulate the viscosity of non-newtonian fluid, namely, small polymer in water solution. Since the system is not a homogenous system, I am not sure periodic perturbation method will be feasible for it. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. From atv55 at msstate.edu Wed Mar 18 06:28:23 2020 From: atv55 at msstate.edu (Anh Vo) Date: Wed, 18 Mar 2020 05:28:23 -0000 Subject: [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules Message-ID: Hi everyone, I am doing just a small simulation of 100 water molecules (after energy minimization, I run only 1 step of NVT and then get the Total energy, Potential and Kinetic energy from .edr file). The Kinetic energy is around 1 kJ/mol, while the Potential and Total energy is below - 2000 kJ/mol (around - 2405 kJ/mol). Similar results are obtained at 310K and 1K, as well as when I run NVE instead of NVT. Is it possible for the energy to be that much negative? If not, what could I have missed? Please see my settings in .mdp file as below for the 1 step NVT (For NVE, similar settings are used, but with tcoupl = no and pcoupl = no). define = -DREST_ON -DSTEP6_1 integrator = md dt = 0.0005 nsteps = 1 nstlog = 1 nstxout = 1 nstvout = 1 nstfout = 1 nstcalcenergy = 1 nstenergy = 1 ; cutoff-scheme = Verlet nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 0.8 rvdw = 1.0 ; tcoupl = berendsen tc_grps = SOL_ION tau_t = 1.0 ref_t = 310 ; pcoupl = no ; constraints = h-bonds constraint_algorithm = LINCS ; nstcomm = 100 comm_mode = linear comm_grps = SOL_ION ; refcoord_scaling = com Thank you very much for your help. I really appreciate it. Best, Anh Vo From atv55 at msstate.edu Wed Mar 18 07:00:52 2020 From: atv55 at msstate.edu (Anh Vo) Date: Wed, 18 Mar 2020 06:00:52 -0000 Subject: [gmx-users] k-space settings in GROMACS Message-ID: Hi everyone, I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare between the two. I'm simulating a lipid bilayer system with 72 POPC lipids and 9072 water molecules, as well as a single lipid system (1 POPC molecule) and water only system (100 H2O molecules). I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS I have *kspace_style* to define a long-range solver and *kspace_modify* to set parameters used by the kspace solvers; but I'm not sure which command I should use for similar settings in GROMACS. (I have read the manual and searched online but haven't figured it out. Please accept my apology if this seems to be an obvious question). In details, these 2 commands in LAMMPS are: * - kspace_style pppm 1e-5 *(pppm is P3M algorithm, 1.0e-5 means that the RMS error will be a factor of 100,000 smaller than the reference force) * - kspace_modify diff ad *(*diff* keyword specifies the differentiation scheme used by the PPPM method to compute forces on particles, *ad* keyword means approach uses only 1 FFT to transfer information back to real space for a total of 2 FFTs per timestep). Please help me to get similar settings in GROMACS (e.g. which command should I use ?). Also, would it make a significant difference (e.g. in the energy of the molecules, in the output pressure, etc.) if I use PME instead of PPPM in GROMACS ? Thank you very much for your help. Best, Anh Vo From mark.j.abraham at gmail.com Wed Mar 18 07:46:37 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:46:37 -0000 Subject: [gmx-users] k-space settings in GROMACS In-Reply-To: References: Message-ID: Hi, On Wed, 18 Mar 2020 at 07:02, Anh Vo wrote: > Hi everyone, > > I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare > between the two. I'm simulating a lipid bilayer system with 72 POPC lipids > and 9072 water molecules, as well as a single lipid system (1 POPC > molecule) and water only system (100 H2O molecules). > Start with a simpler system when proving you understand how to set up equivalent simulations. I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS > I have *kspace_style* to define a long-range solver and *kspace_modify* to > set > parameters used by the kspace solvers; but I'm not sure which command I > should use for similar settings in GROMACS. (I have read the manual and > searched online but haven't figured it out. Please accept my apology if > this seems to be an obvious question). > > In details, these 2 commands in LAMMPS are: > * - kspace_style pppm 1e-5 *(pppm is P3M algorithm, 1.0e-5 means > that the RMS error will be a factor of 100,000 smaller than the reference > force) > Then you'll know that ewald_rtol does exactly that, and that http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-coulombtype=P3M-AD does what you want. * - kspace_modify diff ad *(*diff* keyword specifies the > differentiation scheme used by the PPPM method to compute forces on > particles, *ad* keyword means approach uses only 1 FFT to transfer > information back to real space for a total of 2 FFTs per timestep). > > Please help me to get similar settings in GROMACS (e.g. which command > should I use ?). Also, would it make a significant difference (e.g. in the > energy of the molecules, in the output pressure, etc.) if I use PME instead > of PPPM in GROMACS ? > No need to do that. Mark > Thank you very much for your help. > > Best, > Anh Vo > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 18 07:46:37 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:46:37 -0000 Subject: [gmx-users] k-space settings in GROMACS In-Reply-To: References: Message-ID: Hi, On Wed, 18 Mar 2020 at 07:02, Anh Vo wrote: > Hi everyone, > > I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare > between the two. I'm simulating a lipid bilayer system with 72 POPC lipids > and 9072 water molecules, as well as a single lipid system (1 POPC > molecule) and water only system (100 H2O molecules). > Start with a simpler system when proving you understand how to set up equivalent simulations. I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS > I have *kspace_style* to define a long-range solver and *kspace_modify* to > set > parameters used by the kspace solvers; but I'm not sure which command I > should use for similar settings in GROMACS. (I have read the manual and > searched online but haven't figured it out. Please accept my apology if > this seems to be an obvious question). > > In details, these 2 commands in LAMMPS are: > * - kspace_style pppm 1e-5 *(pppm is P3M algorithm, 1.0e-5 means > that the RMS error will be a factor of 100,000 smaller than the reference > force) > Then you'll know that ewald_rtol does exactly that, and that http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-coulombtype=P3M-AD does what you want. * - kspace_modify diff ad *(*diff* keyword specifies the > differentiation scheme used by the PPPM method to compute forces on > particles, *ad* keyword means approach uses only 1 FFT to transfer > information back to real space for a total of 2 FFTs per timestep). > > Please help me to get similar settings in GROMACS (e.g. which command > should I use ?). Also, would it make a significant difference (e.g. in the > energy of the molecules, in the output pressure, etc.) if I use PME instead > of PPPM in GROMACS ? > No need to do that. Mark > Thank you very much for your help. > > Best, > Anh Vo > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 18 07:48:40 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:48:40 -0000 Subject: [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules In-Reply-To: References: Message-ID: Hi, That's entirely normal for condensed-phase systems. Negative PE means the system doesn't want to fly apart. Conventionally, zero PE is when every particle is infinitely separated - look at the form of the expression for energy in electrostatics (and gravity) Mark On Wed, 18 Mar 2020 at 06:28, Anh Vo wrote: > Hi everyone, > > I am doing just a small simulation of 100 water molecules (after energy > minimization, I run only 1 step of NVT and then get the Total energy, > Potential and Kinetic energy from .edr file). The Kinetic energy is around > 1 kJ/mol, while the Potential and Total energy is below - 2000 kJ/mol > (around - 2405 kJ/mol). Similar results are obtained at 310K and 1K, as > well as when I run NVE instead of NVT. Is it possible for the energy to be > that much negative? If not, what could I have missed? > Please see my settings in .mdp file as below for the 1 step NVT (For NVE, > similar settings are used, but with tcoupl = no and pcoupl = no). > > define = -DREST_ON -DSTEP6_1 > integrator = md > dt = 0.0005 > nsteps = 1 > nstlog = 1 > nstxout = 1 > nstvout = 1 > nstfout = 1 > nstcalcenergy = 1 > nstenergy = 1 > ; > cutoff-scheme = Verlet > nstlist = 10 > rlist = 1.0 > coulombtype = pme > rcoulomb = 1.0 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 0.8 > rvdw = 1.0 > ; > tcoupl = berendsen > tc_grps = SOL_ION > tau_t = 1.0 > ref_t = 310 > ; > pcoupl = no > ; > constraints = h-bonds > constraint_algorithm = LINCS > ; > nstcomm = 100 > comm_mode = linear > comm_grps = SOL_ION > ; > refcoord_scaling = com > > > Thank you very much for your help. I really appreciate it. > > Best, > Anh Vo > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 18 07:48:41 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:48:41 -0000 Subject: [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules In-Reply-To: References: Message-ID: Hi, That's entirely normal for condensed-phase systems. Negative PE means the system doesn't want to fly apart. Conventionally, zero PE is when every particle is infinitely separated - look at the form of the expression for energy in electrostatics (and gravity) Mark On Wed, 18 Mar 2020 at 06:28, Anh Vo wrote: > Hi everyone, > > I am doing just a small simulation of 100 water molecules (after energy > minimization, I run only 1 step of NVT and then get the Total energy, > Potential and Kinetic energy from .edr file). The Kinetic energy is around > 1 kJ/mol, while the Potential and Total energy is below - 2000 kJ/mol > (around - 2405 kJ/mol). Similar results are obtained at 310K and 1K, as > well as when I run NVE instead of NVT. Is it possible for the energy to be > that much negative? If not, what could I have missed? > Please see my settings in .mdp file as below for the 1 step NVT (For NVE, > similar settings are used, but with tcoupl = no and pcoupl = no). > > define = -DREST_ON -DSTEP6_1 > integrator = md > dt = 0.0005 > nsteps = 1 > nstlog = 1 > nstxout = 1 > nstvout = 1 > nstfout = 1 > nstcalcenergy = 1 > nstenergy = 1 > ; > cutoff-scheme = Verlet > nstlist = 10 > rlist = 1.0 > coulombtype = pme > rcoulomb = 1.0 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 0.8 > rvdw = 1.0 > ; > tcoupl = berendsen > tc_grps = SOL_ION > tau_t = 1.0 > ref_t = 310 > ; > pcoupl = no > ; > constraints = h-bonds > constraint_algorithm = LINCS > ; > nstcomm = 100 > comm_mode = linear > comm_grps = SOL_ION > ; > refcoord_scaling = com > > > Thank you very much for your help. I really appreciate it. > > Best, > Anh Vo > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 18 07:53:07 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:53:07 -0000 Subject: [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4) In-Reply-To: References: Message-ID: Hi, That's benign, and probably indicates some kind of mismatch in how hwloc was linked (e.g. headers from one version and libraries from another) or compiled (different compiler or version). mdrun will probably say the same thing, but 2019 has fallback code that means you don't need hwloc support for normal functionality, so you could just cmake -DGMX_HWLOC=off too. Mark On Tue, 17 Mar 2020 at 23:16, Adam Antoszewski wrote: > Hey all, > > I am trying to install GROMACS 2019.4 (patched with plumed 2.5.3) on the > Bridges cluster, which uses Intel > Haswell CPUS. When compiling/installing with GNU compiler (GCC 4.8.4) and > OpenMPI, the compile runs well. The cmake command I used was : > > cmake .. \ > > -DCMAKE_C_COMPILER=mpicc \ > > -DCMAKE_CXX_COMPILER=mpicxx \ > > -DGMX_MPI=ON \ > > -DCMAKE_INSTALL_PREFIX="${INSTALL_ROOT}" \ > > -DGMX_BUILD_OWN_FFTW=OFF \ > > -DGMX_FFT_LIBRARY=fftw3 \ > > -DREGRESSIONTEST_PATH="${BUILD_ROOT}/regressiontests-2019.4" \ > -DGMX_SIMD=AVX2_256 > > Upon running 'make check', I pass 47/48 tests. The only test I fail is the > HardwareUnitTests, specifically the HardwareTopologyTest. The error message > I receive is reproduced below. > > ------- > > 11/46 Test #11: HardwareUnitTests ...................***Failed 0.65 sec > > [==========] Running 5 tests from 2 test cases. > > [----------] Global test environment set-up. > > [----------] 1 test from CpuInfoTest > > [ RUN ] CpuInfoTest.SupportLevel > > [ OK ] CpuInfoTest.SupportLevel (1 ms) > > [----------] 1 test from CpuInfoTest (1 ms total) > > > [----------] 4 tests from HardwareTopologyTest > > [ RUN ] HardwareTopologyTest.Execute > > [ OK ] HardwareTopologyTest.Execute (57 ms) > > [ RUN ] HardwareTopologyTest.HwlocExecute > > > /pylon5/mc5fphp/anto/gromacs_src/gromacs-2019.4/src/gromacs/hardware/tests/hardwaretopology.cpp:88: > Failure > > Expected: (hwTop.supportLevel()) >= > (gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00 > 00-00> vs 4-byte object <02-00 00-00> > > Cannot determine basic hardware topology from hwloc. GROMACS will still > > > work, but it might affect your performance for large nodes. > > Please mail gmx-developers at gromacs.org so we can try to fix it. > > [ FAILED ] HardwareTopologyTest.HwlocExecute (51 ms) > > [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency > > [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms) > > [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency > > [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (48 ms) > > [----------] 4 tests from HardwareTopologyTest (206 ms total) > > > [----------] Global test environment tear-down > > [==========] 5 tests from 2 test cases ran. (207 ms total) > > [ PASSED ] 4 tests. > > [ FAILED ] 1 test, listed below: > > [ FAILED ] HardwareTopologyTest.HwlocExecute > > > 1 FAILED TEST > > > . > > . > > . > > > 98% tests passed, 1 tests failed out of 46 > > > Label Time Summary: > > GTest = 137.68 sec (40 tests) > > IntegrationTest = 103.21 sec (5 tests) > > MpiTest = 1.36 sec (3 tests) > > SlowTest = 15.28 sec (1 test) > > UnitTest = 19.18 sec (34 tests) > > > Total Test time (real) = 1461.58 sec > > > The following tests FAILED: > > 11 - HardwareUnitTests (Failed) > > Errors while running CTest > > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 > > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > > make[1]: *** [CMakeFiles/check > -------- > > The rest of the tests pass without issue, so . Any ideas? Is this some > issue with hwloc, and is there anything I can do to fix it, or do I need to > contact the sys admins? Is this a big issue, even with the failed test? The > nodes only ever have 24 CPUs, so I'm not sure if that counts as a 'large > node' (or if the number of nodes used per simulation would matter). Thanks > in advance for the help! By the way, I am emailing this list because the > error message told me to email gmx-developers, but I don't have permissions > to post there - I apologize if this is the wrong forum. > > Thanks so much! > > -- > Adam Antoszewski, PhD Candidate > Dept. of Chemistry, The University of Chicago > antoszewski at uchicago.edu > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Wed Mar 18 07:53:07 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Wed, 18 Mar 2020 06:53:07 -0000 Subject: [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4) In-Reply-To: References: Message-ID: Hi, That's benign, and probably indicates some kind of mismatch in how hwloc was linked (e.g. headers from one version and libraries from another) or compiled (different compiler or version). mdrun will probably say the same thing, but 2019 has fallback code that means you don't need hwloc support for normal functionality, so you could just cmake -DGMX_HWLOC=off too. Mark On Tue, 17 Mar 2020 at 23:16, Adam Antoszewski wrote: > Hey all, > > I am trying to install GROMACS 2019.4 (patched with plumed 2.5.3) on the > Bridges cluster, which uses Intel > Haswell CPUS. When compiling/installing with GNU compiler (GCC 4.8.4) and > OpenMPI, the compile runs well. The cmake command I used was : > > cmake .. \ > > -DCMAKE_C_COMPILER=mpicc \ > > -DCMAKE_CXX_COMPILER=mpicxx \ > > -DGMX_MPI=ON \ > > -DCMAKE_INSTALL_PREFIX="${INSTALL_ROOT}" \ > > -DGMX_BUILD_OWN_FFTW=OFF \ > > -DGMX_FFT_LIBRARY=fftw3 \ > > -DREGRESSIONTEST_PATH="${BUILD_ROOT}/regressiontests-2019.4" \ > -DGMX_SIMD=AVX2_256 > > Upon running 'make check', I pass 47/48 tests. The only test I fail is the > HardwareUnitTests, specifically the HardwareTopologyTest. The error message > I receive is reproduced below. > > ------- > > 11/46 Test #11: HardwareUnitTests ...................***Failed 0.65 sec > > [==========] Running 5 tests from 2 test cases. > > [----------] Global test environment set-up. > > [----------] 1 test from CpuInfoTest > > [ RUN ] CpuInfoTest.SupportLevel > > [ OK ] CpuInfoTest.SupportLevel (1 ms) > > [----------] 1 test from CpuInfoTest (1 ms total) > > > [----------] 4 tests from HardwareTopologyTest > > [ RUN ] HardwareTopologyTest.Execute > > [ OK ] HardwareTopologyTest.Execute (57 ms) > > [ RUN ] HardwareTopologyTest.HwlocExecute > > > /pylon5/mc5fphp/anto/gromacs_src/gromacs-2019.4/src/gromacs/hardware/tests/hardwaretopology.cpp:88: > Failure > > Expected: (hwTop.supportLevel()) >= > (gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00 > 00-00> vs 4-byte object <02-00 00-00> > > Cannot determine basic hardware topology from hwloc. GROMACS will still > > > work, but it might affect your performance for large nodes. > > Please mail gmx-developers at gromacs.org so we can try to fix it. > > [ FAILED ] HardwareTopologyTest.HwlocExecute (51 ms) > > [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency > > [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (50 ms) > > [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency > > [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (48 ms) > > [----------] 4 tests from HardwareTopologyTest (206 ms total) > > > [----------] Global test environment tear-down > > [==========] 5 tests from 2 test cases ran. (207 ms total) > > [ PASSED ] 4 tests. > > [ FAILED ] 1 test, listed below: > > [ FAILED ] HardwareTopologyTest.HwlocExecute > > > 1 FAILED TEST > > > . > > . > > . > > > 98% tests passed, 1 tests failed out of 46 > > > Label Time Summary: > > GTest = 137.68 sec (40 tests) > > IntegrationTest = 103.21 sec (5 tests) > > MpiTest = 1.36 sec (3 tests) > > SlowTest = 15.28 sec (1 test) > > UnitTest = 19.18 sec (34 tests) > > > Total Test time (real) = 1461.58 sec > > > The following tests FAILED: > > 11 - HardwareUnitTests (Failed) > > Errors while running CTest > > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 > > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 > > make[1]: *** [CMakeFiles/check > -------- > > The rest of the tests pass without issue, so . Any ideas? Is this some > issue with hwloc, and is there anything I can do to fix it, or do I need to > contact the sys admins? Is this a big issue, even with the failed test? The > nodes only ever have 24 CPUs, so I'm not sure if that counts as a 'large > node' (or if the number of nodes used per simulation would matter). Thanks > in advance for the help! By the way, I am emailing this list because the > error message told me to email gmx-developers, but I don't have permissions > to post there - I apologize if this is the wrong forum. > > Thanks so much! > > -- > Adam Antoszewski, PhD Candidate > Dept. of Chemistry, The University of Chicago > antoszewski at uchicago.edu > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From atv55 at msstate.edu Wed Mar 18 08:10:25 2020 From: atv55 at msstate.edu (Anh Vo) Date: Wed, 18 Mar 2020 07:10:25 -0000 Subject: [gmx-users] k-space settings in GROMACS Message-ID: Hi Mark, Thank you very much for your quick response. Would the command 'ewald-rtol = 1e-05' do the same job? I'm not sure because the 1e-5 in 'kspace_style pppm 1e-5' defines how much the RMS error is smaller than the reference force, while 1e-05 in 'ewald-rtol = 1e-05' defines the relative strength of the Ewald-shifted direct potential. Also, would there be much difference (e.g. in the energy of the molecules, in the output pressure, etc.) when PME and P3M are used? Thank you, Anh Vo -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Date: Wed, 18 Mar 2020 07:46:23 +0100 From: Mark Abraham To: Discussion list for GROMACS users Cc: Discussion list for GROMACS users Subject: Re: [gmx-users] k-space settings in GROMACS Message-ID: < CAMNuMAStNtbe8s-QdkChTUBdM-ZrX_ZYdxpGVT-eT--nE2iWAA at mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, On Wed, 18 Mar 2020 at 07:02, Anh Vo wrote: > Hi everyone, > > I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare > between the two. I'm simulating a lipid bilayer system with 72 POPC lipids > and 9072 water molecules, as well as a single lipid system (1 POPC > molecule) and water only system (100 H2O molecules). > Start with a simpler system when proving you understand how to set up equivalent simulations. I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS > I have *kspace_style* to define a long-range solver and *kspace_modify* to > set > parameters used by the kspace solvers; but I'm not sure which command I > should use for similar settings in GROMACS. (I have read the manual and > searched online but haven't figured it out. Please accept my apology if > this seems to be an obvious question). > > In details, these 2 commands in LAMMPS are: > * - kspace_style pppm 1e-5 *(pppm is P3M algorithm, 1.0e-5 means > that the RMS error will be a factor of 100,000 smaller than the reference > force) > Then you'll know that ewald_rtol does exactly that, and that http://secure-web.cisco.com/1bK_dF9SMkoS8dyT5J_HpebY83O47XvhPiIf89xavsJV9dlNvLV7TtA-4DpVUJEkHQGTHa44uJzJBJ807pEGqJfRzXfnyD5srJY1X8Nhys5FdF_nE7ANfoc-7bT5mI2rXACvnYfCjPkft84Do34WkmYwMK1DmKKvmDwjhfiRsZYNEVopvDcmeJcwVnGwLUBbnKOLBPlsvDzkRU9-YHvOZ7pdvASO-6UOuELXEiuPOrFBjxgVL1oY8eOxlKM7C6DE4eUhTZ6K5m-ygWc7iLjDlxbqIkEMSkQx1EFixWuxWnlMum4BQ05zUNCyLGHHudIx7/http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2Fcurrent%2Fuser-guide%2Fmdp-options.html#mdp-value-coulombtype=P3M-AD does what you want. * - kspace_modify diff ad *(*diff* keyword specifies the > differentiation scheme used by the PPPM method to compute forces on > particles, *ad* keyword means approach uses only 1 FFT to transfer > information back to real space for a total of 2 FFTs per timestep). > > Please help me to get similar settings in GROMACS (e.g. which command > should I use ?). Also, would it make a significant difference (e.g. in the > energy of the molecules, in the output pressure, etc.) if I use PME instead > of PPPM in GROMACS ? > No need to do that. Mark > Thank you very much for your help. > > Best, > Anh Vo From alessandra.villa.biosim at gmail.com Wed Mar 18 09:51:11 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 18 Mar 2020 08:51:11 -0000 Subject: [gmx-users] About gmx msd and membrane leaflets In-Reply-To: References: Message-ID: Hi, On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain < poncho_8629 at hotmail.com> wrote: > > > Hello gromacs users: I want to obtain the lateral diffusion for a membrane > with approximately 55 lipids+ions (NA+Cl) but i want to this for each > leaflet of the membrane (outter and inner) and then obtain the average. I > know that i can use gmx msd for lateral diffusion, but i don know how to > know wich lipids are in each leaftlet. ?How can separate the leaflets to > know wich lipid are in each one? After ?Can i make an index for each P > molecule in each lipid for example and then use it in the gmx msd? > > yes you can use index file with gmx msd. gmx make_ndx ( http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html) or gmx select (http://manual.gromacs.org/current/onlinehelp/gmx-select.html )may help to generate the desired index file. Best regards Alessandra > 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 alessandra.villa.biosim at gmail.com Wed Mar 18 09:51:11 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 18 Mar 2020 08:51:11 -0000 Subject: [gmx-users] About gmx msd and membrane leaflets In-Reply-To: References: Message-ID: Hi, On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain < poncho_8629 at hotmail.com> wrote: > > > Hello gromacs users: I want to obtain the lateral diffusion for a membrane > with approximately 55 lipids+ions (NA+Cl) but i want to this for each > leaflet of the membrane (outter and inner) and then obtain the average. I > know that i can use gmx msd for lateral diffusion, but i don know how to > know wich lipids are in each leaftlet. ?How can separate the leaflets to > know wich lipid are in each one? After ?Can i make an index for each P > molecule in each lipid for example and then use it in the gmx msd? > > yes you can use index file with gmx msd. gmx make_ndx ( http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html) or gmx select (http://manual.gromacs.org/current/onlinehelp/gmx-select.html )may help to generate the desired index file. Best regards Alessandra > 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 ibasu788 at gmail.com Wed Mar 18 12:00:11 2020 From: ibasu788 at gmail.com (Ipsita Basu) Date: Wed, 18 Mar 2020 11:00:11 -0000 Subject: [gmx-users] lipid tail order parameter Message-ID: Dear all, I want to calculate lipid tail order parameter as a function of lateral distance from protein for ex the x axis will be the distance of the lipids from the protein in xy plane and y axis will be those sn1/sn2 tail order parameter (time averaged and averaged over the atoms). Is there any other methods rather than combination of g_select and g_order commands. Thanks in advance... Ipsita Basu Post Doctoral Fellow, From thomas.mcdonnell.11 at ucl.ac.uk Wed Mar 18 12:56:48 2020 From: thomas.mcdonnell.11 at ucl.ac.uk (McDonnell, Thomas) Date: Wed, 18 Mar 2020 11:56:48 -0000 Subject: [gmx-users] NDG/BGLC Not Recognised In Force Fields Message-ID: Hey Apologies for not being clearer, the NDG is from the crystal structure, the post CHARMM-GUI now outputs that residue as BGLC, however, this is also not recognised when I run gmx2pdb. I have up to step 5 of the CHARMM-GUI, is there a way of inputting this to Gromacs without going through the GMX gmx2pdb process? Thanks Thomas. On 3/17/20 12:57 PM, McDonnell, Thomas wrote: > Hey > > I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is: > > N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2 > > How do I modify the input files to overcome this, or is there a different forcefield I should be using? What is NDG? There is no such residue or patch in the CHARMM force field so I don't know why CHARMM-GUI produced any file with such a residue name. -Justin From jalemkul at vt.edu Wed Mar 18 13:01:51 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 18 Mar 2020 12:01:51 -0000 Subject: [gmx-users] NDG/BGLC Not Recognised In Force Fields In-Reply-To: References: Message-ID: <13e69fdc-2ada-a652-5cf7-f5f1be8090dd@vt.edu> On 3/18/20 7:56 AM, McDonnell, Thomas wrote: > Hey > > > > Apologies for not being clearer, the NDG is from the crystal structure, the post CHARMM-GUI now outputs that residue as BGLC, however, this is also not recognised when I run gmx2pdb. > > > > I have up to step 5 of the CHARMM-GUI, is there a way of inputting this to Gromacs without going through the GMX gmx2pdb process? > Doesn't CHARMM-GUI give you a GROMACS topology? BGLC is a valid residue in CHARMM so without the actual screen output and error message, there's not much to suggest. The main problem is one intrinsic to pdb2gmx - it's not good at branched polymers. You'll have what it thinks is a discontinuous chain of protein and sugar residues, which you might be able to link/patch via specbond.dat but that requires a lot of work. It's very easy to set up in CHARMM (which is all CHARMM-GUI is doing on the backend). -Justin > > Thanks > > > > Thomas. > > > > > > On 3/17/20 12:57 PM, McDonnell, Thomas wrote: > >> Hey >> I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is: >> N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2 >> How do I modify the input files to overcome this, or is there a different forcefield I should be using? > > > What is NDG? There is no such residue or patch in the CHARMM force field > > so I don't know why CHARMM-GUI produced any file with such a residue name. > > > > -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 Mar 18 13:03:05 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 18 Mar 2020 12:03:05 -0000 Subject: [gmx-users] About gmx msd and membrane leaflets In-Reply-To: References: Message-ID: <534b1f38-2853-3824-daba-2d3a641a5029@vt.edu> On 3/18/20 4:50 AM, Alessandra Villa wrote: > Hi, > > On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain < > poncho_8629 at hotmail.com> wrote: > >> >> Hello gromacs users: I want to obtain the lateral diffusion for a membrane >> with approximately 55 lipids+ions (NA+Cl) but i want to this for each >> leaflet of the membrane (outter and inner) and then obtain the average. I >> know that i can use gmx msd for lateral diffusion, but i don know how to >> know wich lipids are in each leaftlet. ?How can separate the leaflets to >> know wich lipid are in each one? After ?Can i make an index for each P >> molecule in each lipid for example and then use it in the gmx msd? >> >> yes you can use index file with gmx msd. gmx make_ndx ( > http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html) or gmx > select (http://manual.gromacs.org/current/onlinehelp/gmx-select.html > )may > help to generate the desired index file. gmx select is the only way to go here since gmx make_ndx has no ability to separate selections based on geometry. One needs a quick estimate of the middle of the bilayer either from coordinates of terminal methyl carbons or using gmx traj. Any P atom with z-coordinate less than that value is the lower leaflet; larger z-coordinate is the upper leaflet. gmx select can make those selections. -Justin > Best regards > Alessandra > > > >> 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. >> -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 schrodingerscat404 at gmail.com Wed Mar 18 15:00:21 2020 From: schrodingerscat404 at gmail.com (=?UTF-8?B?U3V0YW51IEwnw4l0cmFuZ2Vy?=) Date: Wed, 18 Mar 2020 14:00:21 -0000 Subject: [gmx-users] (no subject) Message-ID: Hi, I've just installed GROMACS on Linux in Virtualbox. But, now I can't find my GROMACS, please tell me how to find it. Thank you. I've used these commands while installing gromacs:- sudo apt update sudo apt upgrade sudo apt install gcc sudo apt install cmake sudo apt install build-essential sudo apt install libfftw3-dev sudo apt install gromacs From T.Piggot at soton.ac.uk Wed Mar 18 15:17:13 2020 From: T.Piggot at soton.ac.uk (Piggot T.) Date: Wed, 18 Mar 2020 14:17:13 -0000 Subject: [gmx-users] lipid tail order parameter In-Reply-To: References: Message-ID: Hi, The modified version of g_order provided as part of the SI in: https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00643# should be able to calculate the order parameters radially from your protein. Cheers Tom On 18 Mar 2020, at 11:02, Ipsita Basu wrote: ?Dear all, I want to calculate lipid tail order parameter as a function of lateral distance from protein for ex the x axis will be the distance of the lipids from the protein in xy plane and y axis will be those sn1/sn2 tail order parameter (time averaged and averaged over the atoms). Is there any other methods rather than combination of g_select and g_order commands. Thanks in advance... Ipsita Basu Post Doctoral Fellow, -- Gromacs Users mailing list * Please search the archive at https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C19046b888fa34aaf74f708d7cb2bcff5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=RJ5Y16bSxGIW0ZPSs1PD%2F4BIVwXiBBsNZnaY%2FHbGgZI%3D&reserved=0 before posting! * Can't post? Read https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C19046b888fa34aaf74f708d7cb2bcff5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=8FHKuAYDZLP2wcjMhnkF4nnve1rD7cNJRRN8MfsQ%2B6I%3D&reserved=0 * For (un)subscribe requests visit https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C19046b888fa34aaf74f708d7cb2bcff5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=IaakpluyP32Ea0PnARGOceAAkM2bpqyVXTVB29sccgo%3D&reserved=0 or send a mail to gmx-users-request at gromacs.org. From schrodingerscat404 at gmail.com Wed Mar 18 15:25:54 2020 From: schrodingerscat404 at gmail.com (=?UTF-8?B?U3V0YW51IEwnw4l0cmFuZ2Vy?=) Date: Wed, 18 Mar 2020 14:25:54 -0000 Subject: [gmx-users] How to find and open Gromacs after installation Message-ID: ---------- Forwarded message --------- From: Sutanu L'?tranger Date: Wed, Mar 18, 2020, 19:31 Subject: [gmx-users] (no subject) To: Hi, I've just installed GROMACS on Linux in Virtualbox. But, now I can't find my GROMACS, please tell me how to find it. Thank you. I've used these commands while installing gromacs:- sudo apt update sudo apt upgrade sudo apt install gcc sudo apt install cmake sudo apt install build-essential sudo apt install libfftw3-dev sudo apt install gromacs From benson_muite at emailplus.org Wed Mar 18 15:50:19 2020 From: benson_muite at emailplus.org (Benson Muite) Date: Wed, 18 Mar 2020 14:50:19 -0000 Subject: [gmx-users] How to find and open Gromacs after installation In-Reply-To: References: Message-ID: <53967f0c-2ca9-45da-a07f-de26f1937c07@www.fastmail.com> It may be helpful to indicate what linux distribution you are using. It may be helpful to also look at the user guide: http://manual.gromacs.org/documentation/current/user-guide/index.html On the linux command line try typing gmx -version Usually the binaries are on the path. You may find it convenient to compile Gromacs yourself for efficient use of any GPUs you have available. Some documentation here: http://manual.gromacs.org/documentation/current/install-guide/index.html On Wed, Mar 18, 2020, at 5:25 PM, Sutanu L'?tranger wrote: > ---------- Forwarded message --------- > From: Sutanu L'?tranger > Date: Wed, Mar 18, 2020, 19:31 > Subject: [gmx-users] (no subject) > To: > > > Hi, > > I've just installed GROMACS on Linux in Virtualbox. But, now I can't find > my GROMACS, please tell me how to find it. > Thank you. > > I've used these commands while installing gromacs:- > > sudo apt update > sudo apt upgrade > sudo apt install gcc > sudo apt install cmake > sudo apt install build-essential > sudo apt install libfftw3-dev > sudo apt install 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 johannes.hermann at tum.de Wed Mar 18 16:50:21 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Wed, 18 Mar 2020 15:50:21 -0000 Subject: [gmx-users] alchemical free energy calculation with physical PBC Message-ID: <4ec1a20f-74e6-4d9e-95a1-864db4ce2bd5@tum.de> Dear all, I am calculating free energy changes with the alchemical free energy framework provided in gromacs. My alchemical transformation involves a charge change in a periodic system, where the periodicity is physical in the bound state but "artificial" in the unbound state. I know there is a bunch of literature dealing with correction schemes when using PME - but it did not find anything when the periodicity is physical, e.g. when simulating a membrane. So: What is the "error" in gromacs free energy calculation? Is it the Interaction with itself in the periodic image or an interaction with a changing neutralizing background charge which sums up? So should I try keeping a zero net charge over all alchemical transition windows also in the physical periodic setup. Thanks and all the best Johannes From kevin.boyd at uconn.edu Wed Mar 18 17:42:53 2020 From: kevin.boyd at uconn.edu (Kevin Boyd) Date: Wed, 18 Mar 2020 16:42:53 -0000 Subject: [gmx-users] About membrane leaflets and msd In-Reply-To: References: Message-ID: Hi, Yes, that's a reasonable approach. Check out gmx select, if say you know your center of membrane's z location, you can select for phosphates > that center point, which will give you your top leaflet. Kevin On Tue, Mar 17, 2020 at 12:49 PM Poncho Arvayo Zatarain < poncho_8629 at hotmail.com> wrote: > *Message sent from a system outside of UConn.* > > > Hello gromacs users: I want to obtain the lateral diffusion for a membrane > with approximately 55 lipids+ions (NA+Cl) but i want to this for each > leaflet of the membrane (outter and inner) and then obtain the average. I > know that i can use gmx msd for lateral diffusion, but i don know how to > know wich lipids are in each leaftlet. ?How can separate the leaflets to > know wich lipid are in each one? After ?Can i make an index for each P > molecule in each lipid for example and then use it in the gmx msd? > > 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 sadafrani6 at gmail.com Thu Mar 19 10:02:37 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Thu, 19 Mar 2020 09:02:37 -0000 Subject: [gmx-users] Error in free energy calculation Message-ID: Dear Gromacs users I am running a free energy calculation, my simulation crashes and generates different PDB structures I have well equilibrated the system before going to the production and the system seems stable. My input file for production run is as below:- ; Run control integrator = sd ; stochastic leap-frog integrator dt = 0.002 nsteps = 1500000 ; 3 ns comm-mode = Linear ; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxout-compressed = 5000 ; Bond parameters continuation = yes ; formerly known as 'unconstrained-start' - useful for exact continuations and reruns constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS ; Neighborsearching and short-range nonbonded interactions cutoff-scheme = verlet nstlist = 20 ns_type = grid rlist = 1.2 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme-order = 4 ; interpolation order for PME (default is 4) fourierspacing = 0.16 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ewald_geometry = 3d ; Ewald sum is performed in all three dimensions ; van der Waals vdwtype = cutoff vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 2.5e-04 rvdw = 1.2 DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) ; velocities gen_vel = no ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 298.15 ; Free energy control stuff free_energy = yes init_lambda_state = 10 delta_lambda = 0 calc_lambda_neighbors = 1 ; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 restraint_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 nstdhdl = 100 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Any help would really be appreciated. Thanks. Sadaf From alessandra.villa.biosim at gmail.com Thu Mar 19 10:03:53 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Thu, 19 Mar 2020 09:03:53 -0000 Subject: [gmx-users] alchemical free energy calculation with physical PBC In-Reply-To: <4ec1a20f-74e6-4d9e-95a1-864db4ce2bd5@tum.de> References: <4ec1a20f-74e6-4d9e-95a1-864db4ce2bd5@tum.de> Message-ID: Hi, On Wed, Mar 18, 2020 at 4:52 PM Johannes Hermann wrote: > Dear all, > > I am calculating free energy changes with the alchemical free energy > framework provided in gromacs. My alchemical transformation involves a > charge change in a periodic system, where the periodicity is physical in > the bound state but "artificial" in the unbound state. I know there is a > bunch of literature dealing with correction schemes when using PME - but > it did not find anything when the periodicity is physical, e.g. when > simulating a membrane. So: > > What is the "error" in gromacs free energy calculation? Is it the > Interaction with itself in the periodic image or an interaction with a > changing neutralizing background charge which sums up? So should I try > keeping a zero net charge over all alchemical transition windows also in > the physical periodic setup. > > Yes that is always good to try to keep zero the net charge change Alessandra > Thanks and all the best > > Johannes > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From liuyujie714 at gmail.com Thu Mar 19 11:48:35 2020 From: liuyujie714 at gmail.com (=?UTF-8?B?bGl1eXVqaWU3MTRAZ21haWwuY29t?=) Date: Thu, 19 Mar 2020 10:48:35 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 Message-ID: <5e734dfe.1c69fb81.d031a.84d9@mx.google.com> From blau at kth.se Thu Mar 19 12:45:51 2020 From: blau at kth.se (Christian Blau) Date: Thu, 19 Mar 2020 11:45:51 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 In-Reply-To: <5e734dfe.1c69fb81.d031a.84d9@mx.google.com> References: <5e734dfe.1c69fb81.d031a.84d9@mx.google.com> Message-ID: <03f995dd-03fd-61d9-a7a5-f06dfc099725@kth.se> Hello Yujie Liu, I am guessing the issue a bit from the brief title, let me know if installing the external program required to run dssp as described below is addressing the issue or if this is something that used to work in GROMACS 2019 and suddenly stopped working, in which case I would need quite a bit more information. Dssp in gromacs relies on an external program to run which you can find here: http://swift.cmbi.ru.nl/gv/dssp , just installing GROMACS does not suffice. The manual is hinting at this here: http://manual.gromacs.org/documentation/current/onlinehelp/gmx-do_dssp.html There is a newer version available on github - see here: https://github.com/cmbi/dssp which might compile better. Best, Christian On 2020-03-19 11:48, liuyujie714 at gmail.com wrote: From liuyujie714 at gmail.com Thu Mar 19 13:15:08 2020 From: liuyujie714 at gmail.com (liuyujie714) Date: Thu, 19 Mar 2020 12:15:08 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 In-Reply-To: <<03f995dd-03fd-61d9-a7a5-f06dfc099725@kth.se>> Message-ID: <20458847-4C90-45D0-B745-E8914289F76F@gmail.com> An HTML attachment was scrubbed... URL: From liuyujie714 at gmail.com Thu Mar 19 13:18:35 2020 From: liuyujie714 at gmail.com (liuyujie714) Date: Thu, 19 Mar 2020 12:18:35 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 In-Reply-To: <<03f995dd-03fd-61d9-a7a5-f06dfc099725@kth.se>> Message-ID: <927945C6-75CB-468D-835C-CA477DA8EFCF@gmail.com> An HTML attachment was scrubbed... URL: From vicente.domarc at gmail.com Thu Mar 19 14:50:21 2020 From: vicente.domarc at gmail.com (=?UTF-8?Q?Vicente_Dom=C3=ADnguez?=) Date: Thu, 19 Mar 2020 13:50:21 -0000 Subject: [gmx-users] About peptide mutation with non-standard residue Message-ID: Dear GROMACS users, I am working with specific peptide formed by a repetition of pentapeptides which sequence is VPGKG. I have built the structure of a protein formed with a determined repetition of those pentapeptides, the function prediction of that protein was carried out with I-TASSER server. Now, I need to mutate a specific residue (K) in some pentapeptides for a non-standard residue (XXXX). I have built successfully the topology of this residue. I am trying to change a K residue for this XXXX residue using several ways and several tools, for example, UCSF Chimera with Join Models tools. The problem always is that I reach a .pdb file with the final structure but I can not use a pdb2gmx tool to reach a .top files to run simulations. I tried to separate in different "chains" the "pieces" of the protein after removing the K, later I joined the XXXX residue in the holes that I made. I insert the .itp of the XXXX residue in .top file, the problem is that when I run grommp there are different numbers of atoms in final .pdb and final .top (Fatal error), this is due to that I needed to remove some H to join the XXXX residue to a specific place. Is there somebody to help me? How I can obtain a final .pdb file with a correct .top? Thanks in advance Vicente Dominguez-Arca PhD Candidate in Applied Physics Biophysics and Interfaces Group University of Santiago de Compostela SPAIN From jochen.hub at uni-saarland.de Thu Mar 19 18:01:23 2020 From: jochen.hub at uni-saarland.de (Jochen Hub) Date: Thu, 19 Mar 2020 17:01:23 -0000 Subject: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? Message-ID: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> Hi developers, I am running a simple DPPC membrane (Berger force field, PME, 1nm cutoff, 4fs time step, all standard) with 2020.1 and comm-mode = Linear nstcomm = 100 comm-grps = DPPC water ; OR System but the membrane rapidly drifts along the z direction: approx. once across the box per 100ps, and accelerating over time. This happens only with mdrun -update gpu -bonded gpu but not with mdrun -update gpu -bonded cpu (no spelling mistake) (with a GTX 1070Ti). Also no problems with 2018.6 or 2019.6. Seems like the center of mass motion removal is broken when doing both *bonded and updating* on the GPU. Is this issue known? Cheers, Jochen -- --------------------------------------------------- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --------------------------------------------------- From adarsh_p130085bt at nitc.ac.in Thu Mar 19 18:25:30 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Thu, 19 Mar 2020 17:25:30 -0000 Subject: [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3 Message-ID: Dear all, How to overcome this error ? ( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in virtual_sites3) I tried after deleting the line which returned an error message but still the problem does not get resolved. Command line: *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* *The above command returns following 'error message' while using with " ions.mdp "* ---------------------------------------------------------- NOTE 1 [file ions.mdp]: ERROR 1 [file lig.itp, line 575]: Duplicate atom index (19) in virtual_sites3 ----------------------------------------------------------- *I tried after deleting the line 575, but it produces another error at a later stage* gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr gmx mdrun -deffnm nvt -v ------------------------------------------------------------------------------------ starting mdrun 'XX in water' 50000 steps, 100.0 ps. Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000442, max 0.021883 (between atoms 5216 and 5218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5216 5217 61.7 0.1111 0.1125 0.1111 5216 5218 36.6 0.1111 0.1135 0.1111 Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 201.336624, max 8789.209961 (between atoms 3384 and 3385) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3384 3385 128.4 0.1111 976.5923 0.1111 4542 4543 103.1 0.1111 806.7125 0.1111 4542 4544 90.0 0.1111 0.4553 0.1111 5216 5217 90.0 0.1125 0.1590 0.1111 5216 5218 50.4 0.1135 0.1079 0.1111 step 5: One or more water molecules can not be settled. Check for bad contacts and/or reduce the time step if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) ------------------------------------------------------------------------------------------ From adarsh_p130085bt at nitc.ac.in Thu Mar 19 18:25:31 2020 From: adarsh_p130085bt at nitc.ac.in (Adarsh V. K.) Date: Thu, 19 Mar 2020 17:25:31 -0000 Subject: [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3 Message-ID: Dear all, How to overcome this error ? ( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in virtual_sites3) I tried after deleting the line which returned an error message but still the problem does not get resolved. Command line: *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* *The above command returns following 'error message' while using with " ions.mdp "* ---------------------------------------------------------- NOTE 1 [file ions.mdp]: ERROR 1 [file lig.itp, line 575]: Duplicate atom index (19) in virtual_sites3 ----------------------------------------------------------- *I tried after deleting the line 575, but it produces another error at a later stage* gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr gmx mdrun -deffnm nvt -v ------------------------------------------------------------------------------------ starting mdrun 'XX in water' 50000 steps, 100.0 ps. Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000442, max 0.021883 (between atoms 5216 and 5218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5216 5217 61.7 0.1111 0.1125 0.1111 5216 5218 36.6 0.1111 0.1135 0.1111 Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 201.336624, max 8789.209961 (between atoms 3384 and 3385) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3384 3385 128.4 0.1111 976.5923 0.1111 4542 4543 103.1 0.1111 806.7125 0.1111 4542 4544 90.0 0.1111 0.4553 0.1111 5216 5217 90.0 0.1125 0.1590 0.1111 5216 5218 50.4 0.1135 0.1079 0.1111 step 5: One or more water molecules can not be settled. Check for bad contacts and/or reduce the time step if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) ------------------------------------------------------------------------------------------ From schrodingerscat404 at gmail.com Thu Mar 19 19:28:30 2020 From: schrodingerscat404 at gmail.com (=?UTF-8?B?U3V0YW51IEwnw4l0cmFuZ2Vy?=) Date: Thu, 19 Mar 2020 18:28:30 -0000 Subject: [gmx-users] pdb2gmx command not found Message-ID: Hi, I've recently installed gromacs latest version, but when I type pdb2gmx, it shows "pdb2gmx command not found", please advise. Thank you. Regards, Sutanu From candrewn at gmail.com Thu Mar 19 23:48:34 2020 From: candrewn at gmail.com (Chris Neale) Date: Thu, 19 Mar 2020 22:48:34 -0000 Subject: [gmx-users] Non-linear slowdown in grompp with very many bonded interactions Message-ID: Hello, I am trying to figure out why grompp is so slow when given a long lists of bonded interactions. For example, my base system takes 7 seconds to run grompp and 37 seconds to do 100 steps of EM. However, when I add ~250,000 distance restraints grompp takes 3 minutes, and when I add ~600,000 distance restraints grompp takes 18 minutes. In both cases, the mdrun command is almost as fast as it was without any distance restraints (~42 seconds in each case). I made a bit of progress by converting the distance restraints to type-6 bonds, in which case the addition of ~250,000 or ~600,000 type-6 bonds results in grompp finishing in 1.5 minutes and 6 minutes, respectively. These numbers indicate to me that there is some type of non-linear slowdown when adding bonded interactions (like possibly a check for duplication of bonded terms as each one is read in, or memory reallocation). I would appreciate it if anybody knows which routine I should look at to see if I can get rid of this grompp lag. I am currently working with gromacs 5.1.2. Newer versions should be OK, but since ideally I want to use energy group exclusions, gromacs-2020 and it's verlet-scheme-only code is probably not an option for me. However, I did verify that I get the same type of non-linear slowdown when adding many bonded terms to gromacs-2020. Thank you, Chris. From candrewn at gmail.com Fri Mar 20 06:28:07 2020 From: candrewn at gmail.com (Chris Neale) Date: Fri, 20 Mar 2020 05:28:07 -0000 Subject: [gmx-users] pdb2gmx command not found Message-ID: Dear Sutanu: try "gmx pdb2gmx" instead. Most older stand-alone commands are now run as options to the gmx command, so pdb2gmx is now gmx pdb2gmx and g_order is now gmx order. Good luck, Chris. From candrewn at gmail.com Fri Mar 20 06:40:08 2020 From: candrewn at gmail.com (Chris Neale) Date: Fri, 20 Mar 2020 05:40:08 -0000 Subject: [gmx-users] About peptide mutation with non-standard residue Message-ID: Dear Vicente: If you can build your own hydrogen atom coordinates in your modified residue, then I suggest that you look at the lysine entry in the .rtp file in your force field directory, copy it, and modify it to match your modified amino acid. This will have a different location based on your force field, but for amber99 it would be here: share/gromacs/top/amber99.ff/aminoacids.rtp Then, you need to modify share/gromacs/top/residuetypes.dat so that it includes your amino acid name as a Protein residue. That should allow you to run gmx pdb2gmx with an input of a regular protein structure and get a .itp file for your protein with the modified residue. If you need gromacs to add hydrogens for you, then that will require also modifying the forcefield .hdb file(s), but it sounds like you might already have that under control. Good luck, this is straightforward but reasonably tricky. Chris. From candrewn at gmail.com Fri Mar 20 07:05:59 2020 From: candrewn at gmail.com (Chris Neale) Date: Fri, 20 Mar 2020 06:05:59 -0000 Subject: [gmx-users] Error in free energy calculation Message-ID: Dear Sadaf: You are starting with lambda = 10, which appears to be a state in which VDW is off, but Coulomb is (partially) on. I?ve not used the FE code in gromacs for quite some time (since it at least used to be unexpectedly slow compared to regular simulations), but I suspect that this is your problem ? with q but no VDW you can get two charged atoms getting really close and generating huge Coulombic forces, leading to system explosion. I believe that it is normal to have q completely off before you start turning off the VDW. Other thoughts, not likely related to your crashes, but I include them since I looked at your .mdp file already: why not use nstlist = 10 ? I?m not sure why nstlist = 20 is ever OK with a 2 fs time step, but I realize that gromacs has made some recent strides in NBlist building, so I might be misinformed here. I get fine sd integrator stability with lincs-order = 6. Not sure how much performance a lincs order of 12 is costing you, but you might be OK with 6 here. Your tau_t is pretty small for velocity Langevin dynamics and you may be in the over-damped regime. You may get more collective dynamics (and better overall sampling) with a 1 ps value of tau_t. Parrinello-Rahman pressure coupling, though giving a better ensemble than Berendsen, is more fragile and will lead to exploding systems more easily than Berendsen pressure coupling if your out of pressure/volume equilibrium. You might at least try using Berendsen pressure coupling and see if it fixes your issues. You have gen_vel = no. Suggest to verify that you are in fact loading in velocities. Good luck, Chris. From cristina.gonzalezfdez at unican.es Fri Mar 20 11:09:03 2020 From: cristina.gonzalezfdez at unican.es (Gonzalez Fernandez, Cristina) Date: Fri, 20 Mar 2020 10:09:03 -0000 Subject: [gmx-users] Problem in protein ligand interaction Message-ID: <5c96913f95e74ea88799d564a75cabeb@unican.es> Dear Gromacs users, I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid in the opposite direction. How could I achieve that the lipid reaches the protein binding site? Could I include some distance restraints that help the lipid to move to the binding pocket and then switch them off or this idea would lead to unreliabe results? Thank you in advance for all your help! Regards, Cristina From liuyujie714 at gmail.com Fri Mar 20 11:34:03 2020 From: liuyujie714 at gmail.com (=?UTF-8?B?bGl1eXVqaWU3MTRAZ21haWwuY29t?=) Date: Fri, 20 Mar 2020 10:34:03 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 Message-ID: <5e749c16.1c69fb81.30a9f.32c1@mx.google.com> From blau at kth.se Fri Mar 20 11:53:43 2020 From: blau at kth.se (Christian Blau) Date: Fri, 20 Mar 2020 10:53:43 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 In-Reply-To: <927945C6-75CB-468D-835C-CA477DA8EFCF@gmail.com> References: <927945C6-75CB-468D-835C-CA477DA8EFCF@gmail.com> Message-ID: <4c742a41-4153-dd67-77b3-d6474902b6ae@kth.se> Hi Yujie, This sounds very much like something we should fix. Can you file a bug report at https://redmine.gromacs.org/ where you can also upload the file that you are trying to run? Let me know if you have any trouble with uploading the report - I'm eager to know what happened. Best, Christian On 2020-03-19 13:18, liuyujie714 wrote: > >I am guessing the issue a bit from the brief title, let me know if > >installing the external program required to run dssp as described below > >is addressing the issue or if this is something that used to work in > >GROMACS 2019 and suddenly stopped working, in which case I would need > >quite a bit more information. > >Dssp in gromacs relies on an external program to run which you can find > >here: http://swift.cmbi.ru.nl/gv/dssp , just installing GROMACS does not > >suffice. > > Thanks Christian! > I post some information as following: > ? This "gmx do_dssp" tool of gmx2020 will report an error > "Segmentation fault" and no xpm and xvg file generated. I tesetd 2.0.4 > and later version of dssp. The gmx2018 and gmx 2019 can work correctly. > ? Then I checked gmx_do_dssp.cpp code and found some parts of matrix > changed a lot, I think this code may have a problem. > ? Thanks > ? Yujie Liu > > > liuyujie714 > liuyujie714 at gmail.com > > > > ??? ?????? > ?? > From ahernandez at unistra.fr Fri Mar 20 12:04:16 2020 From: ahernandez at unistra.fr (Oscar Hernandez Alba) Date: Fri, 20 Mar 2020 11:04:16 -0000 Subject: [gmx-users] distance restraints between different chains Message-ID: <2113997163.924206.1584702252827.JavaMail.zimbra@zstore-b1-027.partage.renater.fr> Dear all, I am trying to run MD with a protein with four different chains. When I convert this structure to gromacs, I have four different molecules in the topology file. I would like to use distance restraints between specific atoms of different chains. I have created the itp file with the information of the atoms involved in distance restraints. However, when I run the MD simulation with distance restraints I always get the same error message : < you have inserted topology section "distance_restraints" in a part belonging to a different molecule than you intended to >. Can someone help me with this problem ? I do not what is the exact place of the < distance-restraints > section in the topology file. Thank you very much. Oscar From vuqv.phys at gmail.com Fri Mar 20 12:16:53 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Fri, 20 Mar 2020 11:16:53 -0000 Subject: [gmx-users] distance restraints between different chains In-Reply-To: <2113997163.924206.1584702252827.JavaMail.zimbra@zstore-b1-027.partage.renater.fr> References: <2113997163.924206.1584702252827.JavaMail.zimbra@zstore-b1-027.partage.renater.fr> Message-ID: I think pulling code can solve the problem, http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba wrote: > Dear all, > > > > I am trying to run MD with a protein with four different chains. When > I > convert this structure to gromacs, I have four different molecules in the > topology file. I would like to use distance restraints between specific > atoms of different chains. I have created the itp file with the information > of the atoms involved in distance restraints. However, when I run the MD > simulation with distance restraints I always get the same error message : < > you have inserted topology section "distance_restraints" in a part > belonging > to a different molecule than you intended to >. Can someone help me with > this problem ? I do not what is the exact place of the < > distance-restraints > > section in the topology file. > > > > Thank you very much. > > > > Oscar > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Fri Mar 20 12:16:53 2020 From: vuqv.phys at gmail.com (Quyen V. Vu) Date: Fri, 20 Mar 2020 11:16:53 -0000 Subject: [gmx-users] distance restraints between different chains In-Reply-To: <2113997163.924206.1584702252827.JavaMail.zimbra@zstore-b1-027.partage.renater.fr> References: <2113997163.924206.1584702252827.JavaMail.zimbra@zstore-b1-027.partage.renater.fr> Message-ID: I think pulling code can solve the problem, http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba wrote: > Dear all, > > > > I am trying to run MD with a protein with four different chains. When > I > convert this structure to gromacs, I have four different molecules in the > topology file. I would like to use distance restraints between specific > atoms of different chains. I have created the itp file with the information > of the atoms involved in distance restraints. However, when I run the MD > simulation with distance restraints I always get the same error message : < > you have inserted topology section "distance_restraints" in a part > belonging > to a different molecule than you intended to >. Can someone help me with > this problem ? I do not what is the exact place of the < > distance-restraints > > section in the topology file. > > > > Thank you very much. > > > > Oscar > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mar 20 13:53:48 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 20 Mar 2020 12:53:48 -0000 Subject: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? In-Reply-To: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> References: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> Message-ID: On 3/19/20 1:01 PM, Jochen Hub wrote: > Hi developers, > > I am running a simple DPPC membrane (Berger force field, PME, 1nm > cutoff, 4fs time step, all standard) with 2020.1 and > > comm-mode??????????????? = Linear > nstcomm????????????????? = 100 > comm-grps??????????????? = DPPC water? ; OR System > > but the membrane rapidly drifts along the z direction: approx. once > across the box per 100ps, and accelerating over time. > > This happens only with > > mdrun -update gpu -bonded gpu > > but not with > > mdrun -update gpu -bonded cpu?? (no spelling mistake) > > (with a GTX 1070Ti). > > Also no problems with 2018.6 or 2019.6. > > Seems like the center of mass motion removal is broken when doing both > *bonded and updating* on the GPU. Is this issue known? > Sounds to me like an important bug that should be reported on Redmine. There was a COM motion bug that was fixed in 2020.1 but perhaps there are lingering issues. -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 Mar 20 13:55:13 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 20 Mar 2020 12:55:13 -0000 Subject: [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3 In-Reply-To: References: Message-ID: On 3/19/20 1:25 PM, Adarsh V. K. wrote: > Dear all, > How to overcome this error ? > ( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in > virtual_sites3) > > I tried after deleting the line which returned an error message > but still the problem does not get resolved. > > Command line: > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* > *The above command returns following 'error message' while using with " > ions.mdp "* > ---------------------------------------------------------- > NOTE 1 [file ions.mdp]: > ERROR 1 [file lig.itp, line 575]: > Duplicate atom index (19) in virtual_sites3 > ----------------------------------------------------------- This comes from our script exploiting a hack allowed in GROMACS 2016 for constructing virtual sites. It is invalid in version 2018 and newer, and you should get the latest version of the script from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs, regenerate the topology, and use GROMACS version 2020, which supports virtual site construction in a manner fully consistent with CHARMM. -Justin > *I tried after deleting the line 575, but it produces another error at a > later stage* > gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o > nvt.tpr > gmx mdrun -deffnm nvt -v > > ------------------------------------------------------------------------------------ > starting mdrun 'XX in water' > 50000 steps, 100.0 ps. > > Step 4, time 0.008 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000442, max 0.021883 (between atoms 5216 and 5218) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 5216 5217 61.7 0.1111 0.1125 0.1111 > 5216 5218 36.6 0.1111 0.1135 0.1111 > > Step 5, time 0.01 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 201.336624, max 8789.209961 (between atoms 3384 and 3385) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3384 3385 128.4 0.1111 976.5923 0.1111 > 4542 4543 103.1 0.1111 806.7125 0.1111 > 4542 4544 90.0 0.1111 0.4553 0.1111 > 5216 5217 90.0 0.1125 0.1590 0.1111 > 5216 5218 50.4 0.1135 0.1079 0.1111 > > step 5: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the time step if appropriate. > Wrote pdb files with previous and current coordinates > Segmentation fault (core dumped) > ------------------------------------------------------------------------------------------ -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 duyu at sioc.ac.cn Fri Mar 20 16:06:11 2020 From: duyu at sioc.ac.cn (Du, Yu) Date: Fri, 20 Mar 2020 15:06:11 -0000 Subject: [gmx-users] Problem in protein ligand interaction In-Reply-To: <5c96913f95e74ea88799d564a75cabeb@unican.es> References: <5c96913f95e74ea88799d564a75cabeb@unican.es> Message-ID: <7d3ebc78.c4e.170f873962c.Coremail.duyu@sioc.ac.cn> Hi Cristina, Previous ultra-long conventional molecular dynamics works have shown that ligand can find its binding pocket and finally bind in a crystal complex pose. Also enhance sampling techniques, e.g. metadynamics, can speeed the binding process. So, if you want ligand to find its binding pocket, you may need long-time simulation or enhance sampling. Distance restraint on the ligand is harmonic force, it indeed can affect the interaction between ligand and protein. > -----????----- > ???: "Gonzalez Fernandez, Cristina" > ????: 2020-03-20 17:59:05 (???) > ???: "gmx-users at gromacs.org" > ??: > ??: [gmx-users] Problem in protein ligand interaction > > Dear Gromacs users, > > > I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid in the opposite direction. How could I achieve that the lipid reaches the protein binding site? Could I include some distance restraints that help the lipid to move to the binding pocket and then switch them off or this idea would lead to unreliabe results? > > > Thank you in advance for all your help! > > > Regards, > > > Cristina > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 From liuyujie714 at gmail.com Sat Mar 21 02:06:16 2020 From: liuyujie714 at gmail.com (yujie Liu) Date: Sat, 21 Mar 2020 01:06:16 -0000 Subject: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1 Message-ID: <1584752677981.vv4yqedfvvmnvbx4s4fpqemd@android.mail.163.com> >This sounds very much like something we should >fix. Can you file a bug report at >https://redmine.gromacs.org/ where you can also >upload the file that you are trying to run? Let me >know if you have any trouble with uploading the >report - I'm eager to know what happened. Best, >Christian I had reported this bug in few days ago, please see this link: https://redmine.gromacs.org/issues/3444 Thanks Yujie Liu From wes.p.michaels at gmail.com Sat Mar 21 03:20:01 2020 From: wes.p.michaels at gmail.com (Wesley Michaels) Date: Sat, 21 Mar 2020 02:20:01 -0000 Subject: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities Message-ID: Hello, I hope this message finds you well! I'm running a pretty simple simulation of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P = 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting large, unstable volume fluctuations when I use the combination of the Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see this behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and pairtype = 1}. I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and set "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing something obvious, but here are the troubleshooting steps I've tried: 1) ensure the simulation is equilibrated (up to 100 nanoseconds with Berendsen barostat beforehand, which is more than plenty I believe); 2) use a smaller time step (down to 0.01 fs); 3) increase the pressure coupling time constant (up to 10 ps); 4) using both GROMACS 2018 and GROMACS 2019. As far as energies go, I don't think there are worryingly large terms that would blow the simulation up. Here's an example prepared with `gmx energy`: Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total Energy Conserved En. Volume Density 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 2.17E+05 2.17E+05 291.0 400.8 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 2.12E+05 1.02E+06 3720.8 31.3 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 1.19E+05 1.25E+06 21855.1 5.3 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 1.31E+05 1.52E+06 88422.7 1.3 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 1.44E+05 1.80E+06 246764.8 0.5 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03 1.57E+05 2.08E+06 538599.2 0.2 Eventually, the volume becomes unphysically large and the density extremely low. I'm sure I'm missing something obvious here (sorry for yet another "my simulation is blowing up" question), so any insight into other steps I could try would be greatly appreciated. If I can provide any additional information (e.g. topology/mdp files), just let me know. Thanks, Wes From dallas.warren at monash.edu Sat Mar 21 06:14:33 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Sat, 21 Mar 2020 05:14:33 -0000 Subject: [gmx-users] pdb2gmx command not found In-Reply-To: References: Message-ID: Versions of GROMACS for awhile now have moved all the scripts underneath "gmx". So now you need use "gmx pdb2gmx" On Fri, 20 Mar. 2020, 5:28 am Sutanu L'?tranger, < schrodingerscat404 at gmail.com> wrote: > Hi, > > I've recently installed gromacs latest version, but when I type pdb2gmx, it > shows "pdb2gmx command not found", please advise. Thank you. > > Regards, > Sutanu > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From alexanderwien2k at gmail.com Sat Mar 21 09:39:13 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sat, 21 Mar 2020 08:39:13 -0000 Subject: [gmx-users] comm-grps Message-ID: Hi all, Using umbrella sampling and WHAM I am calculating the PMF of a single molecule (A) diffusion from water into a thin film made out of another molecule. The thin film is supposed to be an infinite film along X-Y (or have periodicity laterally), also the pbc for the whole system is ON for all three directions pbc = xyz. The reaction coordinate is the film_com to A_com along Z axis. By default the "comm-mode = Linear" for the whole system, however the thin film translate during the PMF simulation in each window causing some artifact in the resulted PMF. Now, for such system my question is that if I am allowed to use: "comm-grps = thin film" and also "comm-mode = Linear-acceleration-correction" ? Thank you Alex From atv55 at msstate.edu Mon Mar 23 00:03:50 2020 From: atv55 at msstate.edu (Anh Vo) Date: Sun, 22 Mar 2020 23:03:50 -0000 Subject: [gmx-users] k-space settings in GROMACS Message-ID: Hi everyone, I have asked about the settings in GROMACS that would do the same job as *kspace_style* and *kspace_modify* in LAMMPS, and got reply from Mark a few days ago, but there are some points I'm still not very clear. Please help me with this again. In details, these 2 commands in LAMMPS are: * - kspace_style pppm 1e-5 *(kspace_style defines a long-range solver, pppm is P3M algorithm, 1.0e-5 means that the RMS error will be a factor of 100,000 smaller than the reference force) * - kspace_modify diff ad *(kspace_modify sets the parameters used by the kspace solvers, *diff* keyword specifies the differentiation scheme used by the PPPM method to compute forces on particles, *ad* keyword means approach uses only 1 FFT to transfer information back to real space for a total of 2 FFTs per timestep). I know that coulombtype *= *P3M-AD can set the pppm algorithm for long range interaction. However, I'm not sure about the *1e-5 *part in* 'kspace_style pppm 1e-5'. *Would the command 'ewald-rtol = 1e-05' do the same job? I'm not sure because the 1e-5 in 'kspace_style pppm 1e-5' defines how much the RMS error is smaller than the reference force, while 1e-05 in 'ewald-rtol = 1e-05' defines the relative strength of the Ewald-shifted direct potential. What values should I set for ewald-rtol to get the same meaning as ' *kspace_style **1e-5'* ? Also, would there be much difference (e.g. in the energy of the molecules, in the output pressure, etc.) when PME is used instead of P3M? (I have tried with some simple systems and got similar results when PME is used instead of P3M-AD) Thank you very much for your help. I really appreciate it. Best regards, Anh Vo From alessandra.villa.biosim at gmail.com Mon Mar 23 11:51:54 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Mon, 23 Mar 2020 10:51:54 -0000 Subject: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities In-Reply-To: References: Message-ID: Hi On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels wrote: > Hello, > > I hope this message finds you well! I'm running a pretty simple simulation > of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P = > 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting > large, unstable volume fluctuations when I use the combination of the > Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see this > behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and > pairtype = 1}. > > I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and set > "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing > something obvious, but here are the troubleshooting steps I've tried: > > Sorry I could not understand the reason behind the modification you did. Standard OPLS-AA force field field has "gen_pairs" to "yes" in forcefield.itp and calculate the 1-4 interaction by uniformly scaling the parameters. No modifications are needed in the [pairs] section of the topol.top for standard simulations with OPLS-AA. Or do you want to do something else? See http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=pair to understand if your setting is inline which the force field. Best regards Alessandra > 1) ensure the simulation is equilibrated (up to 100 nanoseconds with > Berendsen barostat beforehand, which is more than plenty I believe); > 2) use a smaller time step (down to 0.01 fs); > 3) increase the pressure coupling time constant (up to 10 ps); > 4) using both GROMACS 2018 and GROMACS 2019. > > As far as energies go, I don't think there are worryingly large terms that > would blow the simulation up. Here's an example prepared with `gmx energy`: > Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total > Energy Conserved En. Volume Density > 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 2.17E+05 > 2.17E+05 291.0 400.8 > 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 2.12E+05 > 1.02E+06 3720.8 31.3 > 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 1.19E+05 > 1.25E+06 21855.1 5.3 > 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 1.31E+05 > 1.52E+06 88422.7 1.3 > 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 1.44E+05 > 1.80E+06 246764.8 0.5 > 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03 > 1.57E+05 > 2.08E+06 538599.2 0.2 > > > Eventually, the volume becomes unphysically large and the density extremely > low. I'm sure I'm missing something obvious here (sorry for yet another "my > simulation is blowing up" question), so any insight into other steps I > could try would be greatly appreciated. If I can provide any additional > information (e.g. topology/mdp files), just let me know. > > Thanks, > Wes > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From drrahulsuresh at gmail.com Mon Mar 23 12:03:31 2020 From: drrahulsuresh at gmail.com (RAHUL SURESH) Date: Mon, 23 Mar 2020 11:03:31 -0000 Subject: [gmx-users] Gmx bundle regarding Message-ID: Hi I have a 1000ns simulation of gpcr protein. The protein structure have 7 helix. 1. How will I calculate the tilt of each helix? 2. If it has to be done by generating the index file, what groups are meant to be added for index file? 3. What groups should be chosen when gmx bundle prompt to choose it? Kindly share your detailed note. From magnus.lundborg at scilifelab.se Mon Mar 23 13:52:38 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 23 Mar 2020 12:52:38 -0000 Subject: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? In-Reply-To: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> References: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> Message-ID: <1061d43c-7b96-cca9-85da-6507f9133636@scilifelab.se> Hi Jochen, Have you tested if this happens with -update cpu? Perhaps it's the bonded on GPU that's the problem, unrelated to updating. I didn't see a Redmine issue yet. Could you make one? Cheers, Magnus On 2020-03-19 18:01, Jochen Hub wrote: > Hi developers, > > I am running a simple DPPC membrane (Berger force field, PME, 1nm > cutoff, 4fs time step, all standard) with 2020.1 and > > comm-mode??????????????? = Linear > nstcomm????????????????? = 100 > comm-grps??????????????? = DPPC water? ; OR System > > but the membrane rapidly drifts along the z direction: approx. once > across the box per 100ps, and accelerating over time. > > This happens only with > > mdrun -update gpu -bonded gpu > > but not with > > mdrun -update gpu -bonded cpu?? (no spelling mistake) > > (with a GTX 1070Ti). > > Also no problems with 2018.6 or 2019.6. > > Seems like the center of mass motion removal is broken when doing both > *bonded and updating* on the GPU. Is this issue known? > > Cheers, > Jochen > From magnus.lundborg at scilifelab.se Mon Mar 23 13:54:35 2020 From: magnus.lundborg at scilifelab.se (Magnus Lundborg) Date: Mon, 23 Mar 2020 12:54:35 -0000 Subject: [gmx-users] comm-grps In-Reply-To: References: Message-ID: <02c65dcc-6d84-345a-4e74-5f10d951d7ea@scilifelab.se> Hi Alex, Using "comm-grps = thin film" should be right, yes. In theory "comm-mode = Linear-acceleration-correction" could improve things, but is mainly useful if you are actively pulling the molecule through, i.e., what you are probably doing when generating the windows. There was a user report the other day ("2020.1: comm broken with -update gpu -bonded gpu ??") that said that comm removal did not work when combining update and bonded on gpu. That could be the problem in this case as well, especially if it turns out that it's running the bonded interactions on gpu that's the issue. Cheers, Magnus On 2020-03-21 09:38, Alex wrote: > Hi all, > Using umbrella sampling and WHAM I am calculating the PMF of a single > molecule (A) diffusion from water into a thin film made out of another > molecule. The thin film is supposed to be an infinite film along X-Y (or > have periodicity laterally), also the pbc for the whole system is ON for > all three directions pbc = xyz. > The reaction coordinate is the film_com to A_com along Z axis. > > By default the "comm-mode = Linear" for the whole system, however the thin > film translate during the PMF simulation in each window causing some > artifact in the resulted PMF. > > Now, for such system my question is that if I am allowed to use: > "comm-grps = thin film" > and also > "comm-mode = Linear-acceleration-correction" ? > > Thank you > Alex From alexanderwien2k at gmail.com Mon Mar 23 16:10:50 2020 From: alexanderwien2k at gmail.com (Alex) Date: Mon, 23 Mar 2020 15:10:50 -0000 Subject: [gmx-users] comm-grps In-Reply-To: <02c65dcc-6d84-345a-4e74-5f10d951d7ea@scilifelab.se> References: <02c65dcc-6d84-345a-4e74-5f10d951d7ea@scilifelab.se> Message-ID: Hi Magnus, Thanks for the response. As I said before the system contains the "thin film + molecule A ( single molecule) intended for the PMF calculation + Water". And actually by the ?comm-grps = thin film? the gmx grompp failed as some atoms are not part of any center of mass motion removal group (VCM groups). However, the two following options work: ?comm-grps = thin_film Mol_A SOL? or ?comm-grps = Other SOL? Where the Other group contains the thin film and molecule A, the pull_group2 and pull_group1, respectively. Which one do you recommend, please? Thank you Alex On Mon, Mar 23, 2020 at 08:57 Magnus Lundborg wrote: > Hi Alex, > > Using > > "comm-grps = thin film" > > should be right, yes. In theory > > "comm-mode = Linear-acceleration-correction" > > could improve things, but is mainly useful if you are actively pulling > the molecule through, i.e., what you are probably doing when generating > the windows. > > There was a user report the other day ("2020.1: comm broken with -update > gpu -bonded gpu ??") that said that comm removal did not work when > combining update and bonded on gpu. That could be the problem in this > case as well, especially if it turns out that it's running the bonded > interactions on gpu that's the issue. > > Cheers, > > Magnus > > > On 2020-03-21 09:38, Alex wrote: > > Hi all, > > Using umbrella sampling and WHAM I am calculating the PMF of a single > > molecule (A) diffusion from water into a thin film made out of another > > molecule. The thin film is supposed to be an infinite film along X-Y (or > > have periodicity laterally), also the pbc for the whole system is ON for > > all three directions pbc = xyz. > > The reaction coordinate is the film_com to A_com along Z axis. > > > > By default the "comm-mode = Linear" for the whole system, however the > thin > > film translate during the PMF simulation in each window causing some > > artifact in the resulted PMF. > > > > Now, for such system my question is that if I am allowed to use: > > "comm-grps = thin film" > > and also > > "comm-mode = Linear-acceleration-correction" ? > > > > Thank you > > Alex > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From johannes.hermann at tum.de Mon Mar 23 17:06:46 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Mon, 23 Mar 2020 16:06:46 -0000 Subject: [gmx-users] Replica exchange: Coordinates and simulation box size? Message-ID: <7187ee09-3b74-f6e2-4a39-c623f39110f0@tum.de> Dear all, I have slightly different Position Restrains and Box sizes over my lambda windows in an alchemical Free Energy Calculation in NVT ensemble (I know that my calculated Free Energy Difference will not solely depend on the mutation alone..) What happens if I use replica exchange? What exactly is exchanged within different windows: Only the coordinates or also the current simulation box size? Thanks in advance! All the best Johannes From dburns at iastate.edu Mon Mar 23 17:31:13 2020 From: dburns at iastate.edu (Daniel Burns) Date: Mon, 23 Mar 2020 16:31:13 -0000 Subject: [gmx-users] Replica exchange: Coordinates and simulation box size? In-Reply-To: <7187ee09-3b74-f6e2-4a39-c623f39110f0@tum.de> References: <7187ee09-3b74-f6e2-4a39-c623f39110f0@tum.de> Message-ID: Hi Johannes, Somebody please correct me if I'm wrong but I believe it is just the thermostats that are exchanged. A given simulation box's velocities are rescaled accordingly after the exchange and the simulation continues with its own fluctuations in box size assuming it is pressure-coupled. I don't know anything about incorporating free energy calculations with replica exchange though. Aloha, Dan On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann wrote: > Dear all, > > I have slightly different Position Restrains and Box sizes over my > lambda windows in an alchemical Free Energy Calculation in NVT ensemble > (I know that my calculated Free Energy Difference will not solely depend > on the mutation alone..) > > What happens if I use replica exchange? What exactly is exchanged within > different windows: Only the coordinates or also the current simulation > box size? > > Thanks in advance! > > All the best > > Johannes > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mar 23 17:34:19 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Mon, 23 Mar 2020 16:34:19 -0000 Subject: [gmx-users] Replica exchange: Coordinates and simulation box size? In-Reply-To: References: <7187ee09-3b74-f6e2-4a39-c623f39110f0@tum.de> Message-ID: <744e0007-1145-04c9-4bef-8651f4a51ee9@vt.edu> On 3/23/20 12:30 PM, Daniel Burns wrote: > Hi Johannes, > > Somebody please correct me if I'm wrong but I believe it is just the > thermostats that are exchanged. There's a lot of information that is exchanged, including temperature and pressure coupling information, coordinates, velocities, and the box. static void exchange_state(const gmx_multisim_t* ms, int b, t_state* state) { ??? /* When t_state changes, this code should be updated. */ ??? int ngtc, nnhpres; ??? ngtc??? = state->ngtc * state->nhchainlength; ??? nnhpres = state->nnhpres * state->nhchainlength; ??? exchange_rvecs(ms, b, state->box, DIM); ??? exchange_rvecs(ms, b, state->box_rel, DIM); ??? exchange_rvecs(ms, b, state->boxv, DIM); ??? exchange_reals(ms, b, &(state->veta), 1); ??? exchange_reals(ms, b, &(state->vol0), 1); ??? exchange_rvecs(ms, b, state->svir_prev, DIM); ??? exchange_rvecs(ms, b, state->fvir_prev, DIM); ??? exchange_rvecs(ms, b, state->pres_prev, DIM); ??? exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc); ??? exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc); ??? exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres); ??? exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres); ??? exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc); ??? exchange_doubles(ms, b, &state->baros_integral, 1); ??? exchange_rvecs(ms, b, state->x.rvec_array(), state->natoms); ??? exchange_rvecs(ms, b, state->v.rvec_array(), state->natoms); } -Justin > A given simulation box's velocities are rescaled accordingly after the > exchange and the simulation continues with its own fluctuations in box size > assuming it is pressure-coupled. > > I don't know anything about incorporating free energy calculations with > replica exchange though. > > Aloha, > > Dan > > On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann > wrote: > >> Dear all, >> >> I have slightly different Position Restrains and Box sizes over my >> lambda windows in an alchemical Free Energy Calculation in NVT ensemble >> (I know that my calculated Free Energy Difference will not solely depend >> on the mutation alone..) >> >> What happens if I use replica exchange? What exactly is exchanged within >> different windows: Only the coordinates or also the current simulation >> box size? >> >> Thanks in advance! >> >> All the best >> >> Johannes >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe 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 johannes.hermann at tum.de Mon Mar 23 18:18:07 2020 From: johannes.hermann at tum.de (Johannes Hermann) Date: Mon, 23 Mar 2020 17:18:07 -0000 Subject: [gmx-users] Replica exchange: Coordinates and simulation box size? In-Reply-To: <744e0007-1145-04c9-4bef-8651f4a51ee9@vt.edu> References: <7187ee09-3b74-f6e2-4a39-c623f39110f0@tum.de> <744e0007-1145-04c9-4bef-8651f4a51ee9@vt.edu> Message-ID: <9fc715e6-67b4-cc4f-975d-f854b65ef64f@tum.de> Thanks, Justin! On 23.03.20 17:34, Justin Lemkul wrote: > > > On 3/23/20 12:30 PM, Daniel Burns wrote: >> Hi Johannes, >> >> Somebody please correct me if I'm wrong but I believe it is just the >> thermostats that are exchanged. > > There's a lot of information that is exchanged, including temperature > and pressure coupling information, coordinates, velocities, and the box. > > static void exchange_state(const gmx_multisim_t* ms, int b, t_state* > state) > { > ??? /* When t_state changes, this code should be updated. */ > ??? int ngtc, nnhpres; > ??? ngtc??? = state->ngtc * state->nhchainlength; > ??? nnhpres = state->nnhpres * state->nhchainlength; > ??? exchange_rvecs(ms, b, state->box, DIM); > ??? exchange_rvecs(ms, b, state->box_rel, DIM); > ??? exchange_rvecs(ms, b, state->boxv, DIM); > ??? exchange_reals(ms, b, &(state->veta), 1); > ??? exchange_reals(ms, b, &(state->vol0), 1); > ??? exchange_rvecs(ms, b, state->svir_prev, DIM); > ??? exchange_rvecs(ms, b, state->fvir_prev, DIM); > ??? exchange_rvecs(ms, b, state->pres_prev, DIM); > ??? exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc); > ??? exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc); > ??? exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres); > ??? exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres); > ??? exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc); > ??? exchange_doubles(ms, b, &state->baros_integral, 1); > ??? exchange_rvecs(ms, b, state->x.rvec_array(), state->natoms); > ??? exchange_rvecs(ms, b, state->v.rvec_array(), state->natoms); > } > > -Justin > >> A given simulation box's velocities are rescaled accordingly after the >> exchange and the simulation continues with its own fluctuations in >> box size >> assuming it is pressure-coupled. >> >> I don't know anything about incorporating free energy calculations with >> replica exchange though. >> >> Aloha, >> >> Dan >> >> On Mon, Mar 23, 2020 at 11:07 AM Johannes Hermann >> >> wrote: >> >>> Dear all, >>> >>> I have slightly different Position Restrains and Box sizes over my >>> lambda windows in an alchemical Free Energy Calculation in NVT ensemble >>> (I know that my calculated Free Energy Difference will not solely >>> depend >>> on the mutation alone..) >>> >>> What happens if I use replica exchange? What exactly is exchanged >>> within >>> different windows: Only the coordinates or also the current simulation >>> box size? >>> >>> Thanks in advance! >>> >>> All the best >>> >>> Johannes >>> >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-request at gromacs.org. >>> > -- ______________________________________ *Technische Universit?t M?nchen* *Johannes Hermann, M.Sc.* Lehrstuhl f?r Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 89289 15730 Fax: +49 89289 15714 Email: j.hermann at lrz.tum.de http://www.biovt.mw.tum.de/ From jochen.hub at uni-saarland.de Mon Mar 23 19:12:09 2020 From: jochen.hub at uni-saarland.de (Jochen Hub) Date: Mon, 23 Mar 2020 18:12:09 -0000 Subject: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? In-Reply-To: <1061d43c-7b96-cca9-85da-6507f9133636@scilifelab.se> References: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> <1061d43c-7b96-cca9-85da-6507f9133636@scilifelab.se> Message-ID: <08bf06e6-d117-6ad8-cd01-96db34a60a4d@uni-saarland.de> Hi Magnus and Justin, Am 23.03.20 um 13:52 schrieb Magnus Lundborg: > Hi Jochen, > > Have you tested if this happens with -update cpu? Perhaps it's the bonded on GPU that's the problem, unrelated to updating. The problem only appears with -update gpu, not with -update cpu. I didn't see a > Redmine issue yet. Could you make one? I tried, but I seem to lack permissions: On https://redmine.gromacs.org/projects/gromacs/issues/new I get "You are not authorized to access this page." Did I miss something here? Thanks, Jochen Am 23.03.20 um 13:52 schrieb Magnus Lundborg: > Hi Jochen, > > Have you tested if this happens with -update cpu? Perhaps it's the > bonded on GPU that's the problem, unrelated to updating. I didn't see a > Redmine issue yet. Could you make one? > > Cheers, > Magnus > > On 2020-03-19 18:01, Jochen Hub wrote: >> Hi developers, >> >> I am running a simple DPPC membrane (Berger force field, PME, 1nm >> cutoff, 4fs time step, all standard) with 2020.1 and >> >> comm-mode??????????????? = Linear >> nstcomm????????????????? = 100 >> comm-grps??????????????? = DPPC water? ; OR System >> >> but the membrane rapidly drifts along the z direction: approx. once >> across the box per 100ps, and accelerating over time. >> >> This happens only with >> >> mdrun -update gpu -bonded gpu >> >> but not with >> >> mdrun -update gpu -bonded cpu?? (no spelling mistake) >> >> (with a GTX 1070Ti). >> >> Also no problems with 2018.6 or 2019.6. >> >> Seems like the center of mass motion removal is broken when doing both >> *bonded and updating* on the GPU. Is this issue known? >> >> Cheers, >> Jochen >> > -- --------------------------------------------------- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --------------------------------------------------- From paul.bauer.q at gmail.com Mon Mar 23 19:23:45 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 23 Mar 2020 18:23:45 -0000 Subject: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ? In-Reply-To: <08bf06e6-d117-6ad8-cd01-96db34a60a4d@uni-saarland.de> References: <05768139-0c6c-bf54-1315-d8eb3dcb747f@uni-saarland.de> <1061d43c-7b96-cca9-85da-6507f9133636@scilifelab.se> <08bf06e6-d117-6ad8-cd01-96db34a60a4d@uni-saarland.de> Message-ID: Hello, sorry for the confusion, but I'm currently moving our infrastructure over to Gitlab and have set Redmine to read only because of this. I'll update gmx-users and gmx-developers once the process is done, and then you can open the issue on Gitlab using the tracking system there. Cheers Paul On 23/03/2020 19:12, Jochen Hub wrote: > Hi Magnus and Justin, > > Am 23.03.20 um 13:52 schrieb Magnus Lundborg: > > Hi Jochen, > > > > Have you tested if this happens with -update cpu? Perhaps it's the > bonded on GPU that's the problem, unrelated to updating. > > The problem only appears with -update gpu, not with -update cpu. > > ?I didn't see a > > Redmine issue yet. Could you make one? > > I tried, but I seem to lack permissions: On > > https://redmine.gromacs.org/projects/gromacs/issues/new > > I get "You are not authorized to access this page." Did I miss > something here? > > Thanks, > Jochen > > > Am 23.03.20 um 13:52 schrieb Magnus Lundborg: >> Hi Jochen, >> >> Have you tested if this happens with -update cpu? Perhaps it's the >> bonded on GPU that's the problem, unrelated to updating. I didn't see >> a Redmine issue yet. Could you make one? >> >> Cheers, >> Magnus >> >> On 2020-03-19 18:01, Jochen Hub wrote: >>> Hi developers, >>> >>> I am running a simple DPPC membrane (Berger force field, PME, 1nm >>> cutoff, 4fs time step, all standard) with 2020.1 and >>> >>> comm-mode??????????????? = Linear >>> nstcomm????????????????? = 100 >>> comm-grps??????????????? = DPPC water? ; OR System >>> >>> but the membrane rapidly drifts along the z direction: approx. once >>> across the box per 100ps, and accelerating over time. >>> >>> This happens only with >>> >>> mdrun -update gpu -bonded gpu >>> >>> but not with >>> >>> mdrun -update gpu -bonded cpu?? (no spelling mistake) >>> >>> (with a GTX 1070Ti). >>> >>> Also no problems with 2018.6 or 2019.6. >>> >>> Seems like the center of mass motion removal is broken when doing >>> both *bonded and updating* on the GPU. Is this issue known? >>> >>> Cheers, >>> Jochen >>> >> > -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From sadafrani6 at gmail.com Mon Mar 23 21:23:51 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Mon, 23 Mar 2020 20:23:51 -0000 Subject: [gmx-users] Error in free energy calculation (Chris Neale) Message-ID: Dear Chris Thank you very much for giving your comprehensive information on my mdp options. In my current simulation, I am trying to switch off coulombic interactions while keeping VDW on. In gromacs manual, it is mentioned that with parallel simulations and/or non-bonded force calculation on the GPU, a value of 20 or 40 often gives the best performance so I chose nstlist as 20. however, I am not very much sure about the best value. Simulations from lambda window 11 to 20 complete very well without any lincs warning. I am getting following performance with the current selection of mdp:- Core t (s) Wall t (s) (%) Time: 630938.079 39433.648 1600.0 10h57:13 (ns/day) (hour/ns) Performance: 6.573 3.651 Finished mdrun on rank 0 Mon Mar 23 07:41:56 2020 I am running simulations from Lambda 0-1 in 21 different windows. For Lambda 9 I am getting the following error:- Step Time 1100000 2200.00000 Energies (kJ/mol) Bond Restraint Pot. Angle Proper Dih. Improper Dih. 6.18949e+03 2.44298e+00 1.68046e+04 2.06705e+04 9.49832e+02 LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 7.91681e+03 7.10046e+04 2.30248e+05 0.00000e+00 -2.05702e+06 Coul. recip. Angle Rest. Dih. Rest. Potential Kinetic En. 8.96080e+03 7.31848e-01 7.99950e-01 -1.69427e+06 3.28779e+05 Total Energy Temperature Pres. DC (bar) Pressure (bar) dVcoul/dl -1.36549e+06 3.00055e+02 -0.00000e+00 -1.54667e+01 2.05257e+03 dVvdw/dl dVrestraint/dl Constr. rmsd -3.75472e+02 3.97478e+00 3.30377e-06 ------------------------------------------------------- Program: gmx mdrun, version 2020-UNCHECKED Source file: src/gromacs/ewald/pme_redistribute.cpp (line 304) MPI rank: 5 (out of 16) Fatal error: 2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I have equilibrated the system well and pressure is as below:- Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 1.65391 0.58 81.606 -2.0618 (bar) How should I fix this error? Any suggestions for improvement will really help me. Many thanks. Sadaf From wes.p.michaels at gmail.com Tue Mar 24 08:09:53 2020 From: wes.p.michaels at gmail.com (Wesley Michaels) Date: Tue, 24 Mar 2020 07:09:53 -0000 Subject: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities In-Reply-To: References: Message-ID: Hi, Thanks for your reply! I built the topology with my own script, as opposed to using pdb2gmx. Following Bogdan's instructions here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html), I specified all instances of 1-4 pair interactions (i.e. pairs of atom indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] section (i.e. the interaction parameters for pairs of atom types) automatically using "gen_pairs" = "yes". As a second test, I generated a topology using pdb2gmx and the procedure Justin detailed here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html) (using the OPLS-AA FF option in pdb2gmx) and used that in a trial simulation. I experienced the same issue, unfortunately. Happy to provide any files as needed to help clarify the issue. Thanks, Wes On Mon, Mar 23, 2020 at 3:54 AM Alessandra Villa < alessandra.villa.biosim at gmail.com> wrote: > Hi > > On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels > wrote: > > > Hello, > > > > I hope this message finds you well! I'm running a pretty simple > simulation > > of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, > P = > > 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting > > large, unstable volume fluctuations when I use the combination of the > > Parrinello-Rahman barostat and pairtype = 1 for 1-4 pairs. I don't see > this > > behavior with {PR barostat and pairtype = 2} or {Berendsen barostat and > > pairtype = 1}. > > > > I've specified the 1-4 pairs explicitly in the "[ pairs ]" section and > set > > "gen_pairs" to "yes" in the defaults section. I'm sure I'm missing > > something obvious, but here are the troubleshooting steps I've tried: > > > > > Sorry I could not understand the reason behind the modification you did. > Standard OPLS-AA force field field has "gen_pairs" to "yes" in > forcefield.itp and calculate the 1-4 interaction by uniformly scaling the > parameters. > No modifications are needed in the [pairs] section of the topol.top for > standard simulations with OPLS-AA. Or do you want to do something else? > See > > http://manual.gromacs.org/current/reference-manual/topologies/molecule-definition.html?highlight=pair > > to understand if your setting is inline which the force field. > > Best regards > > Alessandra > > > 1) ensure the simulation is equilibrated (up to 100 nanoseconds with > > Berendsen barostat beforehand, which is more than plenty I believe); > > 2) use a smaller time step (down to 0.01 fs); > > 3) increase the pressure coupling time constant (up to 10 ps); > > 4) using both GROMACS 2018 and GROMACS 2019. > > > > As far as energies go, I don't think there are worryingly large terms > that > > would blow the simulation up. Here's an example prepared with `gmx > energy`: > > Time (ps) Bond G96Angle RB LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Total > > Energy Conserved En. Volume Density > > 0 3.10E+04 5.40E+04 2.29E+04 8.76E+03 -1.66E+03 -4.71E+03 5.27E+03 > 2.17E+05 > > 2.17E+05 291.0 400.8 > > 2 5.11E+04 5.71E+04 8.24E+03 5.48E+02 -3.00E+03 -3.68E+03 9.01E+03 > 2.12E+05 > > 1.02E+06 3720.8 31.3 > > 4 2.56E+03 9.53E+03 8.18E+03 4.80E+03 -4.16E+03 -4.27E+03 9.40E+03 > 1.19E+05 > > 1.25E+06 21855.1 5.3 > > 6 4.76E+03 1.48E+04 1.15E+04 5.36E+03 -3.71E+03 -4.02E+03 8.68E+03 > 1.31E+05 > > 1.52E+06 88422.7 1.3 > > 8 6.58E+03 2.07E+04 1.48E+04 6.13E+03 -3.27E+03 -4.02E+03 7.95E+03 > 1.44E+05 > > 1.80E+06 246764.8 0.5 > > 10 1.05E+04 2.80E+04 1.64E+04 6.46E+03 -3.03E+03 -3.98E+03 7.61E+03 > > 1.57E+05 > > 2.08E+06 538599.2 0.2 > > > > > > Eventually, the volume becomes unphysically large and the density > extremely > > low. I'm sure I'm missing something obvious here (sorry for yet another > "my > > simulation is blowing up" question), so any insight into other steps I > > could try would be greatly appreciated. If I can provide any additional > > information (e.g. topology/mdp files), just let me know. > > > > Thanks, > > Wes > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 xz41 at st-andrews.ac.uk Tue Mar 24 11:25:22 2020 From: xz41 at st-andrews.ac.uk (Xiaotong Zhang) Date: Tue, 24 Mar 2020 10:25:22 -0000 Subject: [gmx-users] Free energy change calculation Message-ID: Hi, Sorry to bother you. Recently, I have encountered a problem when running free energy calculation of a dna-ligand complex system. The structure start to getting weird when I try to specify the two state (A,B) in the topology file, which is never spotted in the unconstrained MD simulations. The version I am using is 4.6.7 and the force constant is 1000/nm/rad^2. Could you help me with that? Cheers Xiaotong Xiaotong Zhang PGR student xz41 at st-andrews.ac.uk School of Chemistry, University of St Andrews Purdie Building, North Haugh St Andrews, KY16 9ST From jalemkul at vt.edu Tue Mar 24 11:44:27 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 24 Mar 2020 10:44:27 -0000 Subject: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities In-Reply-To: References: Message-ID: On 3/24/20 3:09 AM, Wesley Michaels wrote: > Hi, > > Thanks for your reply! I built the topology with my own script, as opposed > to using pdb2gmx. Following Bogdan's instructions here ( > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html), > I specified all instances of 1-4 pair interactions (i.e. pairs of atom > indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] > section (i.e. the interaction parameters for pairs of atom types) > automatically using "gen_pairs" = "yes". > > As a second test, I generated a topology using pdb2gmx and the procedure > Justin detailed here ( > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html) > (using the OPLS-AA FF option in pdb2gmx) and used that in a trial > simulation. I experienced the same issue, unfortunately. Happy to provide > any files as needed to help clarify the issue. If pdb2gmx built the topology and you're using an unaltered forcefield.itp [defaults] directive, based on what you've said below, it appears to just be an equilibration issue. Use Berendsen for a while to get the system settled and then switch to Parrinello-Rahman. If you're still experiencing problems, full .mdp file(s) would be helpful. -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 Tue Mar 24 12:30:21 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Tue, 24 Mar 2020 11:30:21 -0000 Subject: [gmx-users] Lincs warning in free energy calculation Message-ID: Dear Gromacs users I ran an MD simulation for 3ns and from the last coordinates started a free energy calculation for 3ns. My system is well equilibrated but after 710725 steps I am getting Lincs warning every time as below:- WARNING: There are no atom pairs for dispersion correction starting mdrun 'GROtesk MACabre and Sinister in water' 1500000 steps, 3000.0 ps. Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000003, max 0.000023 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.8 0.1080 0.1080 0.1080 Step 710726, time 1421.45 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000003, max 0.000021 (between atoms 5470 and 5472) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 43.1 0.1080 0.1080 0.1080 I have added restraints between atoms of ligand and protein and getting Lincs warning between 1 atom included in restraints as below:- [ bonds ] ; i j type r0A r1A r2A fcA r0B r1B r2B fcB *3437* 7908 10 0.418 0.418 10.0 0.0 0.418 0.418 10.0 41840.00 [ angle_restraints ] ; ai aj ak al type thA fcA multA thB fcB multB 3437 7908 7906 7908 1 100.29 0.0 1 100.29 418.40 1 7908 3437 3439 *3437* 1 146.50 0.0 1 146.50 418.40 1 [ dihedral_restraints ] ; ai aj ak al type phiA dphiA fcA phiB dphiB fcB 7906 7908 *3437* 3439 1 156.16 0.0 0.0 156.16 0.0 418.40 7907 7906 7908 *3437* 1 -56.93 0.0 0.0 -56.93 0.0 418.40 7909 *3437* 3430 3435 1 131.32 0.0 0.0 131.32 0.0 418.40 Can anyone please suggest to me how Should I fix this error? Any help will be really appreciated. Thanks. Sadaf From tobias.kloeffel at fau.de Tue Mar 24 16:28:23 2020 From: tobias.kloeffel at fau.de (=?UTF-8?Q?Tobias_Kl=c3=b6ffel?=) Date: Tue, 24 Mar 2020 15:28:23 -0000 Subject: [gmx-users] Various questions related to Gromacs performance tuning Message-ID: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> Dear all, I am very new to Gromacs so maybe some of my problems are very easy to fix:) Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from: https://www.mpibpc.mpg.de/grubmueller/bench 1) OpenMP parallelization: Is it done via OpenMP tasks? If the Intel toolchain is detected and? -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working. Normal? execution via $MPIRUN gmx_mpi mdrun -s ... works 3) As far as I understood, most time of PME is spent in a 3d FFT and hence probably most time is spent in a mpi alltoall communication. For that reason I would like to place all PME tasks on a separate node via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying -ddorder interleave or cartesian works without problems. Is this a known issue? Kind regards, Tobias Kl?ffel -- M.Sc. Tobias Kl?ffel ======================================================= HPC (High Performance Computing) group Erlangen Regional Computing Center(RRZE) Friedrich-Alexander-Universit?t Erlangen-N?rnberg Martensstr. 1 91058 Erlangen Room: 1.133 Phone: +49 (0) 9131 / 85 - 20101 ======================================================= E-mail: tobias.kloeffel at fau.de From paul.bauer.q at gmail.com Tue Mar 24 17:40:16 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Tue, 24 Mar 2020 16:40:16 -0000 Subject: [gmx-users] GROMACS has switched to use Gitlab Message-ID: <10a15f01-43c8-a099-cf8b-f99af85d5340@gmail.com> Hello gmx users! I just finished the transition of our project database to use the Gitlab servers. This means that from now on issues should be reported using the issue tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of redmine.gromacs.org. The redmine and gerrit servers have been set be read only from now on, so that you can still access information there, but it wont be able to report new things there any more. Cheers Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From bauer at cbs.tu-darmstadt.de Tue Mar 24 20:32:50 2020 From: bauer at cbs.tu-darmstadt.de (Daniel Bauer) Date: Tue, 24 Mar 2020 19:32:50 -0000 Subject: [gmx-users] Conversion of improper angles from amber object file to gromacs Message-ID: <416dd056-dd3e-474d-7a95-231a5053f14b@cbs.tu-darmstadt.de> Hi, I? am trying to convert forcefield parameters of zwitterionic glycine from an amber object file format to gromacs .rtp (to use it with amber99sb, which lacks zwitterionic amino acids). The amber library file I plan to use can be found here: https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off This is what i have so far: [ZG] ?[ atoms ] ???? N??? N3????????? -0.408600???? 1 ??? H1??? H??????????? 0.300300???? 2 ??? H2??? H??????????? 0.300300???? 3 ??? H3??? H??????????? 0.300300???? 4 ??? CA??? CT????????? -0.026400???? 5 ?? HA1??? H1?????????? 0.073800???? 6 ?? HA2??? H1?????????? 0.073800???? 7 ???? C??? C??????????? 0.835500???? 8 ???? O??? O2????????? -0.724500???? 9 ?? OXT??? O2????????? -0.724500??? 10 ?[ bonds ] ???? N??? H1 ???? N??? H2 ???? N??? H3 ???? N??? CA ??? CA?? HA1 ??? CA?? HA2 ??? CA???? C ???? C???? O ???? C??? OXT However, I am unsure about the correct conversion of impropers. In the .off file format, those are based on the atom type, while gromacs expects them to be based on atom names. This leaves room for some ambiguity when the same atom type is used multiple types (i.e the COO or NH3 group). The improper parameter section of the .off file looks like this: !entry.zaa_improper.parm.torsions table? str type1? str type2? str type3? str type4? int type? dbl kp? int n? dbl p0? str desc ?"CT" "O2" "C" "O2" 1 10.500000 2 3.141594 "" ?"CT" "N" "C" "O" 1 10.500000 2 3.141594 "" Now, for the CT-O2-C-O2 improper, this would map to two possible combinations: ? [ impropers ] ? ;? atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn ???? CA??? O??? C???? OXT??? 180??????? 43.932??????????? 2 ???? CA??? OXT??? C???? O??? 180??????? 43.932??????????? 2 Are both entries required in the gromacs [ improper ] section or must I put only one of them? Thanks, Daniel -- Daniel Bauer, M.Sc. TU Darmstadt Computational Biology & Simulation Schnittspahnstr. 2 64287 Darmstadt bauer at cbs.tu-darmstadt.de From jalemkul at vt.edu Tue Mar 24 20:35:12 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Tue, 24 Mar 2020 19:35:12 -0000 Subject: [gmx-users] Conversion of improper angles from amber object file to gromacs In-Reply-To: <416dd056-dd3e-474d-7a95-231a5053f14b@cbs.tu-darmstadt.de> References: <416dd056-dd3e-474d-7a95-231a5053f14b@cbs.tu-darmstadt.de> Message-ID: <17d8af08-c16a-220f-6545-dff91fb143fc@vt.edu> On 3/24/20 3:26 PM, Daniel Bauer wrote: > Hi, > > I? am trying to convert forcefield parameters of zwitterionic glycine > from an amber object file format to gromacs .rtp (to use it with > amber99sb, which lacks zwitterionic amino acids). > > The amber library file I plan to use can be found here: > https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off > > This is what i have so far: > > [ZG] > ?[ atoms ] > ???? N??? N3????????? -0.408600???? 1 > ??? H1??? H??????????? 0.300300???? 2 > ??? H2??? H??????????? 0.300300???? 3 > ??? H3??? H??????????? 0.300300???? 4 > ??? CA??? CT????????? -0.026400???? 5 > ?? HA1??? H1?????????? 0.073800???? 6 > ?? HA2??? H1?????????? 0.073800???? 7 > ???? C??? C??????????? 0.835500???? 8 > ???? O??? O2????????? -0.724500???? 9 > ?? OXT??? O2????????? -0.724500??? 10 > ?[ bonds ] > ???? N??? H1 > ???? N??? H2 > ???? N??? H3 > ???? N??? CA > ??? CA?? HA1 > ??? CA?? HA2 > ??? CA???? C > ???? C???? O > ???? C??? OXT > > However, I am unsure about the correct conversion of impropers. In the > .off file format, those are based on the atom type, while gromacs > expects them to be based on atom names. This leaves room for some > ambiguity when the same atom type is used multiple types (i.e the COO or > NH3 group). > > The improper parameter section of the .off file looks like this: > > !entry.zaa_improper.parm.torsions table? str type1? str type2? str > type3? str type4? int type? dbl kp? int n? dbl p0? str desc > ?"CT" "O2" "C" "O2" 1 10.500000 2 3.141594 "" > ?"CT" "N" "C" "O" 1 10.500000 2 3.141594 "" > > Now, for the CT-O2-C-O2 improper, this would map to two possible > combinations: > > ? [ impropers ] > ? ;? atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn > ???? CA??? O??? C???? OXT??? 180??????? 43.932??????????? 2 > ???? CA??? OXT??? C???? O??? 180??????? 43.932??????????? 2 > > Are both entries required in the gromacs [ improper ] section or must I > put only one of them? You only need one, otherwise you end up with double the intended strength of the improper. -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 ckutzne at gwdg.de Tue Mar 24 21:03:35 2020 From: ckutzne at gwdg.de (Kutzner, Carsten) Date: Tue, 24 Mar 2020 20:03:35 -0000 Subject: [gmx-users] Various questions related to Gromacs performance tuning In-Reply-To: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> References: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> Message-ID: <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> Hi, > Am 24.03.2020 um 16:28 schrieb Tobias Kl?ffel : > > Dear all, > I am very new to Gromacs so maybe some of my problems are very easy to fix:) > Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from: > https://www.mpibpc.mpg.de/grubmueller/bench > > 1) OpenMP parallelization: Is it done via OpenMP tasks? Yes, all over the code loops are parallelized via OpenMP via #pragma omp parallel for and similar directives. > If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. GROMACS uses only the serial transposes - allowing mkl to open up its own OpenMP threads would lead to oversubscription of cores and performance degradation. > 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call gmx tune_pme. Most queueing systems don't like it if one parallel program calls another parallel program. > tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working. There should be an output somewhere with the exact command line that tune_pme invoked to test whether mdrun works. That should shed some light on the issue. Side note: Tuning is normally only useful on CPU-nodes. If your nodes also have GPUs, you will probably not want to do this kind of PME tuning. > Normal execution via $MPIRUN gmx_mpi mdrun -s ... works > > > 3) As far as I understood, most time of PME is spent in a 3d FFT and hence probably most time is spent in a mpi alltoall communication. Yes, but that also depends a lot on the number of nodes you are running on. Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number of nodes that you are interested and check the detailed timings at the end of the log file. There you will find how much time is spent in various PME routines. Best, Carsten > For that reason I would like to place all PME tasks on a separate node via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying -ddorder interleave or cartesian works without problems. Is this a known issue? > > Kind regards, > Tobias Kl?ffel > > -- > M.Sc. Tobias Kl?ffel > ======================================================= > HPC (High Performance Computing) group > Erlangen Regional Computing Center(RRZE) > Friedrich-Alexander-Universit?t Erlangen-N?rnberg > Martensstr. 1 > 91058 Erlangen > > Room: 1.133 > Phone: +49 (0) 9131 / 85 - 20101 > > ======================================================= > > E-mail: tobias.kloeffel at fau.de > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa From mark.j.abraham at gmail.com Tue Mar 24 21:59:16 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Tue, 24 Mar 2020 20:59:16 -0000 Subject: [gmx-users] Various questions related to Gromacs performance tuning In-Reply-To: <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> References: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> Message-ID: Hi, There could certainly be a bug with -ddorder pp_pme, as there's no testing done of that. If you can reproduce with a recent version of GROMACS, please do file a bug report. (Though this week we're moving to new infrastructure, so leave it for a day or two before trying to report it! Mark On Tue, 24 Mar 2020 at 21:03, Kutzner, Carsten wrote: > Hi, > > > Am 24.03.2020 um 16:28 schrieb Tobias Kl?ffel : > > > > Dear all, > > I am very new to Gromacs so maybe some of my problems are very easy to > fix:) > > Currently I am trying to compile and benchmark gromacs on AMD rome cpus, > the benchmarks are taken from: > > https://www.mpibpc.mpg.de/grubmueller/bench > > > > 1) OpenMP parallelization: Is it done via OpenMP tasks? > Yes, all over the code loops are parallelized via OpenMP via #pragma omp > parallel for > and similar directives. > > > If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is > set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. > GROMACS uses only the serial transposes - allowing mkl to open up its own > OpenMP threads > would lead to oversubscription of cores and performance degradation. > > > 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do > not really understand what I have to specify for -mdrun. I > Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can > call > gmx tune_pme. Most queueing systems don't like it if one parallel program > calls > another parallel program. > > > tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun > -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS > --report-bindings" But it just complains that mdrun is not working. > There should be an output somewhere with the exact command line that > tune_pme invoked to test whether mdrun works. That should shed some light > on the issue. > > Side note: Tuning is normally only useful on CPU-nodes. If your nodes also > have GPUs, you will probably not want to do this kind of PME tuning. > > > Normal execution via $MPIRUN gmx_mpi mdrun -s ... works > > > > > > 3) As far as I understood, most time of PME is spent in a 3d FFT and > hence probably most time is spent in a mpi alltoall communication. > Yes, but that also depends a lot on the number of nodes you are running on. > Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number > of > nodes that you are interested and check the detailed timings at the end of > the log file. There you will find how much time is spent in various PME > routines. > > Best, > Carsten > > > For that reason I would like to place all PME tasks on a separate node > via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying > -ddorder interleave or cartesian works without problems. Is this a known > issue? > > > > Kind regards, > > Tobias Kl?ffel > > > > -- > > M.Sc. Tobias Kl?ffel > > ======================================================= > > HPC (High Performance Computing) group > > Erlangen Regional Computing Center(RRZE) > > Friedrich-Alexander-Universit?t Erlangen-N?rnberg > > Martensstr. 1 > > 91058 Erlangen > > > > Room: 1.133 > > Phone: +49 (0) 9131 / 85 - 20101 > > > > ======================================================= > > > > E-mail: tobias.kloeffel at fau.de > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From nicolas.rozas at ug.uchile.cl Tue Mar 24 23:54:44 2020 From: nicolas.rozas at ug.uchile.cl (=?UTF-8?Q?Nicol=C3=A1s_Marcelo_Rozas_Castro?=) Date: Tue, 24 Mar 2020 22:54:44 -0000 Subject: [gmx-users] Drude polarization, practical matters Message-ID: Hi everyone, I'll be straight, my questions are: 1. It is possible to use Drude model in GROMACS 5.1.5? 2. How exactly this is done? If someone had an input file example (pdb and/or itp) and can share it i'll appreciate. Thank a lot!! Nicolas Rozas Castro Universidad de Chile From afsane_farhadi at yahoo.com Wed Mar 25 00:58:17 2020 From: afsane_farhadi at yahoo.com (Afsane Farhadi) Date: Tue, 24 Mar 2020 23:58:17 -0000 Subject: [gmx-users] topology of co2 References: <1284100678.1010649.1585094284848.ref@mail.yahoo.com> Message-ID: <1284100678.1010649.1585094284848@mail.yahoo.com> hi allI want to download a topology of co2 ?by opls as forcefield, ?but many servers doesn't answer(like ligpargen and tppmktop). how can I find a topology for this molecule? Sent from Yahoo Mail on Android From neena.susaneappen at mail.utoronto.ca Wed Mar 25 04:17:10 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Wed, 25 Mar 2020 03:17:10 -0000 Subject: [gmx-users] No default bond types Message-ID: Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From b.mijiddorj at gmail.com Wed Mar 25 09:33:18 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Wed, 25 Mar 2020 08:33:18 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations Message-ID: Dear GMX users, I would like to extract the temperatures for specific groups during the simulations. gmx energy gives the system temperature as a function of time. I also tried to get the temperature of a specific group using gmx traj. However, the data of gmx traj much lower values of the system temperatures for any groups in the systems. I also tried to extract GROUP.tpr and GROUP.trr files from original data. Then, I performed rerun for the group. However, these data is more lower than that the data of gmx traj. I have two questions if possible please advise me. 1. Is it possible to make correction for the data of gmx traj? 2. Are there any other methods for this purpose? Best regards, Mijiddorj From harry.greenblatt at weizmann.ac.il Wed Mar 25 11:46:02 2020 From: harry.greenblatt at weizmann.ac.il (Harry Mark Greenblatt) Date: Wed, 25 Mar 2020 10:46:02 -0000 Subject: [gmx-users] compile with intel compiler Message-ID: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> BS?D Dear All, I would like to compile Gromacs 2020 with an intel compiler; I set the following: -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include Despite the fact that I have told it to use the Intel C++ compile is (which it finds), it still looks and finds the system g++, which, of course is quite old. If I have given it the name of a C++ compiler, why is it looking for g++? Thanks 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 marko at kth.se Wed Mar 25 13:10:45 2020 From: marko at kth.se (Marko Petrovic) Date: Wed, 25 Mar 2020 12:10:45 -0000 Subject: [gmx-users] Calculate dihedrals Message-ID: <6C274EDB-6A97-47C4-8111-B21375D9D9F6@kth.se> Hello I want to calculate som singular dihedral values and I know this is simple, but can't figure out the usage of "gmx gangle" . I tried using "gmx angle" but the results were not what I was hoping for as it calculates an average of the specified angles and seems to be meant for averaging many angles calculations. Using the .gro and .ndx files from my call to "gmx angle" gmx angle -f start.gro -n test.ndx -type dihedral to a all to "gmx gangle" gmx gangle -g1 dihedral -f start.gro -n test.ndx this starts a dialogue where I initially tried selecting groups defined in the .ndx file, no error message suggests I've been successful. Pressing ctrl+d ends the run with the following message: > Reading frames from gro file 'GROningen Mixture of Alchemy and Childrens' Stories', 22 atoms. Last frame 0 time 0.000 Analyzed 1 frames, last time 0.000 But I can't find any output anywhere. What am I missing? With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From alessandra.villa.biosim at gmail.com Wed Mar 25 13:40:25 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 25 Mar 2020 12:40:25 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations In-Reply-To: References: Message-ID: HI, On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B wrote: > Dear GMX users, > > I would like to extract the temperatures for specific groups during the > simulations. gmx energy gives the system temperature as a function of time. > I also tried to get the temperature of a specific group using gmx traj. > However, the data of gmx traj much lower values of the system temperatures > for any groups in the systems. I also tried to extract GROUP.tpr and > GROUP.trr files from original data. Then, I performed rerun for the group. > However, these data is more lower than that the data of gmx traj. > > I have two questions if possible please advise me. > 1. Is it possible to make correction for the data of gmx traj? 2. Are there any other methods for this purpose? > > The values you get by gmx traj are calculated on the number of frames that you have saved in trj file (assuming that you have saved velocities in your trajectory file). If you have saved with different frequency the energy and trj files, you may get different temperature values since you are calculated the temperature on different set of data. When you performed a rerun, you have to be sure that you save every step (that you have in your original trajectory) in the new generated energy file. Otherwise also here you will end up to calculate the temperature on a different set of data. Accounting for these points, you should get comparable results with the different approaches. Best regards Alessandra > 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 alessandra.villa.biosim at gmail.com Wed Mar 25 13:40:27 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 25 Mar 2020 12:40:27 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations In-Reply-To: References: Message-ID: HI, On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B wrote: > Dear GMX users, > > I would like to extract the temperatures for specific groups during the > simulations. gmx energy gives the system temperature as a function of time. > I also tried to get the temperature of a specific group using gmx traj. > However, the data of gmx traj much lower values of the system temperatures > for any groups in the systems. I also tried to extract GROUP.tpr and > GROUP.trr files from original data. Then, I performed rerun for the group. > However, these data is more lower than that the data of gmx traj. > > I have two questions if possible please advise me. > 1. Is it possible to make correction for the data of gmx traj? 2. Are there any other methods for this purpose? > > The values you get by gmx traj are calculated on the number of frames that you have saved in trj file (assuming that you have saved velocities in your trajectory file). If you have saved with different frequency the energy and trj files, you may get different temperature values since you are calculated the temperature on different set of data. When you performed a rerun, you have to be sure that you save every step (that you have in your original trajectory) in the new generated energy file. Otherwise also here you will end up to calculate the temperature on a different set of data. Accounting for these points, you should get comparable results with the different approaches. Best regards Alessandra > 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 alessandra.villa.biosim at gmail.com Wed Mar 25 13:43:17 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 25 Mar 2020 12:43:17 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: Hi, On Wed, Mar 25, 2020 at 4:17 AM Neena Susan Eappen < neena.susaneappen at mail.utoronto.ca> wrote: > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond > types and 9 new angle types. Which force field files have you modified? It looks that you did not modify all the necessary files. Best regards Alessandra > However, the command grompp gave a no default error for one bond and 6 > angle types. Is there a way to resolve this? > > Many thanks and Take care, > 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 jalemkul at vt.edu Wed Mar 25 13:44:07 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 25 Mar 2020 12:44:07 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations In-Reply-To: References: Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d19a@vt.edu> On 3/25/20 8:40 AM, Alessandra Villa wrote: > HI, > > On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B wrote: > >> Dear GMX users, >> >> I would like to extract the temperatures for specific groups during the >> simulations. gmx energy gives the system temperature as a function of time. >> I also tried to get the temperature of a specific group using gmx traj. >> However, the data of gmx traj much lower values of the system temperatures >> for any groups in the systems. I also tried to extract GROUP.tpr and >> GROUP.trr files from original data. Then, I performed rerun for the group. >> However, these data is more lower than that the data of gmx traj. >> >> I have two questions if possible please advise me. >> 1. Is it possible to make correction for the data of gmx traj? > 2. Are there any other methods for this purpose? >> > The values you get by gmx traj are calculated on the number of frames that > you have saved in trj file (assuming that you have saved velocities in your > trajectory file). If you have saved with different frequency the energy and > trj files, you may get different temperature values since you are > calculated the temperature on different set of data. > When you performed a rerun, you have to be sure that you save every step > (that you have in your original trajectory) in the new generated energy > file. Otherwise also here you will end up to calculate the temperature on a > different set of data. > > Accounting for these points, you should get comparable results with the > different approaches. The saving interval will only account for a very small difference, one that will likely be within the error estimate. The biggest difference in the outputs of gmx energy and gmx traj is that gmx traj has no knowledge of constraints, so it computes degrees of freedom incorrectly. One can recover the proper temperature by scaling the output of gmx traj after computing the correct number of (unconstrained) degrees of freedom. -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 Wed Mar 25 13:53:47 2020 From: alessandra.villa.biosim at gmail.com (Alessandra Villa) Date: Wed, 25 Mar 2020 12:53:47 -0000 Subject: [gmx-users] Calculate dihedrals In-Reply-To: <6C274EDB-6A97-47C4-8111-B21375D9D9F6@kth.se> References: <6C274EDB-6A97-47C4-8111-B21375D9D9F6@kth.se> Message-ID: Hi, On Wed, Mar 25, 2020 at 1:10 PM Marko Petrovic wrote: > Hello > > I want to calculate som singular dihedral values and I know this is > simple, but can't figure out the usage of "gmx gangle" . I tried using "gmx > angle" but the results were not what I was hoping for as it calculates an > average of the specified angles and seems to be meant for averaging many > angles calculations. > You can use gmx angle with the -all option. With the option -all the first graph is the average and the rest are the individual angles. Or in alternative use an index file with 1 dihedral angle http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-angle.html?highlight=gmx%20angle > Using the .gro and .ndx files from my call to "gmx angle" > > gmx angle -f start.gro -n test.ndx -type dihedral > > to a all to "gmx gangle" > > gmx gangle -g1 dihedral -f start.gro -n test.ndx > > You could try to add the option -group1 selection http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-gangle.html?highlight=gmx%20gangle Best regards Alessandra > this starts a dialogue where I initially tried selecting groups defined in > the .ndx file, no error message suggests I've been successful. Pressing > ctrl+d ends the run with the following message: > > > Reading frames from gro file 'GROningen Mixture of Alchemy and > Childrens' Stories', 22 atoms. > Last frame 0 time 0.000 > Analyzed 1 frames, last time 0.000 > > But I can't find any output anywhere. What am I missing? > > > With Regards > Marko Petrovic > Educator > Computational Science and Technology > School of Electrical Engineering and Computer Science > KTH Royal Institute of Technology > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Mar 25 16:40:17 2020 From: b.mijiddorj at gmail.com (Mijiddorj B) Date: Wed, 25 Mar 2020 15:40:17 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations In-Reply-To: References: Message-ID: Dear Justin and Alessandra, Thank you very much for your prompt response. I saved both velocity and energy data in every 1 ps. > ------------------------------ > > Message: 5 > Date: Wed, 25 Mar 2020 08:43:46 -0400 > From: Justin Lemkul > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] Extracting temperature of specific groups > during the simulations > Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d19a at vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 3/25/20 8:40 AM, Alessandra Villa wrote: > > HI, > > > > On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B > wrote: > > > >> Dear GMX users, > >> > >> I would like to extract the temperatures for specific groups during the > >> simulations. gmx energy gives the system temperature as a function of > time. > >> I also tried to get the temperature of a specific group using gmx traj. > >> However, the data of gmx traj much lower values of the system > temperatures > >> for any groups in the systems. I also tried to extract GROUP.tpr and > >> GROUP.trr files from original data. Then, I performed rerun for the > group. > >> However, these data is more lower than that the data of gmx traj. > >> > >> I have two questions if possible please advise me. > >> 1. Is it possible to make correction for the data of gmx traj? > > 2. Are there any other methods for this purpose? > >> > > The values you get by gmx traj are calculated on the number of frames > that > > you have saved in trj file (assuming that you have saved velocities in > your > > trajectory file). If you have saved with different frequency the energy > and > > trj files, you may get different temperature values since you are > > calculated the temperature on different set of data. > > When you performed a rerun, you have to be sure that you save every step > > (that you have in your original trajectory) in the new generated energy > > file. Otherwise also here you will end up to calculate the temperature > on a > > different set of data. > > > > Accounting for these points, you should get comparable results with the > > different approaches. > > The saving interval will only account for a very small difference, one > that will likely be within the error estimate. The biggest difference in > the outputs of gmx energy and gmx traj is that gmx traj has no knowledge > of constraints, so it computes degrees of freedom incorrectly. One can > recover the proper temperature by scaling the output of gmx traj after > computing the correct number of (unconstrained) degrees of freedom. > Thank you again. I am sorry for further asking. Can you briefly guide me to compute the correct degrees of freedom? How can I scaling the output? Best regards, Mijiddorj > -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. > > End of gromacs.org_gmx-users Digest, Vol 191, Issue 59 > ****************************************************** > From rollyng at gmail.com Wed Mar 25 17:52:38 2020 From: rollyng at gmail.com (Rolly Ng) Date: Wed, 25 Mar 2020 16:52:38 -0000 Subject: [gmx-users] How to reduce the penalty of small molecule from CGenFF Message-ID: <00a401d602c5$c6ff6ed0$54fe4c70$@gmail.com> Dear Gromacs Users, I am new to Gromacs and I followed the Protein-Ligand tutorial on the following webpage, http://www.mdtutorials.com/gmx/complex/02_topology.html It works for the example JZ4 but as I changed to another molecule, the str file produced by the CGenFF server states very high penalty 84.5 Please have a look at my mol2 input and str output below. Your advises are much appreciated! Thank you, Rolly @MOLECULE MF8 20 19 0 0 0 SMALL GASTEIGER @ATOM 1 N08 19.3800 -17.4900 12.2190 N.pl3 1 MF8 -0.2888 2 C07 19.5160 -18.4740 11.4320 C.cat 1 MF8 0.3855 3 N06 20.0120 -18.2750 10.1980 N.pl3 1 MF8 -0.1861 4 N09 19.1990 -19.7060 11.8570 N.pl3 1 MF8 -0.1293 5 C01 18.6460 -20.7310 8.7020 C.3 1 MF8 0.0558 6 N02 19.3290 -19.4990 8.3110 N.pl3 1 MF8 -0.2675 7 N05 18.6660 -17.3520 8.6680 N.pl3 1 MF8 -0.1291 8 C04 19.3130 -18.3670 9.0550 C.cat 1 MF8 0.3896 9 C03 20.0370 -19.6170 7.0360 C.3 1 MF8 0.0558 10 H 19.6101 -16.5820 11.9161 H 1 MF8 0.2547 11 H 19.0443 -17.6336 13.1333 H 1 MF8 0.2547 12 H 20.9660 -18.0428 10.1266 H 1 MF8 0.2707 13 H 19.3013 -20.4766 11.2529 H 1 MF8 0.3062 14 H 18.8055 -21.4799 7.9546 H 1 MF8 0.0619 15 H 17.5973 -20.5420 8.7994 H 1 MF8 0.0619 16 H 19.0353 -21.0729 9.6382 H 1 MF8 0.0619 17 H 18.1443 -17.3894 7.8339 H 1 MF8 0.3062 18 H 19.9010 -20.6026 6.6424 H 1 MF8 0.0619 19 H 21.0802 -19.4349 7.1891 H 1 MF8 0.0619 20 H 19.6476 -18.8997 6.3441 H 1 MF8 0.0619 @BOND 1 1 2 1 2 1 10 1 3 1 11 1 4 2 3 1 5 2 4 2 6 3 8 1 7 3 12 1 8 4 13 1 9 5 6 1 10 5 14 1 11 5 15 1 12 5 16 1 13 6 9 1 14 6 8 1 15 7 8 2 16 7 17 1 17 9 18 1 18 9 19 1 19 9 20 1 * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 1.0.0 * For use with CGenFF version 3.0.1 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 1.0.0 * 36 1 ! "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. RESI MF8 0.000 ! param penalty= 84.500 ; charge penalty= 12.315 GROUP ! CHARGE CH_PENALTY ATOM N08 NG321 -0.603 ! 2.500 ATOM C07 CG2N1 0.547 ! 5.000 ATOM N06 NG311 -0.430 ! 6.533 ATOM N09 NG2D1 -0.907 ! 2.500 ATOM C01 CG331 -0.141 ! 9.593 ATOM N02 NG301 -0.371 ! 12.315 ATOM N05 NG2D1 -0.861 ! 4.101 ATOM C04 CG2N1 0.609 ! 10.954 ATOM C03 CG331 -0.141 ! 9.593 ATOM H1 HGPAM2 0.330 ! 0.000 ATOM H2 HGPAM2 0.330 ! 0.000 ATOM H3 HGPAM1 0.360 ! 0.090 ATOM H4 HGP1 0.369 ! 0.000 ATOM H5 HGA3 0.090 ! 2.518 ATOM H6 HGA3 0.090 ! 2.518 ATOM H7 HGA3 0.090 ! 2.518 ATOM H8 HGP1 0.369 ! 0.030 ATOM H9 HGA3 0.090 ! 2.518 ATOM H10 HGA3 0.090 ! 2.518 ATOM H11 HGA3 0.090 ! 2.518 BOND N08 C07 BOND N08 H1 BOND N08 H2 BOND C07 N06 BOND C07 N09 BOND N06 C04 BOND N06 H3 BOND N09 H4 BOND C01 N02 BOND C01 H5 BOND C01 H6 BOND C01 H7 BOND N02 C03 BOND N02 C04 BOND N05 C04 BOND N05 H8 BOND C03 H9 BOND C03 H10 BOND C03 H11 IMPR C07 N09 N06 N08 IMPR C04 N05 N02 N06 END read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 1.0.0 * ! 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. BONDS CG2N1 NG301 500.00 1.4400 ! MF8 , from CG2N1 NG311, penalty= 5 CG331 NG301 255.00 1.4630 ! MF8 , from CG331 NG311, penalty= 5 ANGLES NG2D1 CG2N1 NG301 50.00 125.00 ! MF8 , from NG2D1 CG2N1 NG311, penalty= 0.6 NG301 CG2N1 NG311 50.00 113.00 ! MF8 , from NG311 CG2N1 NG321, penalty= 1.8 NG301 CG331 HGA3 30.50 109.70 50.00 2.14000 ! MF8 , from NG311 CG331 HGA3, penalty= 0.6 CG2N1 NG301 CG331 43.00 106.00 ! MF8 , from CG2N1 NG311 CG331, penalty= 5 CG331 NG301 CG331 53.00 110.90 ! MF8 , from CG3AM0 NG301 CG3AM0, penalty= 36.6 CG2N1 NG311 CG2N1 40.00 109.00 ! MF8 , from CG2R61 NG311 CG2R61, penalty= 46 DIHEDRALS NG301 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MF8 , from NG311 CG2N1 NG2D1 HGP1, penalty= 0.6 NG2D1 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1 NG311 CG331, penalty= 5 NG311 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 NG311 CG331, penalty= 6.2 NG2D1 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1 NG311 CG331, penalty= 69.9 NG301 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 NG311 CG331, penalty= 71.7 NG301 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MF8 , from NG321 CG2N1 NG311 HGPAM1, penalty= 1.8 NG321 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 NG311 CG331, penalty= 69.9 HGA3 CG331 NG301 CG2N1 0.0000 3 180.00 ! MF8 , from HGA3 CG331 NG311 CG2N1, penalty= 5 HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! MF8 , from HGA2 CG321 NG311 CG2R61, penalty= 84.5 IMPROPERS CG2N1 NG2D1 NG301 NG311 85.0000 0 0.00 ! MF8 , from CG2N1 NG2D1 NG311 NG321, penalty= 1.5 END RETURN From jalemkul at vt.edu Wed Mar 25 18:30:54 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 25 Mar 2020 17:30:54 -0000 Subject: [gmx-users] Extracting temperature of specific groups during the simulations In-Reply-To: References: Message-ID: <74ab9246-a18e-3b68-0ca9-af4a3ae807d7@vt.edu> On 3/25/20 11:40 AM, Mijiddorj B wrote: > Dear Justin and Alessandra, > > Thank you very much for your prompt response. I saved both velocity and > energy data in every 1 ps. > > > > >> ------------------------------ >> >> Message: 5 >> Date: Wed, 25 Mar 2020 08:43:46 -0400 >> From: Justin Lemkul >> To: gmx-users at gromacs.org >> Subject: Re: [gmx-users] Extracting temperature of specific groups >> during the simulations >> Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d19a at vt.edu> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> >> >> On 3/25/20 8:40 AM, Alessandra Villa wrote: >>> HI, >>> >>> On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B >> wrote: >>>> Dear GMX users, >>>> >>>> I would like to extract the temperatures for specific groups during the >>>> simulations. gmx energy gives the system temperature as a function of >> time. >>>> I also tried to get the temperature of a specific group using gmx traj. >>>> However, the data of gmx traj much lower values of the system >> temperatures >>>> for any groups in the systems. I also tried to extract GROUP.tpr and >>>> GROUP.trr files from original data. Then, I performed rerun for the >> group. >>>> However, these data is more lower than that the data of gmx traj. >>>> >>>> I have two questions if possible please advise me. >>>> 1. Is it possible to make correction for the data of gmx traj? >>> 2. Are there any other methods for this purpose? >>> The values you get by gmx traj are calculated on the number of frames >> that >>> you have saved in trj file (assuming that you have saved velocities in >> your >>> trajectory file). If you have saved with different frequency the energy >> and >>> trj files, you may get different temperature values since you are >>> calculated the temperature on different set of data. >>> When you performed a rerun, you have to be sure that you save every step >>> (that you have in your original trajectory) in the new generated energy >>> file. Otherwise also here you will end up to calculate the temperature >> on a >>> different set of data. >>> >>> Accounting for these points, you should get comparable results with the >>> different approaches. >> The saving interval will only account for a very small difference, one >> that will likely be within the error estimate. The biggest difference in >> the outputs of gmx energy and gmx traj is that gmx traj has no knowledge >> of constraints, so it computes degrees of freedom incorrectly. One can >> recover the proper temperature by scaling the output of gmx traj after >> computing the correct number of (unconstrained) degrees of freedom. > > Thank you again. I am sorry for further asking. > Can you briefly guide me to compute the correct degrees of freedom? How can > I scaling the output? Google is your friend... https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090607.html -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From leandro.obt at gmail.com Wed Mar 25 19:34:38 2020 From: leandro.obt at gmail.com (Leandro Bortot) Date: Wed, 25 Mar 2020 18:34:38 -0000 Subject: [gmx-users] gpu_id for more than 10 GPUs? Message-ID: Dear all, I'm running some benchmarks on a shared machine which has 16 GPUs in a single "node". I can specify which GPUs to use with gmx mdrun -gpu_id XYZ. However, the format of XYZ is a string in which each char is a GPU ID. I can't find a way to specify, e.g, GPU #15 because -gpu_id 15 is interpreted as GPUs 1 and 5. Is there a way around this? Thank you for your attention, Leandro ------- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational Biology Brazilian Biosciences National Laboratory (LNBio) Brazilian Center for Research in Energy and Materials (CNPEM) Zip Code 13083-970, Campinas, S?o Paulo, Brazil. From jalemkul at vt.edu Wed Mar 25 19:37:57 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 25 Mar 2020 18:37:57 -0000 Subject: [gmx-users] How to reduce the penalty of small molecule from CGenFF In-Reply-To: <00a401d602c5$c6ff6ed0$54fe4c70$@gmail.com> References: <00a401d602c5$c6ff6ed0$54fe4c70$@gmail.com> Message-ID: On 3/25/20 12:52 PM, Rolly Ng wrote: > Dear Gromacs Users, > > > > I am new to Gromacs and I followed the Protein-Ligand tutorial on the > following webpage, > > http://www.mdtutorials.com/gmx/complex/02_topology.html > > > > It works for the example JZ4 but as I changed to another molecule, the str > file produced by the CGenFF server states very high penalty 84.5 > > > > Please have a look at my mol2 input and str output below. Your advises are > much appreciated! > > Have you read the CGenFF papers? The original 2010 JCC article is basically a tutorial and review of the parametrization theory. -Justin > > Thank you, > > Rolly > > > > @MOLECULE > > MF8 > > 20 19 0 0 0 > > SMALL > > GASTEIGER > > > > @ATOM > > 1 N08 19.3800 -17.4900 12.2190 N.pl3 1 MF8 -0.2888 > > 2 C07 19.5160 -18.4740 11.4320 C.cat 1 MF8 0.3855 > > 3 N06 20.0120 -18.2750 10.1980 N.pl3 1 MF8 -0.1861 > > 4 N09 19.1990 -19.7060 11.8570 N.pl3 1 MF8 -0.1293 > > 5 C01 18.6460 -20.7310 8.7020 C.3 1 MF8 0.0558 > > 6 N02 19.3290 -19.4990 8.3110 N.pl3 1 MF8 -0.2675 > > 7 N05 18.6660 -17.3520 8.6680 N.pl3 1 MF8 -0.1291 > > 8 C04 19.3130 -18.3670 9.0550 C.cat 1 MF8 0.3896 > > 9 C03 20.0370 -19.6170 7.0360 C.3 1 MF8 0.0558 > > 10 H 19.6101 -16.5820 11.9161 H 1 MF8 0.2547 > > 11 H 19.0443 -17.6336 13.1333 H 1 MF8 0.2547 > > 12 H 20.9660 -18.0428 10.1266 H 1 MF8 0.2707 > > 13 H 19.3013 -20.4766 11.2529 H 1 MF8 0.3062 > > 14 H 18.8055 -21.4799 7.9546 H 1 MF8 0.0619 > > 15 H 17.5973 -20.5420 8.7994 H 1 MF8 0.0619 > > 16 H 19.0353 -21.0729 9.6382 H 1 MF8 0.0619 > > 17 H 18.1443 -17.3894 7.8339 H 1 MF8 0.3062 > > 18 H 19.9010 -20.6026 6.6424 H 1 MF8 0.0619 > > 19 H 21.0802 -19.4349 7.1891 H 1 MF8 0.0619 > > 20 H 19.6476 -18.8997 6.3441 H 1 MF8 0.0619 > > @BOND > > 1 1 2 1 > > 2 1 10 1 > > 3 1 11 1 > > 4 2 3 1 > > 5 2 4 2 > > 6 3 8 1 > > 7 3 12 1 > > 8 4 13 1 > > 9 5 6 1 > > 10 5 14 1 > > 11 5 15 1 > > 12 5 16 1 > > 13 6 9 1 > > 14 6 8 1 > > 15 7 8 2 > > 16 7 17 1 > > 17 9 18 1 > > 18 9 19 1 > > 19 9 20 1 > > > > > > * Toppar stream file generated by > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > * For use with CGenFF version 3.0.1 > > * > > > > read rtf card append > > * Topologies generated by > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > * > > 36 1 > > > > ! "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. > > > > RESI MF8 0.000 ! param penalty= 84.500 ; charge penalty= 12.315 > > GROUP ! CHARGE CH_PENALTY > > ATOM N08 NG321 -0.603 ! 2.500 > > ATOM C07 CG2N1 0.547 ! 5.000 > > ATOM N06 NG311 -0.430 ! 6.533 > > ATOM N09 NG2D1 -0.907 ! 2.500 > > ATOM C01 CG331 -0.141 ! 9.593 > > ATOM N02 NG301 -0.371 ! 12.315 > > ATOM N05 NG2D1 -0.861 ! 4.101 > > ATOM C04 CG2N1 0.609 ! 10.954 > > ATOM C03 CG331 -0.141 ! 9.593 > > ATOM H1 HGPAM2 0.330 ! 0.000 > > ATOM H2 HGPAM2 0.330 ! 0.000 > > ATOM H3 HGPAM1 0.360 ! 0.090 > > ATOM H4 HGP1 0.369 ! 0.000 > > ATOM H5 HGA3 0.090 ! 2.518 > > ATOM H6 HGA3 0.090 ! 2.518 > > ATOM H7 HGA3 0.090 ! 2.518 > > ATOM H8 HGP1 0.369 ! 0.030 > > ATOM H9 HGA3 0.090 ! 2.518 > > ATOM H10 HGA3 0.090 ! 2.518 > > ATOM H11 HGA3 0.090 ! 2.518 > > > > BOND N08 C07 > > BOND N08 H1 > > BOND N08 H2 > > BOND C07 N06 > > BOND C07 N09 > > BOND N06 C04 > > BOND N06 H3 > > BOND N09 H4 > > BOND C01 N02 > > BOND C01 H5 > > BOND C01 H6 > > BOND C01 H7 > > BOND N02 C03 > > BOND N02 C04 > > BOND N05 C04 > > BOND N05 H8 > > BOND C03 H9 > > BOND C03 H10 > > BOND C03 H11 > > IMPR C07 N09 N06 N08 > > IMPR C04 N05 N02 N06 > > > > END > > > > read param card flex append > > * Parameters generated by analogy by > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > * > > > > ! 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. > > > > BONDS > > CG2N1 NG301 500.00 1.4400 ! MF8 , from CG2N1 NG311, penalty= 5 > > CG331 NG301 255.00 1.4630 ! MF8 , from CG331 NG311, penalty= 5 > > > > ANGLES > > NG2D1 CG2N1 NG301 50.00 125.00 ! MF8 , from NG2D1 CG2N1 NG311, > penalty= 0.6 > > NG301 CG2N1 NG311 50.00 113.00 ! MF8 , from NG311 CG2N1 NG321, > penalty= 1.8 > > NG301 CG331 HGA3 30.50 109.70 50.00 2.14000 ! MF8 , from NG311 > CG331 HGA3, penalty= 0.6 > > CG2N1 NG301 CG331 43.00 106.00 ! MF8 , from CG2N1 NG311 CG331, > penalty= 5 > > CG331 NG301 CG331 53.00 110.90 ! MF8 , from CG3AM0 NG301 CG3AM0, > penalty= 36.6 > > CG2N1 NG311 CG2N1 40.00 109.00 ! MF8 , from CG2R61 NG311 CG2R61, > penalty= 46 > > > > DIHEDRALS > > NG301 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MF8 , from NG311 CG2N1 > NG2D1 HGP1, penalty= 0.6 > > NG2D1 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1 > NG311 CG331, penalty= 5 > > NG311 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 > NG311 CG331, penalty= 6.2 > > NG2D1 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG2D1 CG2N1 > NG311 CG331, penalty= 69.9 > > NG301 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 > NG311 CG331, penalty= 71.7 > > NG301 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MF8 , from NG321 CG2N1 > NG311 HGPAM1, penalty= 1.8 > > NG321 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 CG2N1 > NG311 CG331, penalty= 69.9 > > HGA3 CG331 NG301 CG2N1 0.0000 3 180.00 ! MF8 , from HGA3 CG331 > NG311 CG2N1, penalty= 5 > > HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! MF8 , from HGA2 CG321 > NG311 CG2R61, penalty= 84.5 > > > > IMPROPERS > > CG2N1 NG2D1 NG301 NG311 85.0000 0 0.00 ! MF8 , from CG2N1 NG2D1 > NG311 NG321, penalty= 1.5 > > > > END > > RETURN > > > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel 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 dorosh at ualberta.ca Wed Mar 25 19:48:50 2020 From: dorosh at ualberta.ca (Lyudmyla Dorosh) Date: Wed, 25 Mar 2020 18:48:50 -0000 Subject: [gmx-users] compile with intel compiler In-Reply-To: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> References: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> Message-ID: Dear Harry, I'm not an expert, but before running gromacs install I "sourced" all Intel libraries, and specified SIMD for my processor: source /opt/intel/bin/compilervars.sh intel64 source /opt/intel/impi/2019.5.281/intel64/bin/mpivars.sh source /opt/intel/mkl/bin/mklvars.sh intel64 sudo cmake .. -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=on -DGMX_OPENMP=on -DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/opt/intel/bin/icc" -DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on Hope it helps, Luda On Wed, Mar 25, 2020 at 4:46 AM Harry Mark Greenblatt < harry.greenblatt at weizmann.ac.il> wrote: > BS?D > > Dear All, > > I would like to compile Gromacs 2020 with an intel compiler; I set the > following: > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on > -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include > > Despite the fact that I have told it to use the Intel C++ compile is > (which it finds), it still looks and finds the system g++, which, of course > is quite old. If I have given it the name of a C++ compiler, why is it > looking for g++? > > > > Thanks > > 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. -- Regards, Lyudmyla Dorosh, PhD ------------------------------------------------------------ University of Alberta Department of Electrical and Computer Engineering, 4-030A ECERF Edmonton, AB, T6G 2G8 Canada Email: dorosh at ualberta.ca From jalemkul at vt.edu Wed Mar 25 20:07:49 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 25 Mar 2020 19:07:49 -0000 Subject: [gmx-users] gpu_id for more than 10 GPUs? In-Reply-To: References: Message-ID: On 3/25/20 2:34 PM, Leandro Bortot wrote: > Dear all, > I'm running some benchmarks on a shared machine which has 16 GPUs in a > single "node". > I can specify which GPUs to use with gmx mdrun -gpu_id XYZ. However, > the format of XYZ is a string in which each char is a GPU ID. I can't find > a way to specify, e.g, GPU #15 because -gpu_id 15 is interpreted as GPUs 1 > and 5. > Is there a way around this? Use a comma-delimited string. http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalemkul at vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== From neena.susaneappen at mail.utoronto.ca Wed Mar 25 21:23:47 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Wed, 25 Mar 2020 20:23:47 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From jalemkul at vt.edu Wed Mar 25 21:25:35 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Wed, 25 Mar 2020 20:25:35 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: <72079c92-3fc3-00b4-8263-0d9ba4826477@vt.edu> On 3/25/20 4:23 PM, Neena Susan Eappen wrote: > Hi Alessandra, > > For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? Check to make sure they're correctly defined in ffbonded.itp. grompp doesn't lie; if it cannot find parameters for something, it tells you exactly which ones it's missing. -Justin > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 3:17 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] No default bond types > > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? > > Many thanks and Take care, > 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 roland.schulz at intel.com Wed Mar 25 21:26:36 2020 From: roland.schulz at intel.com (Schulz, Roland) Date: Wed, 25 Mar 2020 20:26:36 -0000 Subject: [gmx-users] compile with intel compiler In-Reply-To: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> References: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> Message-ID: Hi, Are you referring to this type of error: -- Performing Test USING_LIBSTDCXX -- Performing Test USING_LIBSTDCXX - Success CMake Error at cmake/FindLibStdCpp.cmake:119 (message): Found g++ at /usr/bin/g++. Its version is 4.8.5. GROMACS requires at least version 5.1. Please specify a different g++ using GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH. This is because GROMACS needs both a C++ compiler and a C++ standard library. The Intel compiler doesn't come with a standard library but utilizes libstdc++ for that. GROMACS automatically looks for the right version of g++ to find the proper version of libstdc++ If you are referring to a different error please be more specific and post the exact error. Roland > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of Harry > Mark Greenblatt > Sent: Wednesday, March 25, 2020 3:46 AM > To: gmx-users at gromacs.org > Subject: [gmx-users] compile with intel compiler > > BS?D > > Dear All, > > I would like to compile Gromacs 2020 with an intel compiler; I set the > following: > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc - > DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=OFF - > DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 - > DMKL_INCLUDE_DIR=$MKLROOT/include > > Despite the fact that I have told it to use the Intel C++ compile is (which it > finds), it still looks and finds the system g++, which, of course is quite old. If I > have given it the name of a C++ compiler, why is it looking for g++? > > > > Thanks > > 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 neena.susaneappen at mail.utoronto.ca Thu Mar 26 00:59:54 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Wed, 25 Mar 2020 23:59:54 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: , Message-ID: Hi Justin, Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 8:23 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From jalemkul at vt.edu Thu Mar 26 01:02:29 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 26 Mar 2020 00:02:29 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: <59c15541-aa07-929a-dad3-57afaf06dc24@vt.edu> On 3/25/20 7:59 PM, Neena Susan Eappen wrote: > Hi Justin, > > Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... You haven't provided any information from which we can diagnose the issue, but if you're still having errors related to missing parameters, you have still not correctly added the required parameters. If you need further help, you'll have to provide the exact error messages and any other relevant information about what you're doing, topology snippets, etc. -Justin > > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 8:23 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > Hi Alessandra, > > For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 3:17 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] No default bond types > > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? > > Many thanks and Take care, > 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 neena.susaneappen at mail.utoronto.ca Thu Mar 26 01:47:10 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Thu, 26 Mar 2020 00:47:10 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: , , Message-ID: I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: On grompp, following error came up: ERROR 1 [file topol.top, line 84]: No default bond types Line 84 in topol.top : 14 20 1 Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: CA C15 1 0.14900 334720.0 Problem solved by changing that line 84 in topology file Line 84: 14 20 1 0.14900 334720.0 ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 11:59 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Justin, Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 8:23 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From jalemkul at vt.edu Thu Mar 26 01:48:21 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 26 Mar 2020 00:48:21 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: <42c78436-362a-8ff6-9b59-6e82a5327830@vt.edu> On 3/25/20 8:47 PM, Neena Susan Eappen wrote: > I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: > > On grompp, following error came up: > > ERROR 1 [file topol.top, line 84]: > No default bond types > > Line 84 in topol.top : 14 20 1 > > Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: > > CA C15 1 0.14900 334720.0 This didn't work because ffbonded.itp requires atom types, not atom names. -Justin > Problem solved by changing that line 84 in topology file > > Line 84: 14 20 1 0.14900 334720.0 > > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 11:59 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > Hi Justin, > > Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... > > > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 8:23 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > Hi Alessandra, > > For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 3:17 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] No default bond types > > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? > > Many thanks and Take care, > 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 neena.susaneappen at mail.utoronto.ca Thu Mar 26 02:04:22 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Thu, 26 Mar 2020 01:04:22 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: , , , Message-ID: Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH (modified alanine) opls_968 12.01100 ; C15 in ALH ________________________________ From: Neena Susan Eappen Sent: Thursday, March 26, 2020 12:47 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: On grompp, following error came up: ERROR 1 [file topol.top, line 84]: No default bond types Line 84 in topol.top : 14 20 1 Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: CA C15 1 0.14900 334720.0 Problem solved by changing that line 84 in topology file Line 84: 14 20 1 0.14900 334720.0 ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 11:59 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Justin, Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 8:23 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From jalemkul at vt.edu Thu Mar 26 02:06:34 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Thu, 26 Mar 2020 01:06:34 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: Message-ID: <1cba5878-752f-1608-bff7-5a3978ef36bc@vt.edu> On 3/25/20 9:04 PM, Neena Susan Eappen wrote: > Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH (modified alanine) > > opls_968 12.01100 ; C15 in ALH atomtypes.atp is irrelevant after pdb2gmx, so grompp has no knowledge of it. You need to add it to ffnonbonded.itp and include the bonded atom type (C15 in this case) as the second column so that grompp understands the translated atom type. -Justin > ________________________________ > From: Neena Susan Eappen > Sent: Thursday, March 26, 2020 12:47 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: > > On grompp, following error came up: > > ERROR 1 [file topol.top, line 84]: > No default bond types > > Line 84 in topol.top : 14 20 1 > > Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: > > CA C15 1 0.14900 334720.0 > > Problem solved by changing that line 84 in topology file > > Line 84: 14 20 1 0.14900 334720.0 > > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 11:59 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > Hi Justin, > > Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... > > > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 8:23 PM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: Re: [gmx-users] No default bond types > > Hi Alessandra, > > For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? > ________________________________ > From: Neena Susan Eappen > Sent: Wednesday, March 25, 2020 3:17 AM > To: gromacs.org_gmx-users at maillist.sys.kth.se > Subject: [gmx-users] No default bond types > > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? > > Many thanks and Take care, > 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 neena.susaneappen at mail.utoronto.ca Thu Mar 26 03:21:26 2020 From: neena.susaneappen at mail.utoronto.ca (Neena Susan Eappen) Date: Thu, 26 Mar 2020 02:21:26 -0000 Subject: [gmx-users] No default bond types In-Reply-To: References: , , , , Message-ID: Interesting, I did have that line in ffnonbonded.itp opls_968 C15 6 12.01100 0.641 A 3.55000e-01 3.17984e-01 ________________________________ From: Neena Susan Eappen Sent: Thursday, March 26, 2020 1:04 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH (modified alanine) opls_968 12.01100 ; C15 in ALH ________________________________ From: Neena Susan Eappen Sent: Thursday, March 26, 2020 12:47 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference: On grompp, following error came up: ERROR 1 [file topol.top, line 84]: No default bond types Line 84 in topol.top : 14 20 1 Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below: CA C15 1 0.14900 334720.0 Problem solved by changing that line 84 in topology file Line 84: 14 20 1 0.14900 334720.0 ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 11:59 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Justin, Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors.... ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 8:23 PM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: Re: [gmx-users] No default bond types Hi Alessandra, For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this? ________________________________ From: Neena Susan Eappen Sent: Wednesday, March 25, 2020 3:17 AM To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] No default bond types Hello gromacs users, I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this? Many thanks and Take care, Neena From harry.greenblatt at weizmann.ac.il Thu Mar 26 08:11:22 2020 From: harry.greenblatt at weizmann.ac.il (Harry Mark Greenblatt) Date: Thu, 26 Mar 2020 07:11:22 -0000 Subject: [gmx-users] compile with intel compiler In-Reply-To: References: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il>, Message-ID: BS"D Yes, indeed, that was the error. I did try to define the GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4; that worked to compile and install gromacs. But when it came to executing the program it couldn't find the libstdc++ for gcc 6.4. This is on a cluster, and when I have compiled gromacs in the past with gcc 6.4, I can set up the environment by loading the gcc 6.4 module, but this of course displaces the intel compiler module. If I add the gcc 6.4 library path in the GMXRC file, would that interfere with the intel stuff? Thanks Harry Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il> Weizmann Institute of Science Phone: 972-8-934-3625 234 Herzl St. Facsimile: 972-8-934-4159 Rehovot, 76100 Israel ________________________________ From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Schulz, Roland Sent: Wednesday, March 25, 2020 10:25:24 PM To: gmx-users at gromacs.org Subject: Re: [gmx-users] compile with intel compiler Hi, Are you referring to this type of error: -- Performing Test USING_LIBSTDCXX -- Performing Test USING_LIBSTDCXX - Success CMake Error at cmake/FindLibStdCpp.cmake:119 (message): Found g++ at /usr/bin/g++. Its version is 4.8.5. GROMACS requires at least version 5.1. Please specify a different g++ using GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH. This is because GROMACS needs both a C++ compiler and a C++ standard library. The Intel compiler doesn't come with a standard library but utilizes libstdc++ for that. GROMACS automatically looks for the right version of g++ to find the proper version of libstdc++ If you are referring to a different error please be more specific and post the exact error. Roland > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of Harry > Mark Greenblatt > Sent: Wednesday, March 25, 2020 3:46 AM > To: gmx-users at gromacs.org > Subject: [gmx-users] compile with intel compiler > > BS?D > > Dear All, > > I would like to compile Gromacs 2020 with an intel compiler; I set the > following: > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc - > DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=OFF - > DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64 - > DMKL_INCLUDE_DIR=$MKLROOT/include > > Despite the fact that I have told it to use the Intel C++ compile is (which it > finds), it still looks and finds the system g++, which, of course is quite old. If I > have given it the name of a C++ compiler, why is it looking for g++? > > > > Thanks > > 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. From herbert.fruchtl at st-andrews.ac.uk Thu Mar 26 13:15:21 2020 From: herbert.fruchtl at st-andrews.ac.uk (Herbert Fruchtl) Date: Thu, 26 Mar 2020 12:15:21 -0000 Subject: [gmx-users] compilation error in multidimarray.h Message-ID: Folks, I am trying to compile gromacs 2020.1 with the Intel compilers (version 17.0.2). It fails with: /home/herbert/gromacs-2020.1/src/gromacs/math/multidimarray.h(153): error: expression must have a constant value template>> In file included from /home/herbert/gromacs-2020.1/src/gromacs/math/densityfit.cpp(49): /opt/rh/devtoolset-6/root/usr/include/c++/6.3.1/type_traits(2523): error: class "std::enable_if<, void>" has no member "type" using enable_if_t = typename enable_if<_Cond, _Tp>::type; That last part seems to indicate that the problem is in the g++ libraries. Why does it use them at all? I have set CXX to icpc and sourced compilervars.sh. How do I get around this? Thanks, Herbert -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From mark.j.abraham at gmail.com Thu Mar 26 14:19:25 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Thu, 26 Mar 2020 13:19:25 -0000 Subject: [gmx-users] compilation error in multidimarray.h In-Reply-To: References: Message-ID: Hi, Intel doesn't supply a standard library, it always gets one from either a gcc or msvc installed on the system. Which versions of gcc libstdc++ are supported varies with the intel version, so you could follow the advice at http://manual.gromacs.org/documentation/2020/install-guide/index.html#compiler to try a different one, perhaps in a newer devtoolset. Mark On Thu, 26 Mar 2020 at 13:15, Herbert Fruchtl < herbert.fruchtl at st-andrews.ac.uk> wrote: > Folks, > > I am trying to compile gromacs 2020.1 with the Intel compilers (version > 17.0.2). It fails with: > > /home/herbert/gromacs-2020.1/src/gromacs/math/multidimarray.h(153): > error: expression must have a constant value > template std::enable_if_t>> > > In file included from > /home/herbert/gromacs-2020.1/src/gromacs/math/densityfit.cpp(49): > /opt/rh/devtoolset-6/root/usr/include/c++/6.3.1/type_traits(2523): > error: class "std::enable_if<, void>" has no member "type" > using enable_if_t = typename enable_if<_Cond, _Tp>::type; > > That last part seems to indicate that the problem is in the g++ > libraries. Why does it use them at all? I have set CXX to icpc and > sourced compilervars.sh. How do I get around this? > > Thanks, > > Herbert > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics University of > St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From erik.marklund at kemi.uu.se Thu Mar 26 14:41:00 2020 From: erik.marklund at kemi.uu.se (Erik Marklund) Date: Thu, 26 Mar 2020 13:41:00 -0000 Subject: [gmx-users] Force field for urea and urea-TMAO mixture In-Reply-To: References: Message-ID: <11BB5B42-F738-4197-8534-737E92B41BCB@kemi.uu.se> Dear Ishrat, I recommend this article and references therein for TMAO + urea parameters: http://dx.doi.org/10.1021/jacs.7b11695. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4562 erik.marklund at kemi.uu.se On 5 Mar 2020, at 10:05, Alessandra Villa > wrote: Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any suggestions regarding this will be highly appreciated. Thank you Regards -- Ishrat Jahan Research Scholar Department Of Chemistry A.M.U Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy From herbert.fruchtl at st-andrews.ac.uk Thu Mar 26 14:48:50 2020 From: herbert.fruchtl at st-andrews.ac.uk (Herbert Fruchtl) Date: Thu, 26 Mar 2020 13:48:50 -0000 Subject: [gmx-users] compilation error in multidimarray.h In-Reply-To: References: Message-ID: <5d7c2a48-b3c3-1190-18d0-9ec215fecfc7@st-andrews.ac.uk> Thanks, I had devtoolset-7 first, but then cmake already stops in the dependencies, and says the gcc included there is not supported by Intel 17. Will have to compile the complete toolchain with gcc... Herbert On 26/03/2020 13:12, Mark Abraham wrote: > Hi, > > Intel doesn't supply a standard library, it always gets one from either a > gcc or msvc installed on the system. Which versions of gcc libstdc++ are > supported varies with the intel version, so you could follow the advice at > http://manual.gromacs.org/documentation/2020/install-guide/index.html#compiler > to try a different one, perhaps in a newer devtoolset. > > Mark > > On Thu, 26 Mar 2020 at 13:15, Herbert Fruchtl < > herbert.fruchtl at st-andrews.ac.uk> wrote: > >> Folks, >> >> I am trying to compile gromacs 2020.1 with the Intel compilers (version >> 17.0.2). It fails with: >> >> /home/herbert/gromacs-2020.1/src/gromacs/math/multidimarray.h(153): >> error: expression must have a constant value >> template> std::enable_if_t>> >> >> In file included from >> /home/herbert/gromacs-2020.1/src/gromacs/math/densityfit.cpp(49): >> /opt/rh/devtoolset-6/root/usr/include/c++/6.3.1/type_traits(2523): >> error: class "std::enable_if<, void>" has no member "type" >> using enable_if_t = typename enable_if<_Cond, _Tp>::type; >> >> That last part seems to indicate that the problem is in the g++ >> libraries. Why does it use them at all? I have set CXX to icpc and >> sourced compilervars.sh. How do I get around this? >> >> Thanks, >> >> Herbert >> -- >> Herbert Fruchtl >> Senior Scientific Computing Officer >> School of Chemistry, School of Mathematics and Statistics University of >> St Andrews >> -- >> The University of St Andrews is a charity registered in Scotland: >> No SC013532 >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From tobias.kloeffel at fau.de Thu Mar 26 17:00:31 2020 From: tobias.kloeffel at fau.de (=?UTF-8?Q?Tobias_Kl=c3=b6ffel?=) Date: Thu, 26 Mar 2020 16:00:31 -0000 Subject: [gmx-users] Various questions related to Gromacs performance tuning In-Reply-To: <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> References: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> Message-ID: <708acde1-8281-f169-9d0d-25ae8370e5ba@fau.de> Hi Carsten, On 3/24/20 9:02 PM, Kutzner, Carsten wrote: > Hi, > >> Am 24.03.2020 um 16:28 schrieb Tobias Kl?ffel : >> >> Dear all, >> I am very new to Gromacs so maybe some of my problems are very easy to fix:) >> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from: >> https://www.mpibpc.mpg.de/grubmueller/bench >> >> 1) OpenMP parallelization: Is it done via OpenMP tasks? > Yes, all over the code loops are parallelized via OpenMP via #pragma omp parallel for > and similar directives. Ok but that's not OpenMP tasking:) > >> If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. > GROMACS uses only the serial transposes - allowing mkl to open up its own OpenMP threads > would lead to oversubscription of cores and performance degradation. Ah I see. But then it should be noted somewhere in the docu that all FFTW/MKL calls are inside a parallel region. Is there a specific reason for this? Normally you can achieve much better performance if you call a threaded library outside of a parallel region and let the library use its own threads. >> 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I > Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call > gmx tune_pme. Most queueing systems don't like it if one parallel program calls > another parallel program. > >> tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working. > There should be an output somewhere with the exact command line that > tune_pme invoked to test whether mdrun works. That should shed some light > on the issue. > > Side note: Tuning is normally only useful on CPU-nodes. If your nodes also > have GPUs, you will probably not want to do this kind of PME tuning. Yes it's CPU only... I will tune pp:ppme procs manually. However, most of the times it is failing with 'too large prime number' what is considered to be 'too large'? Thanks, Tobias >> Normal execution via $MPIRUN gmx_mpi mdrun -s ... works >> >> >> 3) As far as I understood, most time of PME is spent in a 3d FFT and hence probably most time is spent in a mpi alltoall communication. > Yes, but that also depends a lot on the number of nodes you are running on. > Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number of > nodes that you are interested and check the detailed timings at the end of > the log file. There you will find how much time is spent in various PME > routines. > > Best, > Carsten > >> For that reason I would like to place all PME tasks on a separate node via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying -ddorder interleave or cartesian works without problems. Is this a known issue? >> >> Kind regards, >> Tobias Kl?ffel >> >> -- >> M.Sc. Tobias Kl?ffel >> ======================================================= >> HPC (High Performance Computing) group >> Erlangen Regional Computing Center(RRZE) >> Friedrich-Alexander-Universit?t Erlangen-N?rnberg >> Martensstr. 1 >> 91058 Erlangen >> >> Room: 1.133 >> Phone: +49 (0) 9131 / 85 - 20101 >> >> ======================================================= >> >> E-mail: tobias.kloeffel at fau.de >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. > -- > Dr. Carsten Kutzner > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics > Am Fassberg 11, 37077 Goettingen, Germany > Tel. +49-551-2012313, Fax: +49-551-2012302 > http://www.mpibpc.mpg.de/grubmueller/kutzner > http://www.mpibpc.mpg.de/grubmueller/sppexa > -- M.Sc. Tobias Kl?ffel ======================================================= HPC (High Performance Computing) group Erlangen Regional Computing Center(RRZE) Friedrich-Alexander-Universit?t Erlangen-N?rnberg Martensstr. 1 91058 Erlangen Room: 1.133 Phone: +49 (0) 9131 / 85 - 20101 ======================================================= E-mail: tobias.kloeffel at fau.de From roland.schulz at intel.com Thu Mar 26 17:35:17 2020 From: roland.schulz at intel.com (Schulz, Roland) Date: Thu, 26 Mar 2020 16:35:17 -0000 Subject: [gmx-users] compile with intel compiler In-Reply-To: References: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il>, Message-ID: This isn't really a GROMACS question. You might need to set LD_LIBRARY_PATH manual. If you don't know how you should ask e.g. your cluster admin. Or you could use a static build (see GROMACS install guide). Roland > -----Original Message----- > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > On Behalf Of Harry > Mark Greenblatt > Sent: Thursday, March 26, 2020 12:11 AM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] compile with intel compiler > > BS"D > > > Yes, indeed, that was the error. I did try to define the > GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4; that > worked to compile and install gromacs. But when it came to executing the > program it couldn't find the libstdc++ for gcc 6.4. This is on a cluster, and > when I have compiled gromacs in the past with gcc 6.4, I can set up the > environment by loading the gcc 6.4 module, but this of course displaces the > intel compiler module. If I add the gcc 6.4 library path in the GMXRC file, > would that interfere with the intel stuff? > > > Thanks > > > Harry > > > > > > Harry M. Greenblatt > Associate Staff Scientist > Dept of Structural Biology > harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs > 5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.& > URL=mailto%3aharry.greenblatt%40weizmann.ac.il> > Weizmann Institute of Science Phone: 972-8-934-3625 > 234 Herzl St. Facsimile: 972-8-934-4159 > Rehovot, 76100 > Israel > ________________________________ > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > on behalf of Schulz, > Roland > Sent: Wednesday, March 25, 2020 10:25:24 PM > To: gmx-users at gromacs.org > Subject: Re: [gmx-users] compile with intel compiler > > Hi, > > > Are you referring to this type of error: > > -- Performing Test USING_LIBSTDCXX > -- Performing Test USING_LIBSTDCXX - Success CMake Error at > cmake/FindLibStdCpp.cmake:119 (message): > Found g++ at /usr/bin/g++. Its version is 4.8.5. GROMACS requires at > least version 5.1. Please specify a different g++ using > GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH. > > This is because GROMACS needs both a C++ compiler and a C++ standard > library. The Intel compiler doesn't come with a standard library but utilizes > libstdc++ for that. GROMACS automatically looks for the right version of g++ > to find the proper version of libstdc++ > > If you are referring to a different error please be more specific and post the > exact error. > > Roland > > > -----Original Message----- > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > On Behalf Of Harry > > Mark Greenblatt > > Sent: Wednesday, March 25, 2020 3:46 AM > > To: gmx-users at gromacs.org > > Subject: [gmx-users] compile with intel compiler > > > > BS"D > > > > Dear All, > > > > I would like to compile Gromacs 2020 with an intel compiler; I set > > the > > following: > > > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc - > DGMX_MPI=on > > -DGMX_BUILD_OWN_FFTW=OFF - DGMX_FFT_LIBRARY=mkl > > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 - > > DMKL_INCLUDE_DIR=$MKLROOT/include > > > > Despite the fact that I have told it to use the Intel C++ compile is > > (which it finds), it still looks and finds the system g++, which, of > > course is quite old. If I have given it the name of a C++ compiler, why is it > looking for g++? > > > > > > > > Thanks > > > > 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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe 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 dave.gromax at gmail.com Fri Mar 27 05:28:30 2020 From: dave.gromax at gmail.com (Dave M) Date: Fri, 27 Mar 2020 04:28:30 -0000 Subject: [gmx-users] interpolating frames between extremes Message-ID: Hi All, I have a question/confusion regarding interpolate frames option '-nframes' in gmx anaeig. One can find the extreme conformations as dot products projected on a selected eigenvector (to simplify say first eigenvector PC1). As the manual says, with -nframes (in anaeig) one can interpolate between the two extremes. I am confused with 'interpolating' here: a) Are these interpolated frames, between extremes, the 'real' conformations extracted from the trajectory? Which in that case one cannot define nframes > total frames falling between the extremes (dot product projections min and max on selected eigenvector). I don't think am right here because I could simply use a filtering option in anaeig. Or b) Are these interpolated smoothened frames some kind of predicted conformations along a path? In that case these interpolated conformations cannot be considered as 'real' conformational changes (that is they are not extracted from the trajectory) occurring between the extremes. Many times people show beautiful animations (interpolations between extremes), then they are not true conformational changes extracted from the trajectory. In that case I should not trust their visual explanations about the conformational changes. But I believe, please correct me, the interpolation is done using some intermediate real frames extracted from the trajectory otherwise it will not look so smooth. I hope I was able to ask my source of confusion clearly. Thanks Dave From compbioph at gmail.com Fri Mar 27 10:20:51 2020 From: compbioph at gmail.com (Emran Heshmati) Date: Fri, 27 Mar 2020 09:20:51 -0000 Subject: [gmx-users] Inexpected rmsd Message-ID: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as shown in arttached graph. What is the problem? From jordencabal at gmail.com Fri Mar 27 10:43:02 2020 From: jordencabal at gmail.com (Jorden Cabal) Date: Fri, 27 Mar 2020 09:43:02 -0000 Subject: [gmx-users] Inexpected rmsd In-Reply-To: References: Message-ID: Dear Emran Heshmati, I can not see any graph? Did you attach it. Please verify. Thank you On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote: > I am working on a protein consisting 2 chains. After performing regular MD > simulation and analysis the outputs, I got unexpecter rmsd, as shown in > arttached graph. What is the problem? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Fri Mar 27 10:44:33 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Fri, 27 Mar 2020 09:44:33 -0000 Subject: [gmx-users] Inexpected rmsd In-Reply-To: References: Message-ID: <458cbb21-89ca-cb80-1b9c-359736f91967@gmail.com> Hello, you can't attach files here on the mailing list. Please upload the file somewhere and share a link to it. Cheers Paul On 27/03/2020 10:35, Jorden Cabal wrote: > Dear Emran Heshmati, > I can not see any graph? Did you attach it. Please verify. > Thank you > > On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote: > >> I am working on a protein consisting 2 chains. After performing regular MD >> simulation and analysis the outputs, I got unexpecter rmsd, as shown in >> arttached graph. What is the problem? >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From compbioph at gmail.com Fri Mar 27 16:10:32 2020 From: compbioph at gmail.com (Emran Heshmati) Date: Fri, 27 Mar 2020 15:10:32 -0000 Subject: [gmx-users] unexpecter rmsd Message-ID: Thanks to Paul and jorden, I repost my question: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as seen in link below. What is the problem?? https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html From jalemkul at vt.edu Fri Mar 27 16:16:52 2020 From: jalemkul at vt.edu (Justin Lemkul) Date: Fri, 27 Mar 2020 15:16:52 -0000 Subject: [gmx-users] unexpecter rmsd In-Reply-To: References: Message-ID: <542cb4fb-8a22-696f-9921-46809f70f2cc@vt.edu> On 3/27/20 11:10 AM, Emran Heshmati wrote: > Thanks to Paul and jorden, I repost my question: > I am working on a protein consisting 2 chains. After performing > regular MD simulation > and analysis the outputs, I got unexpecter rmsd, as seen in link below. > What is the problem?? > https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html This is a PBC effect, with one or more protein chains jumping across a periodic boundary. Recenter with trjconv. You may have to center on one of the chains individually to get proper wrapping of the unit cell. -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 compbioph at gmail.com Fri Mar 27 17:14:23 2020 From: compbioph at gmail.com (Emran Heshmati) Date: Fri, 27 Mar 2020 16:14:23 -0000 Subject: [gmx-users] unexpecter rmsd In-Reply-To: <542cb4fb-8a22-696f-9921-46809f70f2cc@vt.edu> References: <542cb4fb-8a22-696f-9921-46809f70f2cc@vt.edu> Message-ID: Thank you Justin On Fri, Mar 27, 2020, 19:47 Justin Lemkul wrote: > > > On 3/27/20 11:10 AM, Emran Heshmati wrote: > > Thanks to Paul and jorden, I repost my question: > > I am working on a protein consisting 2 chains. After performing > > regular MD simulation > > and analysis the outputs, I got unexpecter rmsd, as seen in link below. > > What is the problem?? > > https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html > > This is a PBC effect, with one or more protein chains jumping across a > periodic boundary. Recenter with trjconv. You may have to center on one > of the chains individually to get proper wrapping of the unit cell. > > -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 bjorn.wesen at gmail.com Fri Mar 27 17:14:50 2020 From: bjorn.wesen at gmail.com (Bjorn Wesen) Date: Fri, 27 Mar 2020 16:14:50 -0000 Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? Message-ID: Hi list, I have a working sim of the solvated SARS-CoV-2 main protease dimer from https://www.rcsb.org/structure/6Y84 using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to proceed by adding some of the various proposed inhibitor ligands to the sim for further workflow testing, for example, this one: "COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1". So I made a pdb of this and generated a .gro and .itp through one of the online Acpype servers (the one at http://bio2byte.be/acpype ), but there is no option to generate gmx vsites for getting rid of the hydrogen bond-angles so I simply assume the result will blow up when running with the longer timesteps the rest of the sim now uses. I found a 5 year old post on this list with the same problem, with this advice from Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html "At present, the simplest way forward is to take the information you have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand." I was wondering, is this still the recommended method? I'm not super-knowledgeable in the details of how to port something from the ITP to the RTP formats. Should I just give up on doing it this way or is it an "opportunity to learn the details" ;) Or is there a better way. Maybe some other gmx tool to build the vsites for a ligand without having to go all the way by creating the rtp stuff. Also, yes, I could simply give up the vsites and run everything slower. This is the fallback. Maybe some of these ligands simply won't work well with these constructions at any rate. Regards /Bjorn From rollyng at gmail.com Fri Mar 27 17:34:55 2020 From: rollyng at gmail.com (Rolly Ng) Date: Fri, 27 Mar 2020 16:34:55 -0000 Subject: [gmx-users] compile with intel compiler In-Reply-To: References: <67069E1B-9F36-493C-844C-1186165F451F@weizmann.ac.il> Message-ID: Hi, I use the following combination with Intel PSXE. It works and your problem is likely related to the name of the Intel CXX compiler. source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 source /opt/intel/impi/2018.4.274/bin64/mpivars.sh source /opt/intel/mkl/bin/mklvars.sh intel64 FLAGS="-xCORE-AVX2"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS; cmake .. -DCMAKE_C_COMPILER=mpiicc \ -DCMAKE_CXX_COMPILER=mpiicpc \ -DCMAKE_INSTALL_PREFIX=/home/user/Gromacs/gromacs-2020/install \ -DGMX_FFT_LIBRARY=mkl \ -DGMX_MPI=ON \ -DGMX_SIMD=AVX2_256 \ -DMPIEXEC=srun \ -DMPIEXEC_NUMPROC_FLAG=-n \ -DMPIEXEC_PREFLAGS= \ -DMPIEXEC_POSTFLAGS= make -j 16 make install On Fri, Mar 27, 2020 at 12:35 AM Schulz, Roland wrote: > This isn't really a GROMACS question. You might need to set > LD_LIBRARY_PATH manual. If you don't know how you should ask e.g. your > cluster admin. Or you could use a static build (see GROMACS install guide). > > Roland > > > -----Original Message----- > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > On Behalf Of Harry > > Mark Greenblatt > > Sent: Thursday, March 26, 2020 12:11 AM > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] compile with intel compiler > > > > BS"D > > > > > > Yes, indeed, that was the error. I did try to define the > > GMX_GPLUSPLUS_PATH, and have that point to a local install of gcc 6.4; > that > > worked to compile and install gromacs. But when it came to executing the > > program it couldn't find the libstdc++ for gcc 6.4. This is on a > cluster, and > > when I have compiled gromacs in the past with gcc 6.4, I can set up the > > environment by loading the gcc 6.4 module, but this of course displaces > the > > intel compiler module. If I add the gcc 6.4 library path in the GMXRC > file, > > would that interfere with the intel stuff? > > > > > > Thanks > > > > > > Harry > > > > > > > > > > > > Harry M. Greenblatt > > Associate Staff Scientist > > Dept of Structural Biology > > harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs > > 5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.& > > URL=mailto%3aharry.greenblatt%40weizmann.ac.il> > > Weizmann Institute of Science Phone: 972-8-934-3625 > > 234 Herzl St. Facsimile: 972-8-934-4159 > > Rehovot, 76100 > > Israel > > ________________________________ > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > on behalf of Schulz, > > Roland > > Sent: Wednesday, March 25, 2020 10:25:24 PM > > To: gmx-users at gromacs.org > > Subject: Re: [gmx-users] compile with intel compiler > > > > Hi, > > > > > > Are you referring to this type of error: > > > > -- Performing Test USING_LIBSTDCXX > > -- Performing Test USING_LIBSTDCXX - Success CMake Error at > > cmake/FindLibStdCpp.cmake:119 (message): > > Found g++ at /usr/bin/g++. Its version is 4.8.5. GROMACS requires at > > least version 5.1. Please specify a different g++ using > > GMX_GPLUSPLUS_PATH, PATH or CMAKE_PREFIX_PATH. > > > > This is because GROMACS needs both a C++ compiler and a C++ standard > > library. The Intel compiler doesn't come with a standard library but > utilizes > > libstdc++ for that. GROMACS automatically looks for the right version of > g++ > > to find the proper version of libstdc++ > > > > If you are referring to a different error please be more specific and > post the > > exact error. > > > > Roland > > > > > -----Original Message----- > > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se > > > On Behalf Of Harry > > > Mark Greenblatt > > > Sent: Wednesday, March 25, 2020 3:46 AM > > > To: gmx-users at gromacs.org > > > Subject: [gmx-users] compile with intel compiler > > > > > > BS"D > > > > > > Dear All, > > > > > > I would like to compile Gromacs 2020 with an intel compiler; I set > > > the > > > following: > > > > > > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc - > > DGMX_MPI=on > > > -DGMX_BUILD_OWN_FFTW=OFF - DGMX_FFT_LIBRARY=mkl > > > -DMKL_LIBRARIES=$MKLROOT/lib/intel64 - > > > DMKL_INCLUDE_DIR=$MKLROOT/include > > > > > > Despite the fact that I have told it to use the Intel C++ compile is > > > (which it finds), it still looks and finds the system g++, which, of > > > course is quite old. If I have given it the name of a C++ compiler, > why is it > > looking for g++? > > > > > > > > > > > > Thanks > > > > > > 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. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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 leandro.obt at gmail.com Fri Mar 27 20:30:07 2020 From: leandro.obt at gmail.com (Leandro Bortot) Date: Fri, 27 Mar 2020 19:30:07 -0000 Subject: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported" Message-ID: Dear users, I'm trying to optimize the execution of a system composed by 10 million atoms on a multi-GPU machine with GROMACS 2020.1. I've followed the instructions given at https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ . However, when I run my simulation, mdrun tells me this: " *Update task on the GPU was required, by the GMX_FORCE_UPDATE_DEFAULT_GPU environment variable, but the following condition(s) were not satisfied:Domain decomposition without GPU halo exchange is not supported.* " My understanding was that exporting *GMX_GPU_DD_COMMS=true* would enable such halo communications. My simulation runs, however the performance is not scaling well with the number of GPUs. I've done the following: " *export GMX_GPU_DD_COMMS=trueexport GMX_GPU_PME_PP_COMMS=trueexport GMX_FORCE_UPDATE_DEFAULT_GPU=true*" And my execution line is: "*mpirun -np 4 gmx_mpi mdrun -s eq.1.tpr -v -deffnm eq.1 -pin on -ntomp 6 -npme 1 -nb gpu -bonded gpu -pme gpu -nstlist 400*" If I add "-update gpu" to this same line I have the following error: " *Inconsistency in user input:Update task on the GPU was required,but the following condition(s) were not satisfied:Domain decomposition without GPU halo exchange is not supported. With separate PME rank(s), PME must use direct communication.*" Also, I'm using constraints = h-bonds in my .mdp file. Am I doing something wrong? Thank you for your attention, Leandro ------- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational Biology Brazilian Biosciences National Laboratory (LNBio) Brazilian Center for Research in Energy and Materials (CNPEM) Zip Code 13083-970, Campinas, S?o Paulo, Brazil. From blau at kth.se Fri Mar 27 20:55:34 2020 From: blau at kth.se (blau) Date: Fri, 27 Mar 2020 19:55:34 -0000 Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? In-Reply-To: Message-ID: Hi Bjorn,?This is still the recommended procedure.?Contact me directly if you need help with the conversion to an rtp file.Best,?Christian -------- Original message --------From: Bjorn Wesen Date: 27/03/2020 17:16 (GMT+01:00) To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? Hi list, I have a working sim of the solvated SARS-CoV-2 main proteasedimer fromhttps://www.rcsb.org/structure/6Y84using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted toproceed by adding some of the various proposed inhibitor ligands to the simfor further workflow testing, for example, this one:"COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1".So I made a pdb of this and generated a .gro and .itp through one of theonline Acpype servers (the one at http://bio2byte.be/acpype ), but there isno option to generate gmx vsites for getting rid of the hydrogenbond-angles so I simply assume the result will blow up when running withthe longer timesteps the rest of the sim now uses.I found a 5 year old post on this list with the same problem, with thisadvice from Justin:https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html"At present, the simplest way forward is to take the information you havein yourligand topology from acpype and create an .rtp entry, then allow pdb2gmx toprocess the whole thing and build the virtual sites on the ligand."I was wondering, is this still the recommended method? I'm notsuper-knowledgeable in the details of how to port something from the ITP tothe RTP formats. Should I just give up on doing it this way or is it an"opportunity to learn the details" ;) Or is there a better way. Maybe someother gmx tool to build the vsites for a ligand without having to go allthe way by creating the rtp stuff.Also, yes, I could simply give up the vsites and run everything slower.This is the fallback. Maybe some of these ligands simply won't work wellwith these constructions at any rate.Regards/Bjorn-- Gromacs Users mailing list* Please search the archive at http://www.gromacs.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 blau at kth.se Fri Mar 27 20:55:34 2020 From: blau at kth.se (blau) Date: Fri, 27 Mar 2020 19:55:34 -0000 Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? In-Reply-To: Message-ID: Hi Bjorn,?This is still the recommended procedure.?Contact me directly if you need help with the conversion to an rtp file.Best,?Christian -------- Original message --------From: Bjorn Wesen Date: 27/03/2020 17:16 (GMT+01:00) To: gromacs.org_gmx-users at maillist.sys.kth.se Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? Hi list, I have a working sim of the solvated SARS-CoV-2 main proteasedimer fromhttps://www.rcsb.org/structure/6Y84using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted toproceed by adding some of the various proposed inhibitor ligands to the simfor further workflow testing, for example, this one:"COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1".So I made a pdb of this and generated a .gro and .itp through one of theonline Acpype servers (the one at http://bio2byte.be/acpype ), but there isno option to generate gmx vsites for getting rid of the hydrogenbond-angles so I simply assume the result will blow up when running withthe longer timesteps the rest of the sim now uses.I found a 5 year old post on this list with the same problem, with thisadvice from Justin:https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html"At present, the simplest way forward is to take the information you havein yourligand topology from acpype and create an .rtp entry, then allow pdb2gmx toprocess the whole thing and build the virtual sites on the ligand."I was wondering, is this still the recommended method? I'm notsuper-knowledgeable in the details of how to port something from the ITP tothe RTP formats. Should I just give up on doing it this way or is it an"opportunity to learn the details" ;) Or is there a better way. Maybe someother gmx tool to build the vsites for a ligand without having to go allthe way by creating the rtp stuff.Also, yes, I could simply give up the vsites and run everything slower.This is the fallback. Maybe some of these ligands simply won't work wellwith these constructions at any rate.Regards/Bjorn-- Gromacs Users mailing list* Please search the archive at http://www.gromacs.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 addiw7 at googlemail.com Fri Mar 27 21:45:58 2020 From: addiw7 at googlemail.com (Dawid das) Date: Fri, 27 Mar 2020 20:45:58 -0000 Subject: [gmx-users] Water molecules fill in gaps in protein Message-ID: Dear Gromacs Users, I noticed that quite often after adding the solvent (water) to the protein, the water molecules fill in gaps inside the protein which are not occupied. I am afraid that since their position may not be optimal (they actually should not be there), it will lead to artifacts as the MD simulation progresses. What is your opinion on removing these water molecules on some occasions? Best wishes, Dawid Grabarek From wes.p.michaels at gmail.com Sat Mar 28 01:32:41 2020 From: wes.p.michaels at gmail.com (Wesley Michaels) Date: Sat, 28 Mar 2020 00:32:41 -0000 Subject: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities In-Reply-To: References: Message-ID: Hey y'all, Ran some additional simulations and, unfortunately, I'm still experiencing problems. Here's the mdp file that I used: integrator = md nsteps = 20000000 ; 20 ns dt = 0.001000 nstlist = 20 ns_type = grid nstxout = 25000 nstvout = 25000 nstenergy = 25000 nstlog = 25000 continuation = yes constraints = none lincs_iter = 1 lincs_order = 4 cutoff-scheme = Verlet rcoulomb = 1.4 rvdw = 1.4 coulombtype = PME vdwtype = PME pme_order = 4 fourierspacing = 0.12 tcoupl = Nose-Hoover tc-grps = System tau_t = 0.100000 ref_t = 300.000000 nsttcouple = 5 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.000000 ref_p = 1.000000 compressibility = 0.000045 refcoord_scaling = com pbc = xyz periodic-molecules = no DispCorr = EnerPres gen_vel = no The simulation ran for 40ns with the Berendsen barostat just fine - density and volume were well-equilibrated within 1ns of the simulation starting. Unstable density fluctuations began immediately after switching to the PR barostat (from the output configuration of the previous 40ns run) and the simulation failed within 0.4ns. Here are some links to: - topology file: https://drive.google.com/open?id=1NF5EPbM2mnTGilXpOf7pQK5qlelBd8KC - initial configuration: https://drive.google.com/file/d/1kxMOKQcsAEheBCEAbkGcXqfBDwsHKpwr/view?usp=sharing - log file of second half of Berendsen run: https://drive.google.com/file/d/15TgbOOr6_fb8FkqR-nFHR8j1qbhTNT-Q/view?usp=sharing - log file of PR run: https://drive.google.com/file/d/1CPobb3ddDsd4I6Fce1tEpwHiBd5yq-tE/view?usp=sharing Thanks! If you need any other files or information, please let me know. -Wes On Tue, Mar 24, 2020 at 3:44 AM Justin Lemkul wrote: > > > On 3/24/20 3:09 AM, Wesley Michaels wrote: > > Hi, > > > > Thanks for your reply! I built the topology with my own script, as > opposed > > to using pdb2gmx. Following Bogdan's instructions here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html > ), > > I specified all instances of 1-4 pair interactions (i.e. pairs of atom > > indices) in the [ pairs ] section, but let GMX specify the [ pairtypes ] > > section (i.e. the interaction parameters for pairs of atom types) > > automatically using "gen_pairs" = "yes". > > > > As a second test, I generated a topology using pdb2gmx and the procedure > > Justin detailed here ( > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html > ) > > (using the OPLS-AA FF option in pdb2gmx) and used that in a trial > > simulation. I experienced the same issue, unfortunately. Happy to provide > > any files as needed to help clarify the issue. > > If pdb2gmx built the topology and you're using an unaltered > forcefield.itp [defaults] directive, based on what you've said below, it > appears to just be an equilibration issue. Use Berendsen for a while to > get the system settled and then switch to Parrinello-Rahman. If you're > still experiencing problems, full .mdp file(s) would be helpful. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalemkul at vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From sadafrani6 at gmail.com Sat Mar 28 02:11:35 2020 From: sadafrani6 at gmail.com (Sadaf Rani) Date: Sat, 28 Mar 2020 01:11:35 -0000 Subject: [gmx-users] no atom pairs for dispersion correction Message-ID: Dear Gromacs users I am running an MD simulation of the protein-ligand complex. At the start of the production run, I am getting this warning. What does it mean and how should I fix it? *WARNING: There are no atom pairs for dispersion correction* Thanks in advance. Sadaf From fnabi at myamu.ac.in Sat Mar 28 02:25:36 2020 From: fnabi at myamu.ac.in (FAISAL NABI) Date: Sat, 28 Mar 2020 01:25:36 -0000 Subject: [gmx-users] Lincs warning in free energy calculation In-Reply-To: References: Message-ID: Check the forcefield you are using is appropriate for your system or there might be some problem with the ligand parameters. On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote: > Dear Gromacs users > I ran an MD simulation for 3ns and from the last coordinates started a free > energy calculation for 3ns. My system is well equilibrated but after 710725 > steps I am getting Lincs warning every time as below:- > > WARNING: There are no atom pairs for dispersion correction > starting mdrun 'GROtesk MACabre and Sinister in water' > 1500000 steps, 3000.0 ps. > > Step 710726, time 1421.45 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000003, max 0.000023 (between atoms 5470 and 5472) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3437 3438 43.8 0.1080 0.1080 0.1080 > > Step 710726, time 1421.45 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000003, max 0.000021 (between atoms 5470 and 5472) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3437 3438 43.1 0.1080 0.1080 0.1080 > > I have added restraints between atoms of ligand and protein and getting > Lincs warning between 1 atom included in restraints as below:- > > [ bonds ] > ; i j type r0A r1A r2A fcA r0B r1B r2B > fcB > *3437* 7908 10 0.418 0.418 10.0 0.0 0.418 0.418 10.0 > 41840.00 > > [ angle_restraints ] > ; ai aj ak al type thA fcA multA thB fcB > multB > 3437 7908 7906 7908 1 100.29 0.0 1 100.29 418.40 > 1 > 7908 3437 3439 *3437* 1 146.50 0.0 1 146.50 418.40 > 1 > > [ dihedral_restraints ] > ; ai aj ak al type phiA dphiA fcA phiB dphiB > fcB > 7906 7908 *3437* 3439 1 156.16 0.0 0.0 156.16 0.0 > 418.40 > 7907 7906 7908 *3437* 1 -56.93 0.0 0.0 -56.93 0.0 > 418.40 > 7909 *3437* 3430 3435 1 131.32 0.0 0.0 131.32 0.0 > 418.40 > > Can anyone please suggest to me how Should I fix this error? Any help will > be really appreciated. > > 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. > -- Faisal Nabi *Pre-Doctoral Fellow (CSIR-JRF)* C/o Professor Rizwan Hassan Khan Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP, INDIA. Email- *fnabi at myamy.ac.in * * faisalbiochem at gmail.com * Contact no. - *+91-8923713214* From gcarneiroq at pos.iq.ufrj.br Sat Mar 28 04:02:46 2020 From: gcarneiroq at pos.iq.ufrj.br (Guilherme Carneiro Queiroz da Silva) Date: Sat, 28 Mar 2020 03:02:46 -0000 Subject: [gmx-users] Per atom energies Message-ID: Hi all, I look on google for any answers for such question in this maillist, and I found related questions but no final answer. I wish to compute the heat flux for my system using GK relations. I found the gromacs extension force the calculation of the per atom stress (http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the per atom energies. Did someone manage to extract such properties? I'm aware i could use enemat but had to do a large numbers of reruns in order to cover each atom obeying the group limit of gromacs, since this could be tedious I'm looking for other solutions. Could editing the trajectory code in order to extract not only forces but also the energies be the only solution? Thanks for any help, Guilherme Carneiro mdStress.org :: MDStressLib MDStress Library. MDStressLib is a standalone C++ library developed for local stress calculations. This library can be integrated into any molecular simulation code to compute local stress fields in 3D. www.mdstress.org From mark.j.abraham at gmail.com Sat Mar 28 09:57:55 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 28 Mar 2020 08:57:55 -0000 Subject: [gmx-users] Per atom energies In-Reply-To: References: Message-ID: Hi, On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, < gcarneiroq at pos.iq.ufrj.br> wrote: > Hi all, > > I look on google for any answers for such question in this maillist, and I > found related questions but no final answer. > > I wish to compute the heat flux for my system using GK relations. I found > the gromacs extension force the calculation of the per atom stress ( > http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks > the per atom energies. Did someone manage to extract such properties? > > I'm aware i could use enemat but had to do a large numbers of reruns in > order to cover each atom obeying the group limit of gromacs, since this > could be tedious I'm looking for other solutions. Could editing the > trajectory code in order to extract not only forces but also the energies > be the only solution? > The energies are computed as a sum over interactions and saved only in aggregate. There's no support for anything more useful than reruns with energy groups. Mark Thanks for any help, > > Guilherme Carneiro > > > mdStress.org :: MDStressLib > > MDStress Library. MDStressLib is a standalone C++ library developed for > local stress calculations. This library can be integrated into any > molecular simulation code to compute local stress fields in 3D. > www.mdstress.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 mark.j.abraham at gmail.com Sat Mar 28 09:57:55 2020 From: mark.j.abraham at gmail.com (Mark Abraham) Date: Sat, 28 Mar 2020 08:57:55 -0000 Subject: [gmx-users] Per atom energies In-Reply-To: References: Message-ID: Hi, On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, < gcarneiroq at pos.iq.ufrj.br> wrote: > Hi all, > > I look on google for any answers for such question in this maillist, and I > found related questions but no final answer. > > I wish to compute the heat flux for my system using GK relations. I found > the gromacs extension force the calculation of the per atom stress ( > http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks > the per atom energies. Did someone manage to extract such properties? > > I'm aware i could use enemat but had to do a large numbers of reruns in > order to cover each atom obeying the group limit of gromacs, since this > could be tedious I'm looking for other solutions. Could editing the > trajectory code in order to extract not only forces but also the energies > be the only solution? > The energies are computed as a sum over interactions and saved only in aggregate. There's no support for anything more useful than reruns with energy groups. Mark Thanks for any help, > > Guilherme Carneiro > > > mdStress.org :: MDStressLib > > MDStress Library. MDStressLib is a standalone C++ library developed for > local stress calculations. This library can be integrated into any > molecular simulation code to compute local stress fields in 3D. > www.mdstress.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 erik.marklund at kemi.uu.se Sat Mar 28 15:14:09 2020 From: erik.marklund at kemi.uu.se (Erik Marklund) Date: Sat, 28 Mar 2020 14:14:09 -0000 Subject: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites? In-Reply-To: References: Message-ID: <0AB0A7ED-41D3-463D-9007-8DFAF62D8B5C@kemi.uu.se> Hi Bjorn (and others interested in virtual sites for non-protein molecules), We have an article in press where we describe our new tool Mkvsites, which is a great help when you want virtual sites for a new residue, ligand, etc. I will announce the article once it is available, but I might as well provide the tool already now: https://github.com/ErikMarklund/mkvsites In short: Use topinspect.py to identify any atomtypes and interactions in your itp/top file that need to be added to the force field (not needed for some things, like nucleic acids already present in the force field, but for which no vsite parameters exist). topinspect.py optionally produces an rtp file, which is very helpful because it enables you to use pdb2gmx to place all dummy masses etc at a later stage. Then use Mkvsites.py to generate the required vsite parameters, including angle constraints for -OH groups. Put that in your force field, then prepare your system with pdb2gmx etc like you would for a vanilla protein system. Look at the examples provided and get in touch if you need help. I am sure there are things we can do to improve the usability, so input is welcome. We have NOT automated the actual modification of force field files, since we have noticed that some of the input we have used for testing need human interpretation (e.g. to decide element type for new atom types). While we could implement some logic for that, it is difficult to foresee all possible flavours of input, and that strategy risk causing silent errors in the simulations. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4562 erik.marklund at kemi.uu.se On 27 Mar 2020, at 17:14, Bjorn Wesen > wrote: Hi list, I have a working sim of the solvated SARS-CoV-2 main protease dimer from https://www.rcsb.org/structure/6Y84 using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to proceed by adding some of the various proposed inhibitor ligands to the sim for further workflow testing, for example, this one: "COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1". So I made a pdb of this and generated a .gro and .itp through one of the online Acpype servers (the one at http://bio2byte.be/acpype ), but there is no option to generate gmx vsites for getting rid of the hydrogen bond-angles so I simply assume the result will blow up when running with the longer timesteps the rest of the sim now uses. I found a 5 year old post on this list with the same problem, with this advice from Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html "At present, the simplest way forward is to take the information you have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand." I was wondering, is this still the recommended method? I'm not super-knowledgeable in the details of how to port something from the ITP to the RTP formats. Should I just give up on doing it this way or is it an "opportunity to learn the details" ;) Or is there a better way. Maybe some other gmx tool to build the vsites for a ligand without having to go all the way by creating the rtp stuff. Also, yes, I could simply give up the vsites and run everything slower. This is the fallback. Maybe some of these ligands simply won't work well with these constructions at any rate. Regards /Bjorn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org. N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy From spoel at xray.bmc.uu.se Sat Mar 28 17:00:45 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sat, 28 Mar 2020 16:00:45 -0000 Subject: [gmx-users] Per atom energies In-Reply-To: References: Message-ID: <2fb64d25-d83e-184a-663d-84afc330f65e@xray.bmc.uu.se> Den 2020-03-28 kl. 04:01, skrev Guilherme Carneiro Queiroz da Silva: > Hi all, > > I look on google for any answers for such question in this maillist, and I found related questions but no final answer. > > I wish to compute the heat flux for my system using GK relations. I found the gromacs extension force the calculation of the per atom stress (http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the per atom energies. Did someone manage to extract such properties? > > I'm aware i could use enemat but had to do a large numbers of reruns in order to cover each atom obeying the group limit of gromacs, since this could be tedious I'm looking for other solutions. Could editing the trajectory code in order to extract not only forces but also the energies be the only solution? > The reason that there is no support is that it is not physically meaningful, at least not to my knowledge. How would you partition the bond energy in a HCl molecule into atoms? In an isolated system it is in principle possible to compute interaction energies, using the typical pair potentials that classical force fields apply. However, these force fields ignore higher order interactions, which means this is a crude approximation. In a periodic system the computation of energies and energy components is even more cumbersome, although we have attempted that using potential of mean force calculation in JCTC 9 pp. 4542-4551 (2013). > Thanks for any help, > > Guilherme Carneiro > > > mdStress.org :: MDStressLib > MDStress Library. MDStressLib is a standalone C++ library developed for local stress calculations. This library can be integrated into any molecular simulation code to compute local stress fields in 3D. > www.mdstress.org > -- 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 ckutzne at gwdg.de Sat Mar 28 19:32:37 2020 From: ckutzne at gwdg.de (Kutzner, Carsten) Date: Sat, 28 Mar 2020 18:32:37 -0000 Subject: [gmx-users] Various questions related to Gromacs performance tuning In-Reply-To: <708acde1-8281-f169-9d0d-25ae8370e5ba@fau.de> References: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> <708acde1-8281-f169-9d0d-25ae8370e5ba@fau.de> Message-ID: > Am 26.03.2020 um 17:00 schrieb Tobias Kl?ffel : > > Hi Carsten, > > > On 3/24/20 9:02 PM, Kutzner, Carsten wrote: >> Hi, >> >>> Am 24.03.2020 um 16:28 schrieb Tobias Kl?ffel : >>> >>> Dear all, >>> I am very new to Gromacs so maybe some of my problems are very easy to fix:) >>> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from: >>> https://www.mpibpc.mpg.de/grubmueller/bench >>> >>> 1) OpenMP parallelization: Is it done via OpenMP tasks? >> Yes, all over the code loops are parallelized via OpenMP via #pragma omp parallel for >> and similar directives. > Ok but that's not OpenMP tasking:) >> >>> If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. >> GROMACS uses only the serial transposes - allowing mkl to open up its own OpenMP threads >> would lead to oversubscription of cores and performance degradation. > Ah I see. But then it should be noted somewhere in the docu that all FFTW/MKL calls are inside a parallel region. Is there a specific reason for this? Normally you can achieve much better performance if you call a threaded library outside of a parallel region and let the library use its own threads. >>> 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I >> Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call >> gmx tune_pme. Most queueing systems don't like it if one parallel program calls >> another parallel program. >> >>> tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working. >> There should be an output somewhere with the exact command line that >> tune_pme invoked to test whether mdrun works. That should shed some light >> on the issue. >> >> Side note: Tuning is normally only useful on CPU-nodes. If your nodes also >> have GPUs, you will probably not want to do this kind of PME tuning. > Yes it's CPU only... I will tune pp:ppme procs manually. However, most of the times it is failing with 'too large prime number' what is considered to be 'too large'? I think 2, 3, 5, 7, 11, and 13 and multiples of these are ok, but not larger prime numbers. So for a fixed number of procs only some of the combinations PP:PME will actually work. The ones that don't work would not be wise to choose from a performance point of view. Best, Carsten From benson_muite at emailplus.org Sat Mar 28 19:42:38 2020 From: benson_muite at emailplus.org (Benson Muite) Date: Sat, 28 Mar 2020 18:42:38 -0000 Subject: [gmx-users] =?utf-8?q?Various_questions_related_to_Gromacs_perfor?= =?utf-8?q?mance_tuning?= In-Reply-To: References: <71a9703e-0f2c-e305-81e9-a13dbfd07ff0@fau.de> <2171CA21-0C61-4275-8585-82A7D95DE558@mpibpc.mpg.de> <708acde1-8281-f169-9d0d-25ae8370e5ba@fau.de> Message-ID: <866b83f2-2ec5-4649-941b-ca27b12066a9@www.fastmail.com> On Sat, Mar 28, 2020, at 9:32 PM, Kutzner, Carsten wrote: > > > > Am 26.03.2020 um 17:00 schrieb Tobias Kl?ffel : > > > > Hi Carsten, > > > > > > On 3/24/20 9:02 PM, Kutzner, Carsten wrote: > >> Hi, > >> > >>> Am 24.03.2020 um 16:28 schrieb Tobias Kl?ffel : > >>> > >>> Dear all, > >>> I am very new to Gromacs so maybe some of my problems are very easy to fix:) > >>> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from: > >>> https://www.mpibpc.mpg.de/grubmueller/bench > >>> > >>> 1) OpenMP parallelization: Is it done via OpenMP tasks? > >> Yes, all over the code loops are parallelized via OpenMP via #pragma omp parallel for > >> and similar directives. > > Ok but that's not OpenMP tasking:) > >> > >>> If the Intel toolchain is detected and -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set. > >> GROMACS uses only the serial transposes - allowing mkl to open up its own OpenMP threads > >> would lead to oversubscription of cores and performance degradation. > > Ah I see. But then it should be noted somewhere in the docu that all FFTW/MKL calls are inside a parallel region. Is there a specific reason for this? Normally you can achieve much better performance if you call a threaded library outside of a parallel region and let the library use its own threads. Creating and destroying threads can sometimes be slow, which is what threaded libraries do upon entry and exit. Thus if a progam is already using threads, it can be faster to have multiple threads call threadsafe versions of the serial library if this is what the library does - likely the case for FFTW. > >>> 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I > >> Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call > >> gmx tune_pme. Most queueing systems don't like it if one parallel program calls > >> another parallel program. > >> > >>> tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working. > >> There should be an output somewhere with the exact command line that > >> tune_pme invoked to test whether mdrun works. That should shed some light > >> on the issue. > >> > >> Side note: Tuning is normally only useful on CPU-nodes. If your nodes also > >> have GPUs, you will probably not want to do this kind of PME tuning. > > Yes it's CPU only... I will tune pp:ppme procs manually. However, > most of the times it is failing with 'too large prime number' what is > considered to be 'too large'? > I think 2, 3, 5, 7, 11, and 13 and multiples of these are ok, but not > larger prime numbers. > So for a fixed number of procs only some of the combinations PP:PME > will actually work. > The ones that don't work would not be wise to choose from a performance > point of view. > > Best, > Carsten > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Sun Mar 29 03:55:45 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sun, 29 Mar 2020 01:55:45 -0000 Subject: [gmx-users] replica exchange simulations performance issues. Message-ID: Hi everybody. I've been experimenting with REMD for my system running on 48 cores with 4 gpus (I will need to scale up to 73 replicas because this is a complicated system with many DOF I'm open to being told this is all a silly idea). My run configuration is mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 the best I can squeeze out of this is 9ns/day. In a non-replica simulation I can hit 50ns/day with a single GPU and 12 cores. Looking at my accounting, for a single replica 52% of time is being spent on the "Force" category with 92% of my Mflops going into NxN Ewald Elec. + LJ [F] I'm wondering what I could do to reduce this bottle neck if anything. Thank you. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From miro.astore at gmail.com Sun Mar 29 03:57:31 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sun, 29 Mar 2020 01:57:31 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: References: Message-ID: correction: 99.3% is going into NxN Ewald Elec. + LJ [F] On Sun, Mar 29, 2020 at 12:55 PM Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea). > > My run configuration is > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > the best I can squeeze out of this is 9ns/day. In a non-replica > simulation I can hit 50ns/day with a single GPU and 12 cores. > > Looking at my accounting, for a single replica 52% of time is being > spent on the "Force" category with 92% of my Mflops going into NxN > Ewald Elec. + LJ [F] > > I'm wondering what I could do to reduce this bottle neck if anything. > > Thank you. > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From alexanderwien2k at gmail.com Sun Mar 29 05:25:18 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 29 Mar 2020 03:25:18 -0000 Subject: [gmx-users] Thin film drifting Message-ID: Dear all, In a system, I have a thin_film (infinitive in x-y directions) with water on top and bottom of it, PBC = xyz. By the below flags I try to remove the motion of the center of mass of the two group separately. comm-grps = thin_film Water comm-mode = Linear nstcomm = 100 However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex From rollyng at gmail.com Sun Mar 29 07:30:10 2020 From: rollyng at gmail.com (Rolly Ng) Date: Sun, 29 Mar 2020 05:30:10 -0000 Subject: [gmx-users] How to reduce the penalty of small molecule from CGenFF In-Reply-To: References: <00a401d602c5$c6ff6ed0$54fe4c70$@gmail.com> Message-ID: Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what are these parameters in water_constr.inp? what values should I use in my case? if @stage eq 4 echo ######## USING MP2 GEOMETRY!!! ######## echo QM dipole (Debye) echo mp2/6-31g*: X= -3.1938 Y= 1.2595 Z= 0.0011 Tot= 3.4332 echo hf/6-31g*: X= -3.4411 Y= 1.3570 Z= 0.0012 Tot= 3.6990 (2) How can I get the correct value for the IC table for surface of interest? I suppose H2O molecules are placed one at a time to the C and N atoms of my molecule but where to place the dummy? generate dum first none last none setup warn noangle nodihedral join @residue dum renumber !preparation of IC table for surface of interest ic edit dihe 1 N2 1 C1 1 H1 3 dum 0.0 dihe 1 C1 1 H1 3 dum 4 dum 0.0 dihe 4 dum 3 dum 1 H1 2 oh2 180.0 end ic fill preserve ic edit dihe 3 dum 1 H1 2 oh2 2 h1 90.0 dihe 3 dum 1 H1 2 oh2 2 h2 -90.0 bond 1 H1 3 dum 1. bond 3 dum 4 dum 1. bond 1 H1 2 oh2 @d !varied bond 2 oh2 2 h1 0.9572 bond 2 oh2 2 h2 0.9572 angl 1 C1 1 H1 3 dum 90.0 angl 1 H1 3 dum 4 dum 90.0 angl 3 dum 1 H1 2 oh2 90.0 angl 1 H1 2 oh2 2 h1 127.74 angl 1 H1 2 oh2 2 h2 127.74 end How can I know the bond, angle and dihedral without a GUI show these parameters? Thanks for your patient. Regards, Rolly On Thu, Mar 26, 2020 at 2:38 AM Justin Lemkul wrote: > > > On 3/25/20 12:52 PM, Rolly Ng wrote: > > Dear Gromacs Users, > > > > > > > > I am new to Gromacs and I followed the Protein-Ligand tutorial on the > > following webpage, > > > > http://www.mdtutorials.com/gmx/complex/02_topology.html > > > > > > > > It works for the example JZ4 but as I changed to another molecule, the > str > > file produced by the CGenFF server states very high penalty 84.5 > > > > > > > > Please have a look at my mol2 input and str output below. Your advises > are > > much appreciated! > > > > > > Have you read the CGenFF papers? The original 2010 JCC article is > basically a tutorial and review of the parametrization theory. > > -Justin > > > > > Thank you, > > > > Rolly > > > > > > > > @MOLECULE > > > > MF8 > > > > 20 19 0 0 0 > > > > SMALL > > > > GASTEIGER > > > > > > > > @ATOM > > > > 1 N08 19.3800 -17.4900 12.2190 N.pl3 1 MF8 > -0.2888 > > > > 2 C07 19.5160 -18.4740 11.4320 C.cat 1 MF8 > 0.3855 > > > > 3 N06 20.0120 -18.2750 10.1980 N.pl3 1 MF8 > -0.1861 > > > > 4 N09 19.1990 -19.7060 11.8570 N.pl3 1 MF8 > -0.1293 > > > > 5 C01 18.6460 -20.7310 8.7020 C.3 1 MF8 > 0.0558 > > > > 6 N02 19.3290 -19.4990 8.3110 N.pl3 1 MF8 > -0.2675 > > > > 7 N05 18.6660 -17.3520 8.6680 N.pl3 1 MF8 > -0.1291 > > > > 8 C04 19.3130 -18.3670 9.0550 C.cat 1 MF8 > 0.3896 > > > > 9 C03 20.0370 -19.6170 7.0360 C.3 1 MF8 > 0.0558 > > > > 10 H 19.6101 -16.5820 11.9161 H 1 MF8 > 0.2547 > > > > 11 H 19.0443 -17.6336 13.1333 H 1 MF8 > 0.2547 > > > > 12 H 20.9660 -18.0428 10.1266 H 1 MF8 > 0.2707 > > > > 13 H 19.3013 -20.4766 11.2529 H 1 MF8 > 0.3062 > > > > 14 H 18.8055 -21.4799 7.9546 H 1 MF8 > 0.0619 > > > > 15 H 17.5973 -20.5420 8.7994 H 1 MF8 > 0.0619 > > > > 16 H 19.0353 -21.0729 9.6382 H 1 MF8 > 0.0619 > > > > 17 H 18.1443 -17.3894 7.8339 H 1 MF8 > 0.3062 > > > > 18 H 19.9010 -20.6026 6.6424 H 1 MF8 > 0.0619 > > > > 19 H 21.0802 -19.4349 7.1891 H 1 MF8 > 0.0619 > > > > 20 H 19.6476 -18.8997 6.3441 H 1 MF8 > 0.0619 > > > > @BOND > > > > 1 1 2 1 > > > > 2 1 10 1 > > > > 3 1 11 1 > > > > 4 2 3 1 > > > > 5 2 4 2 > > > > 6 3 8 1 > > > > 7 3 12 1 > > > > 8 4 13 1 > > > > 9 5 6 1 > > > > 10 5 14 1 > > > > 11 5 15 1 > > > > 12 5 16 1 > > > > 13 6 9 1 > > > > 14 6 8 1 > > > > 15 7 8 2 > > > > 16 7 17 1 > > > > 17 9 18 1 > > > > 18 9 19 1 > > > > 19 9 20 1 > > > > > > > > > > > > * Toppar stream file generated by > > > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > > > * For use with CGenFF version 3.0.1 > > > > * > > > > > > > > read rtf card append > > > > * Topologies generated by > > > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > > > * > > > > 36 1 > > > > > > > > ! "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. > > > > > > > > RESI MF8 0.000 ! param penalty= 84.500 ; charge penalty= > 12.315 > > > > GROUP ! CHARGE CH_PENALTY > > > > ATOM N08 NG321 -0.603 ! 2.500 > > > > ATOM C07 CG2N1 0.547 ! 5.000 > > > > ATOM N06 NG311 -0.430 ! 6.533 > > > > ATOM N09 NG2D1 -0.907 ! 2.500 > > > > ATOM C01 CG331 -0.141 ! 9.593 > > > > ATOM N02 NG301 -0.371 ! 12.315 > > > > ATOM N05 NG2D1 -0.861 ! 4.101 > > > > ATOM C04 CG2N1 0.609 ! 10.954 > > > > ATOM C03 CG331 -0.141 ! 9.593 > > > > ATOM H1 HGPAM2 0.330 ! 0.000 > > > > ATOM H2 HGPAM2 0.330 ! 0.000 > > > > ATOM H3 HGPAM1 0.360 ! 0.090 > > > > ATOM H4 HGP1 0.369 ! 0.000 > > > > ATOM H5 HGA3 0.090 ! 2.518 > > > > ATOM H6 HGA3 0.090 ! 2.518 > > > > ATOM H7 HGA3 0.090 ! 2.518 > > > > ATOM H8 HGP1 0.369 ! 0.030 > > > > ATOM H9 HGA3 0.090 ! 2.518 > > > > ATOM H10 HGA3 0.090 ! 2.518 > > > > ATOM H11 HGA3 0.090 ! 2.518 > > > > > > > > BOND N08 C07 > > > > BOND N08 H1 > > > > BOND N08 H2 > > > > BOND C07 N06 > > > > BOND C07 N09 > > > > BOND N06 C04 > > > > BOND N06 H3 > > > > BOND N09 H4 > > > > BOND C01 N02 > > > > BOND C01 H5 > > > > BOND C01 H6 > > > > BOND C01 H7 > > > > BOND N02 C03 > > > > BOND N02 C04 > > > > BOND N05 C04 > > > > BOND N05 H8 > > > > BOND C03 H9 > > > > BOND C03 H10 > > > > BOND C03 H11 > > > > IMPR C07 N09 N06 N08 > > > > IMPR C04 N05 N02 N06 > > > > > > > > END > > > > > > > > read param card flex append > > > > * Parameters generated by analogy by > > > > * CHARMM General Force Field (CGenFF) program version 1.0.0 > > > > * > > > > > > > > ! 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. > > > > > > > > BONDS > > > > CG2N1 NG301 500.00 1.4400 ! MF8 , from CG2N1 NG311, penalty= 5 > > > > CG331 NG301 255.00 1.4630 ! MF8 , from CG331 NG311, penalty= 5 > > > > > > > > ANGLES > > > > NG2D1 CG2N1 NG301 50.00 125.00 ! MF8 , from NG2D1 CG2N1 NG311, > > penalty= 0.6 > > > > NG301 CG2N1 NG311 50.00 113.00 ! MF8 , from NG311 CG2N1 NG321, > > penalty= 1.8 > > > > NG301 CG331 HGA3 30.50 109.70 50.00 2.14000 ! MF8 , from > NG311 > > CG331 HGA3, penalty= 0.6 > > > > CG2N1 NG301 CG331 43.00 106.00 ! MF8 , from CG2N1 NG311 CG331, > > penalty= 5 > > > > CG331 NG301 CG331 53.00 110.90 ! MF8 , from CG3AM0 NG301 CG3AM0, > > penalty= 36.6 > > > > CG2N1 NG311 CG2N1 40.00 109.00 ! MF8 , from CG2R61 NG311 CG2R61, > > penalty= 46 > > > > > > > > DIHEDRALS > > > > NG301 CG2N1 NG2D1 HGP1 5.2000 2 180.00 ! MF8 , from NG311 > CG2N1 > > NG2D1 HGP1, penalty= 0.6 > > > > NG2D1 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG2D1 > CG2N1 > > NG311 CG331, penalty= 5 > > > > NG311 CG2N1 NG301 CG331 0.5000 2 180.00 ! MF8 , from NG321 > CG2N1 > > NG311 CG331, penalty= 6.2 > > > > NG2D1 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG2D1 > CG2N1 > > NG311 CG331, penalty= 69.9 > > > > NG301 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 > CG2N1 > > NG311 CG331, penalty= 71.7 > > > > NG301 CG2N1 NG311 HGPAM1 2.8000 2 180.00 ! MF8 , from NG321 > CG2N1 > > NG311 HGPAM1, penalty= 1.8 > > > > NG321 CG2N1 NG311 CG2N1 0.5000 2 180.00 ! MF8 , from NG321 > CG2N1 > > NG311 CG331, penalty= 69.9 > > > > HGA3 CG331 NG301 CG2N1 0.0000 3 180.00 ! MF8 , from HGA3 > CG331 > > NG311 CG2N1, penalty= 5 > > > > HGA3 CG331 NG301 CG331 0.0000 3 180.00 ! MF8 , from HGA2 > CG321 > > NG311 CG2R61, penalty= 84.5 > > > > > > > > IMPROPERS > > > > CG2N1 NG2D1 NG301 NG311 85.0000 0 0.00 ! MF8 , from CG2N1 > NG2D1 > > NG311 NG321, penalty= 1.5 > > > > > > > > END > > > > RETURN > > > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel 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 spoel at xray.bmc.uu.se Sun Mar 29 08:43:57 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 29 Mar 2020 06:43:57 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: References: Message-ID: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> Den 2020-03-29 kl. 05:24, skrev Alex: > Dear all, > In a system, I have a thin_film (infinitive in x-y directions) with water > on top and bottom of it, PBC = xyz. > By the below flags I try to remove the motion of the center of mass of the > two group separately. > comm-grps = thin_film Water > comm-mode = Linear > nstcomm = 100 > > However the thin film drift specially in x and y directions whereas I was > expecting to have no drifting for the thin film, If I understood correctly > the usage of the comm-grps! > > Would you please let me know how I can stop drifting of the thin film? > > Thank you, > Alex > Is that a liquid film? Are there interactions within the film and with water? The comm removal will calculate the center of mass taking periodic boundaries into account so if your film moves one molecule at a time the COM will stay in place. In a realistic system the friction between water and film should prevent this, hav eyou tried turning off comm? Historically this has been a fix for the Berendsen thermostat that accumulates energy, however with a stochastic thermostat it should not be necessary. Not sure about Nose-Hoover though. -- 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 benson_muite at emailplus.org Sun Mar 29 12:04:19 2020 From: benson_muite at emailplus.org (Benson Muite) Date: Sun, 29 Mar 2020 10:04:19 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: References: Message-ID: <62b8a3f6-2c0a-4d38-8c9e-99c946c536a2@www.fastmail.com> On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea). > > My run configuration is > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > the best I can squeeze out of this is 9ns/day. In a non-replica > simulation I can hit 50ns/day with a single GPU and 12 cores. What happens for a small number of replicas? > > Looking at my accounting, for a single replica 52% of time is being > spent on the "Force" category with 92% of my Mflops going into NxN > Ewald Elec. + LJ [F] > > I'm wondering what I could do to reduce this bottle neck if anything. Do you have access to more hardware? There area number of HPC centers in Australia. > > Thank you. > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Sun Mar 29 12:51:20 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sun, 29 Mar 2020 10:51:20 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: <62b8a3f6-2c0a-4d38-8c9e-99c946c536a2@www.fastmail.com> References: <62b8a3f6-2c0a-4d38-8c9e-99c946c536a2@www.fastmail.com> Message-ID: After much experimentation I managed to run mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 on a single node at 27 ns/day. This scaled up for 73 replicas on my 190 000 atom system ( using the same logic -np num_sims*12) on our gadi cluster in australia. I will soon see if i can get away with fewer replicas. Thanks for your help. Miro On Sun, Mar 29, 2020 at 9:04 PM Benson Muite wrote: > > > On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > because this is a complicated system with many DOF I'm open to being > > told this is all a silly idea). > > > > My run configuration is > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > What happens for a small number of replicas? > > > > > Looking at my accounting, for a single replica 52% of time is being > > spent on the "Force" category with 92% of my Mflops going into NxN > > Ewald Elec. + LJ [F] > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > Do you have access to more hardware? There area number of HPC centers in Australia. > > > > > Thank you. > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From miro.astore at gmail.com Sun Mar 29 12:52:08 2020 From: miro.astore at gmail.com (Miro Astore) Date: Sun, 29 Mar 2020 10:52:08 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: <62b8a3f6-2c0a-4d38-8c9e-99c946c536a2@www.fastmail.com> References: <62b8a3f6-2c0a-4d38-8c9e-99c946c536a2@www.fastmail.com> Message-ID: After much experimentation I managed to run mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 on a single node at 27 ns/day. This scaled up for 73 replicas on my 190 000 atom system ( using the same logic -np num_sims*12) on our gadi cluster in australia. I will soon see if i can get away with fewer replicas. Thanks for your help. Miro On Sun, Mar 29, 2020 at 9:04 PM Benson Muite wrote: > > > On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > because this is a complicated system with many DOF I'm open to being > > told this is all a silly idea). > > > > My run configuration is > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > What happens for a small number of replicas? > > > > > Looking at my accounting, for a single replica 52% of time is being > > spent on the "Force" category with 92% of my Mflops going into NxN > > Ewald Elec. + LJ [F] > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > Do you have access to more hardware? There area number of HPC centers in Australia. > > > > > Thank you. > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From alexanderwien2k at gmail.com Sun Mar 29 15:16:53 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 29 Mar 2020 13:16:53 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> Message-ID: Thank Prof. van der Spoel for the response. No, it isn't. The thin film is solid. There are interaction within the thin film and with water in the interface. Please find a short movie of the unwrapped trajectory of the simulation in below link (water molecules are hidden); It shows minimization, then equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl = v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = v-rescale and pcoupl = Parrinello-Rahman). https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf The thin film starts drifting significantly in the production along both x and y directions. Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel wrote: > Den 2020-03-29 kl. 05:24, skrev Alex: > > Dear all, > > In a system, I have a thin_film (infinitive in x-y directions) with water > > on top and bottom of it, PBC = xyz. > > By the below flags I try to remove the motion of the center of mass of > the > > two group separately. > > comm-grps = thin_film Water > > comm-mode = Linear > > nstcomm = 100 > > > > However the thin film drift specially in x and y directions whereas I was > > expecting to have no drifting for the thin film, If I understood > correctly > > the usage of the comm-grps! > > > > Would you please let me know how I can stop drifting of the thin film? > > > > Thank you, > > Alex > > > Is that a liquid film? Are there interactions within the film and with > water? The comm removal will calculate the center of mass taking > periodic boundaries into account so if your film moves one molecule at a > time the COM will stay in place. In a realistic system the friction > between water and film should prevent this, hav eyou tried turning off > comm? > > Historically this has been a fix for the Berendsen thermostat that > accumulates energy, however with a stochastic thermostat it should not > be necessary. Not sure about Nose-Hoover though. > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From nelgho at gmail.com Sun Mar 29 17:50:39 2020 From: nelgho at gmail.com (Nadia Elghobashi-Meinhardt) Date: Sun, 29 Mar 2020 15:50:39 -0000 Subject: [gmx-users] geometry optimization of metalloenzyme Message-ID: Hello everyone, I am trying to minimize the potential energy of a metalloenzyme containing Ni and Fe atoms. What is the best way to constrain (fix?) the position of the active site atoms during the geometry optimization? I have tried introducing bonds with relatively high force constants and alternatively, tried introducing a [constraints] section, but the atoms are still not staying put. Or should one use extra position restraints? Any tips are welcome! Thank you. From spoel at xray.bmc.uu.se Sun Mar 29 17:59:11 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 29 Mar 2020 15:59:11 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> Message-ID: <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> Den 2020-03-29 kl. 15:16, skrev Alex: > Thank Prof. van der Spoel for the response. > No, it isn't. The thin film is solid. There are interaction within the thin > film and with water in the interface. > > Please find a short movie of the unwrapped trajectory of the simulation in > below link (water molecules are hidden); It shows minimization, then > equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl = > v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = > v-rescale and pcoupl = Parrinello-Rahman). > > https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf > > The thin film starts drifting significantly in the production along both x > and y directions. Thanks, do you have isotropic pressure scaling? Is the shift towards higher x and y values? Maybe you can open an issue here: https://gitlab.com/gromacs/gromacs/-/issues > > Best regards, > Alex > > On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel > wrote: > >> Den 2020-03-29 kl. 05:24, skrev Alex: >>> Dear all, >>> In a system, I have a thin_film (infinitive in x-y directions) with water >>> on top and bottom of it, PBC = xyz. >>> By the below flags I try to remove the motion of the center of mass of >> the >>> two group separately. >>> comm-grps = thin_film Water >>> comm-mode = Linear >>> nstcomm = 100 >>> >>> However the thin film drift specially in x and y directions whereas I was >>> expecting to have no drifting for the thin film, If I understood >> correctly >>> the usage of the comm-grps! >>> >>> Would you please let me know how I can stop drifting of the thin film? >>> >>> Thank you, >>> Alex >>> >> Is that a liquid film? Are there interactions within the film and with >> water? The comm removal will calculate the center of mass taking >> periodic boundaries into account so if your film moves one molecule at a >> time the COM will stay in place. In a realistic system the friction >> between water and film should prevent this, hav eyou tried turning off >> comm? >> >> Historically this has been a fix for the Berendsen thermostat that >> accumulates energy, however with a stochastic thermostat it should not >> be necessary. Not sure about Nose-Hoover though. >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From alexanderwien2k at gmail.com Sun Mar 29 19:44:10 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 29 Mar 2020 17:44:10 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> Message-ID: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: > Den 2020-03-29 kl. 15:16, skrev Alex: > > Thank Prof. van der Spoel for the response. > > No, it isn't. The thin film is solid. There are interaction within the > thin > > film and with water in the interface. > > > > Please find a short movie of the unwrapped trajectory of the simulation > in > > below link (water molecules are hidden); It shows minimization, then > > equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl > = > > v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = > > v-rescale and pcoupl = Parrinello-Rahman). > > > > https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf > > > > The thin film starts drifting significantly in the production along both > x > > and y directions. > Thanks, do you have isotropic pressure scaling? > Yes, the pcoupltype is isotropic. Please find the mdp file in below link. https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa > > Is the shift towards higher x and y values? > The shift is toward higher y value (+y). It also firstly goes toward higher x value (+x ) for a very short time and then switches the direction to toward lower x value (-x) and finally shifts toward lower x value (-x). Maybe you can open an issue here: > https://gitlab.com/gromacs/gromacs/-/issues I will open an issue. Actually, in the later steps of the simulations, using umbrella sampling and wham, I want to simulate the PMF a single molecule (called A; 26 atoms) when it comes from water and diffuses inside the thin film till mid (com) of thin film. pull_group1 and pull_group2 would be the Mol_A and thin_film, respectively. I don't know if this kind of drifting would affect on the PMF, if so, how? If the comm-grps works I have the two following options to consider: ?comm-grps = thin_film Mol_A SOL? or ?comm-grps = Other SOL? Where the Other group contains the thin film and molecule A. Which one do you recommend, please? Thank you, Alex > > > > > Best regards, > > Alex > > > > On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < > spoel at xray.bmc.uu.se> > > wrote: > > > >> Den 2020-03-29 kl. 05:24, skrev Alex: > >>> Dear all, > >>> In a system, I have a thin_film (infinitive in x-y directions) with > water > >>> on top and bottom of it, PBC = xyz. > >>> By the below flags I try to remove the motion of the center of mass of > >> the > >>> two group separately. > >>> comm-grps = thin_film Water > >>> comm-mode = Linear > >>> nstcomm = 100 > >>> > >>> However the thin film drift specially in x and y directions whereas I > was > >>> expecting to have no drifting for the thin film, If I understood > >> correctly > >>> the usage of the comm-grps! > >>> > >>> Would you please let me know how I can stop drifting of the thin film? > >>> > >>> Thank you, > >>> Alex > >>> > >> Is that a liquid film? Are there interactions within the film and with > >> water? The comm removal will calculate the center of mass taking > >> periodic boundaries into account so if your film moves one molecule at a > >> time the COM will stay in place. In a realistic system the friction > >> between water and film should prevent this, hav eyou tried turning off > >> comm? > >> > >> Historically this has been a fix for the Berendsen thermostat that > >> accumulates energy, however with a stochastic thermostat it should not > >> be necessary. Not sure about Nose-Hoover though. > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Sun Mar 29 20:49:28 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Sun, 29 Mar 2020 18:49:28 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> Message-ID: <9f755a0e-3e76-dec2-6583-7124090192c0@xray.bmc.uu.se> Den 2020-03-29 kl. 19:43, skrev Alex: > Thanks. > > On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel > wrote: > >> Den 2020-03-29 kl. 15:16, skrev Alex: >>> Thank Prof. van der Spoel for the response. >>> No, it isn't. The thin film is solid. There are interaction within the >> thin >>> film and with water in the interface. >>> >>> Please find a short movie of the unwrapped trajectory of the simulation >> in >>> below link (water molecules are hidden); It shows minimization, then >>> equalization (NVT : tcoupl = v-rescale), then equalization (NpT : tcoupl >> = >>> v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = >>> v-rescale and pcoupl = Parrinello-Rahman). >>> >>> https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf >>> >>> The thin film starts drifting significantly in the production along both >> x >>> and y directions. >> Thanks, do you have isotropic pressure scaling? >> > Yes, the pcoupltype is isotropic. Please find the mdp file in below link. > https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa > >> >> Is the shift towards higher x and y values? >> > The shift is toward higher y value (+y). > It also firstly goes toward higher x value (+x ) for a very short time and > then switches the direction to toward lower x value (-x) and finally shifts > toward lower x value (-x). > But how is the solid modeled? Are there covalent bonds? It is not certain there is a problem, at least I am not convinced. In P scaling the coordinates of all particles are scaled by a constant and then certain atoms can hop over PBC. If you plot the center of mass including periodic boundaries (i.e. without unwrapping) it will be nicely in the center of the box with few fluctuations. gmx traj may do this for you. I and many others have done PMFs of small compounds over membranes of different types, but not sure that anyone has noticed problems with moving membranes. > Maybe you can open an issue here: >> https://gitlab.com/gromacs/gromacs/-/issues > > I will open an issue. > > Actually, in the later steps of the simulations, using umbrella sampling > and wham, I want to simulate the PMF a single molecule (called A; 26 atoms) > when it comes from water and diffuses inside the thin film till mid (com) > of thin film. pull_group1 and pull_group2 would be the Mol_A and thin_film, > respectively. > > I don't know if this kind of drifting would affect on the PMF, if so, how? > If the comm-grps works I have the two following options to consider: > ?comm-grps = thin_film Mol_A SOL? > or > ?comm-grps = Other SOL? > Where the Other group contains the thin film and molecule A. > Which one do you recommend, please? > > Thank you, > Alex > >> >>> >>> Best regards, >>> Alex >>> >>> On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < >> spoel at xray.bmc.uu.se> >>> wrote: >>> >>>> Den 2020-03-29 kl. 05:24, skrev Alex: >>>>> Dear all, >>>>> In a system, I have a thin_film (infinitive in x-y directions) with >> water >>>>> on top and bottom of it, PBC = xyz. >>>>> By the below flags I try to remove the motion of the center of mass of >>>> the >>>>> two group separately. >>>>> comm-grps = thin_film Water >>>>> comm-mode = Linear >>>>> nstcomm = 100 >>>>> >>>>> However the thin film drift specially in x and y directions whereas I >> was >>>>> expecting to have no drifting for the thin film, If I understood >>>> correctly >>>>> the usage of the comm-grps! >>>>> >>>>> Would you please let me know how I can stop drifting of the thin film? >>>>> >>>>> Thank you, >>>>> Alex >>>>> >>>> Is that a liquid film? Are there interactions within the film and with >>>> water? The comm removal will calculate the center of mass taking >>>> periodic boundaries into account so if your film moves one molecule at a >>>> time the COM will stay in place. In a realistic system the friction >>>> between water and film should prevent this, hav eyou tried turning off >>>> comm? >>>> >>>> Historically this has been a fix for the Berendsen thermostat that >>>> accumulates energy, however with a stochastic thermostat it should not >>>> be necessary. Not sure about Nose-Hoover though. >>>> -- >>>> David van der Spoel, Ph.D., Professor of Biology >>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>> http://www.icm.uu.se >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From alexanderwien2k at gmail.com Sun Mar 29 22:47:13 2020 From: alexanderwien2k at gmail.com (Alex) Date: Sun, 29 Mar 2020 20:47:13 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: <9f755a0e-3e76-dec2-6583-7124090192c0@xray.bmc.uu.se> References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> <9f755a0e-3e76-dec2-6583-7124090192c0@xray.bmc.uu.se> Message-ID: On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: > Den 2020-03-29 kl. 19:43, skrev Alex: > > Thanks. > > > > On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < > spoel at xray.bmc.uu.se> > > wrote: > > > >> Den 2020-03-29 kl. 15:16, skrev Alex: > >>> Thank Prof. van der Spoel for the response. > >>> No, it isn't. The thin film is solid. There are interaction within the > >> thin > >>> film and with water in the interface. > >>> > >>> Please find a short movie of the unwrapped trajectory of the simulation > >> in > >>> below link (water molecules are hidden); It shows minimization, then > >>> equalization (NVT : tcoupl = v-rescale), then equalization (NpT : > tcoupl > >> = > >>> v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = > >>> v-rescale and pcoupl = Parrinello-Rahman). > >>> > >>> https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf > >>> > >>> The thin film starts drifting significantly in the production along > both > >> x > >>> and y directions. > >> Thanks, do you have isotropic pressure scaling? > >> > > Yes, the pcoupltype is isotropic. Please find the mdp file in below link. > > https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa > > > >> > >> Is the shift towards higher x and y values? > >> > > The shift is toward higher y value (+y). > > It also firstly goes toward higher x value (+x ) for a very short time > and > > then switches the direction to toward lower x value (-x) and finally > shifts > > toward lower x value (-x). > > > But how is the solid modeled? Are there covalent bonds? It is not > certain there is a problem, at least I am not convinced. In P scaling > the coordinates of all particles are scaled by a constant and then > certain atoms can hop over PBC. If you plot the center of mass including > periodic boundaries (i.e. without unwrapping) it will be nicely in the > center of the box with few fluctuations. gmx traj may do this for you. > The thin film contains 1075 epoxy molecules in which there is no inter-molecule covalent bond. Below are the COM of the thin film with and without pbc in gmx traj. I admit you are right and the comm-grps works fine as gmx traj -pbc yes shows, thanks. PBC : Yes https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp PBC: No https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx > > I and many others have done PMFs of small compounds over membranes of > different types, but not sure that anyone has noticed problems with > moving membranes. I would also be so appreciated if you give me your preferences of the following two choices I have in the PMF calculation of Mol_A to the thin-film. ?comm-grps = *thin_film* *Mol_A* *SOL*? or ?comm-grps = *Other* *SOL*? Where the Other group contains the thin film and molecule A. Best regards, Alex > > > > Maybe you can open an issue here: > >> https://gitlab.com/gromacs/gromacs/-/issues > > > > I will open an issue. > > > > Actually, in the later steps of the simulations, using umbrella sampling > > and wham, I want to simulate the PMF a single molecule (called A; 26 > atoms) > > when it comes from water and diffuses inside the thin film till mid (com) > > of thin film. pull_group1 and pull_group2 would be the Mol_A and > thin_film, > > respectively. > > > > I don't know if this kind of drifting would affect on the PMF, if so, > how? > > If the comm-grps works I have the two following options to consider: > > ?comm-grps = thin_film Mol_A SOL? > > or > > ?comm-grps = Other SOL? > > Where the Other group contains the thin film and molecule A. > > Which one do you recommend, please? > > > > Thank you, > > Alex > > > >> > >>> > >>> Best regards, > >>> Alex > >>> > >>> On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < > >> spoel at xray.bmc.uu.se> > >>> wrote: > >>> > >>>> Den 2020-03-29 kl. 05:24, skrev Alex: > >>>>> Dear all, > >>>>> In a system, I have a thin_film (infinitive in x-y directions) with > >> water > >>>>> on top and bottom of it, PBC = xyz. > >>>>> By the below flags I try to remove the motion of the center of mass > of > >>>> the > >>>>> two group separately. > >>>>> comm-grps = thin_film Water > >>>>> comm-mode = Linear > >>>>> nstcomm = 100 > >>>>> > >>>>> However the thin film drift specially in x and y directions whereas I > >> was > >>>>> expecting to have no drifting for the thin film, If I understood > >>>> correctly > >>>>> the usage of the comm-grps! > >>>>> > >>>>> Would you please let me know how I can stop drifting of the thin > film? > >>>>> > >>>>> Thank you, > >>>>> Alex > >>>>> > >>>> Is that a liquid film? Are there interactions within the film and with > >>>> water? The comm removal will calculate the center of mass taking > >>>> periodic boundaries into account so if your film moves one molecule > at a > >>>> time the COM will stay in place. In a realistic system the friction > >>>> between water and film should prevent this, hav eyou tried turning off > >>>> comm? > >>>> > >>>> Historically this has been a fix for the Berendsen thermostat that > >>>> accumulates energy, however with a stochastic thermostat it should not > >>>> be necessary. Not sure about Nose-Hoover though. > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>> http://www.icm.uu.se > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From m.b.abdelaal at gmail.com Mon Mar 30 03:29:23 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Mon, 30 Mar 2020 01:29:23 -0000 Subject: [gmx-users] Temperature and Pressure coupling in NVT.mdp, NPT.mdp and md.mdp Message-ID: Hello everybody, Can anybody please help me as I am confused between the Temperature and Pressure coupling in the different .mdp files. Can you please tell me what is the difference between the Temperature and Pressure coupling in the NVT.mdp, NPT.mdp during the equilibration and in the md.mdp during the production run? In my project I am simulating the vacuum evaporation, So, I am inserting molecules in the vacuum and they should be at high temperatures (evaporation temperature) and at vacuum pressure. Should I add these 2 conditions through temperature and pressure coupling in the NVT.mdp and NPT.mdp during equilibration and also in the md.mdp during the production run? If yes, is there any difference between the NVT.mdp, NPT.mdp and the md.mdp in terms of temperature and pressure coupling ? If my molecules are moving with a specific velocity, should I generate the velocity in the NVT.mdp, NPT.mdp and in the md.mdp ? Many Thanks, Mohamed From m.b.abdelaal at gmail.com Mon Mar 30 03:29:24 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Mon, 30 Mar 2020 01:29:24 -0000 Subject: [gmx-users] Temperature and Pressure coupling in NVT.mdp, NPT.mdp and md.mdp Message-ID: Hello everybody, Can anybody please help me as I am confused between the Temperature and Pressure coupling in the different .mdp files. Can you please tell me what is the difference between the Temperature and Pressure coupling in the NVT.mdp, NPT.mdp during the equilibration and in the md.mdp during the production run? In my project I am simulating the vacuum evaporation, So, I am inserting molecules in the vacuum and they should be at high temperatures (evaporation temperature) and at vacuum pressure. Should I add these 2 conditions through temperature and pressure coupling in the NVT.mdp and NPT.mdp during equilibration and also in the md.mdp during the production run? If yes, is there any difference between the NVT.mdp, NPT.mdp and the md.mdp in terms of temperature and pressure coupling ? If my molecules are moving with a specific velocity, should I generate the velocity in the NVT.mdp, NPT.mdp and in the md.mdp ? Many Thanks, Mohamed From hfarag2 at illinois.edu Mon Mar 30 08:01:40 2020 From: hfarag2 at illinois.edu (Farag, Hossam Mostafa Abdelhamid Mostafa) Date: Mon, 30 Mar 2020 06:01:40 -0000 Subject: [gmx-users] gmx rdf (Angular Dependence) Message-ID: Hi, In the 2020.1 Release of Gromacs Documentation, it is written in page 486 the following: "With gmx rdf (page 135) it is also possible to calculate an angle dependent rdf g_AB(r, theta), where the angle theta is defined with respect to a certain laboratory axis e, see Fig. 5.50 B" However, when I go to "gmx rdf" command, I can't find any options to compute the anisotropic distribution. I only found an option called -xy, which I am not sure how to use if this is the one relevant to what I am looking for. Looking forward for your help. Many thanks! Hossam Farag Graduate Research Assistant Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 3614 Beckman Institute 405 N. Mathews Ave. Urbana, IL 61801 217.418.3196 | hfarag2 at illinois.edu [cid:e3f6c7fd-050f-4257-b3e1-c9207270e649] From nicolas.rozas at ug.uchile.cl Mon Mar 30 08:22:28 2020 From: nicolas.rozas at ug.uchile.cl (=?UTF-8?Q?Nicol=C3=A1s_Marcelo_Rozas_Castro?=) Date: Mon, 30 Mar 2020 06:22:28 -0000 Subject: [gmx-users] GROMACS 2019-rc1 install issues Message-ID: Hi everyone, I'm a beginner user of GROMACS, and I'm having some troubles with the installation. I follow the instruction in http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html , but when i run "make", appear the error shown in file attached. Any advice will be appreciated. Regards, Nicolas Rozas Castro Universidad de Chile, Faculty of Science. From spoel at xray.bmc.uu.se Mon Mar 30 08:46:17 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Mon, 30 Mar 2020 06:46:17 -0000 Subject: [gmx-users] Thin film drifting In-Reply-To: References: <8bfc3373-feb0-238b-ae07-813df9d20840@xray.bmc.uu.se> <7710fd90-4fcd-a292-6fe4-40f0b16c7cd5@xray.bmc.uu.se> <9f755a0e-3e76-dec2-6583-7124090192c0@xray.bmc.uu.se> Message-ID: <1da7d144-dee3-6616-8957-6bd1361a2b01@xray.bmc.uu.se> Den 2020-03-29 kl. 22:46, skrev Alex: > On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel > wrote: > >> Den 2020-03-29 kl. 19:43, skrev Alex: >>> Thanks. >>> >>> On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < >> spoel at xray.bmc.uu.se> >>> wrote: >>> >>>> Den 2020-03-29 kl. 15:16, skrev Alex: >>>>> Thank Prof. van der Spoel for the response. >>>>> No, it isn't. The thin film is solid. There are interaction within the >>>> thin >>>>> film and with water in the interface. >>>>> >>>>> Please find a short movie of the unwrapped trajectory of the simulation >>>> in >>>>> below link (water molecules are hidden); It shows minimization, then >>>>> equalization (NVT : tcoupl = v-rescale), then equalization (NpT : >> tcoupl >>>> = >>>>> v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl = >>>>> v-rescale and pcoupl = Parrinello-Rahman). >>>>> >>>>> https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf >>>>> >>>>> The thin film starts drifting significantly in the production along >> both >>>> x >>>>> and y directions. >>>> Thanks, do you have isotropic pressure scaling? >>>> >>> Yes, the pcoupltype is isotropic. Please find the mdp file in below link. >>> https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa >>> >>>> >>>> Is the shift towards higher x and y values? >>>> >>> The shift is toward higher y value (+y). >>> It also firstly goes toward higher x value (+x ) for a very short time >> and >>> then switches the direction to toward lower x value (-x) and finally >> shifts >>> toward lower x value (-x). >>> >> But how is the solid modeled? Are there covalent bonds? It is not >> certain there is a problem, at least I am not convinced. In P scaling >> the coordinates of all particles are scaled by a constant and then >> certain atoms can hop over PBC. If you plot the center of mass including >> periodic boundaries (i.e. without unwrapping) it will be nicely in the >> center of the box with few fluctuations. gmx traj may do this for you. >> > The thin film contains 1075 epoxy molecules in which there is no > inter-molecule covalent bond. > Below are the COM of the thin film with and without pbc in gmx traj. > > I admit you are right and the comm-grps works fine as gmx traj -pbc yes > shows, thanks. > PBC : Yes > https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp > > PBC: No > https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx Note that the net movement is a lot smaller than the fluctuations in the in the one with PBC, I don't think there is any problem. > >> >> I and many others have done PMFs of small compounds over membranes of >> different types, but not sure that anyone has noticed problems with >> moving membranes. > > I would also be so appreciated if you give me your preferences of the > following two choices I have in the PMF calculation of Mol_A to the > thin-film. > ?comm-grps = *thin_film* *Mol_A* *SOL*? > or > ?comm-grps = *Other* *SOL*? > Where the Other group contains the thin film and molecule A. > I would go for comm-grps = system. Make sure to compute the pmf based on the relative distance between your compound and the membrane. > Best regards, > Alex > >> >> >>> Maybe you can open an issue here: >>>> https://gitlab.com/gromacs/gromacs/-/issues >>> >>> I will open an issue. >>> >>> Actually, in the later steps of the simulations, using umbrella sampling >>> and wham, I want to simulate the PMF a single molecule (called A; 26 >> atoms) >>> when it comes from water and diffuses inside the thin film till mid (com) >>> of thin film. pull_group1 and pull_group2 would be the Mol_A and >> thin_film, >>> respectively. >>> >>> I don't know if this kind of drifting would affect on the PMF, if so, >> how? >>> If the comm-grps works I have the two following options to consider: >>> ?comm-grps = thin_film Mol_A SOL? >>> or >>> ?comm-grps = Other SOL? >>> Where the Other group contains the thin film and molecule A. >>> Which one do you recommend, please? >>> >>> Thank you, >>> Alex >>> >>>> >>>>> >>>>> Best regards, >>>>> Alex >>>>> >>>>> On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel < >>>> spoel at xray.bmc.uu.se> >>>>> wrote: >>>>> >>>>>> Den 2020-03-29 kl. 05:24, skrev Alex: >>>>>>> Dear all, >>>>>>> In a system, I have a thin_film (infinitive in x-y directions) with >>>> water >>>>>>> on top and bottom of it, PBC = xyz. >>>>>>> By the below flags I try to remove the motion of the center of mass >> of >>>>>> the >>>>>>> two group separately. >>>>>>> comm-grps = thin_film Water >>>>>>> comm-mode = Linear >>>>>>> nstcomm = 100 >>>>>>> >>>>>>> However the thin film drift specially in x and y directions whereas I >>>> was >>>>>>> expecting to have no drifting for the thin film, If I understood >>>>>> correctly >>>>>>> the usage of the comm-grps! >>>>>>> >>>>>>> Would you please let me know how I can stop drifting of the thin >> film? >>>>>>> >>>>>>> Thank you, >>>>>>> Alex >>>>>>> >>>>>> Is that a liquid film? Are there interactions within the film and with >>>>>> water? The comm removal will calculate the center of mass taking >>>>>> periodic boundaries into account so if your film moves one molecule >> at a >>>>>> time the COM will stay in place. In a realistic system the friction >>>>>> between water and film should prevent this, hav eyou tried turning off >>>>>> comm? >>>>>> >>>>>> Historically this has been a fix for the Berendsen thermostat that >>>>>> accumulates energy, however with a stochastic thermostat it should not >>>>>> be necessary. Not sure about Nose-Hoover though. >>>>>> -- >>>>>> David van der Spoel, Ph.D., Professor of Biology >>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>>>> http://www.icm.uu.se >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>> >>>> >>>> >>>> -- >>>> David van der Spoel, Ph.D., Professor of Biology >>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>> http://www.icm.uu.se >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From paul.bauer.q at gmail.com Mon Mar 30 08:56:01 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 30 Mar 2020 06:56:01 -0000 Subject: [gmx-users] GROMACS 2019-rc1 install issues In-Reply-To: References: Message-ID: <57c3a663-57ae-13dc-80f5-52932fdfd255@gmail.com> Hello, you can't attach files to the list here, either paste the error directly from the terminal or upload the file somewhere and share the link. Cheers Paul On 30/03/2020 08:22, Nicol?s Marcelo Rozas Castro wrote: > Hi everyone, > > I'm a beginner user of GROMACS, and I'm having some troubles with the > installation. I follow the instruction in > http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html , > but when i run "make", appear the error shown in file attached. > Any advice will be appreciated. > > Regards, > > Nicolas Rozas Castro > Universidad de Chile, Faculty of Science. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From paul.bauer.q at gmail.com Mon Mar 30 08:57:00 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 30 Mar 2020 06:57:00 -0000 Subject: [gmx-users] GROMACS 2019-rc1 install issues In-Reply-To: References: Message-ID: <4d85332a-b973-e0e9-fb11-7e67b35b801b@gmail.com> Also, please don't use Release candidate versions for anything serious. Instead use the latest official release that suits you. Cheers Paul On 30/03/2020 08:22, Nicol?s Marcelo Rozas Castro wrote: > Hi everyone, > > I'm a beginner user of GROMACS, and I'm having some troubles with the > installation. I follow the instruction in > http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html , > but when i run "make", appear the error shown in file attached. > Any advice will be appreciated. > > Regards, > > Nicolas Rozas Castro > Universidad de Chile, Faculty of Science. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From J.Sindt at ed.ac.uk Mon Mar 30 11:43:19 2020 From: J.Sindt at ed.ac.uk (SINDT Julien) Date: Mon, 30 Mar 2020 09:43:19 -0000 Subject: [gmx-users] Coupled Gromacs+CP2K QM/MM user survey Message-ID: Dear Gromacs users, My name is Julien Sindt and I am a member of the BioExcel Centre of Excellence. We aim to provide support to academic and industrial researchers in the use of high-performance computing (HPC) and high-throughput computing (HTC) in biomolecular research (if you're interested, please check out bioexcel.eu). One of the projects we are working on is coupling Gromacs with the quantum chemistry package CP2K to enable QM/MM simulation of biomolecular systems -- we are working in close collaboration with the developers of Gromacs to create this feature and hope that it will be available soon. We will support users of coupled Gromacs+CP2K on this mailing list and on the BioExcel QM/MM support forum at https://ask.bioexcel.eu/c/qmmm-biosim/. We've developed a survey to get a better idea of the interests and needs of the biomolecular simulation community with regards to QM/MM to help shape the user support and training that we provide, and very much welcome input from Gromacs users. If you would like a say in this, please contribute by filling out the survey here: https://bioexcel.eu/bioexcel-qm-mm-survey/ (deadline April 5th). The overall insights from the survey will be shared publicly later in the year. If you have any further questions, please feel free to contact me, either on this mailing list or by emailing J.Sindt at epcc.ed.ac.uk. Regards, Julien -------------------------------------------- Dr Julien Sindt HPC Applications Consultant, EPCC 2.20 The Bayes Centre 47 Potterrow Edinburgh, EH8 9BT Email: J.Sindt at epcc.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From jkozuch at stanford.edu Mon Mar 30 18:09:52 2020 From: jkozuch at stanford.edu (Jacek Artur Kozuch) Date: Mon, 30 Mar 2020 16:09:52 -0000 Subject: [gmx-users] GROMACS - tip7p itp and gro files - couldn't find them anywhere Message-ID: Hi all, I've seen that recent tip7p water model (https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out. However, I couldn't find or I missed where the itp and gro files are deposited. Anybody knows where to find them? Thanks a lot in advance! Best, Jacek [https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jpcbfk/2019/jpcbfk.2019.123.issue-21/acs.jpcb.9b03149/20190523/images/large/jp-2019-03149k_0011.jpeg] Seven-Site Effective Pair Potential for Simulating Liquid Water | The Journal of Physical Chemistry B Constant pressure simulations were carried out to construct a new rigid nonpolarizable seven-site water model (TIP7P), which is an effective and efficient version of flexible seven-fluctuating-charge water model. In this model, the positive charges are located on three nuclei and the negative charges disperse on two bond sites at the geometric center of each OH bond and two lone-pair sites ... pubs.acs.org ________________________________________________ Dr. Jacek Kozuch Postdoctoral Researcher - Boxer Lab Stanford University Department of Chemistry Keck Science Building 380 Roth Way Stanford, California 94305-5012 phone +1 (650) 723-0386 https://web.stanford.edu/group/boxer/ ________________________________________________ From sinaomrani96 at gmail.com Mon Mar 30 22:51:34 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Mon, 30 Mar 2020 20:51:34 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: Message-ID: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: > Hi, I would like to calculate the Onsager coefficient but after months of > study, I'm not able to do that. if anybody can help me I would really > appreciate it. I don't know if there is a specific command to do it or it > needs a series of analyses. > > P.S. I attached a picture of a formula that calculates the Onsager > coefficient from MD. > > sincerely, > Sina Omrani > From pall.szilard at gmail.com Tue Mar 31 00:57:04 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Mon, 30 Mar 2020 22:57:04 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: References: Message-ID: On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote: > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea). > It is a bad idea, you should have at least 1 physical core per replica and with a large system ideally more. However, if you are going for high efficiency (aggregate ns/day per phyical node), always put at least 2 replicas per GPU. > > My run configuration is > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > the best I can squeeze out of this is 9ns/day. In a non-replica > simulation I can hit 50ns/day with a single GPU and 12 cores. > That is abnormal and indicates that: - either something is wrong with the hardware mapping / assignment in your run or; do use simply "-pin on" and let mdrun manage threads pinning (that map-by-numa is certainly not optimal); also I advise against tweaking the thread count and using weird numbers like 11 (just use quarter); - your exchange overhead is very high (check the communication cost in the log) If you share some log files of a standalone and a replex run, we can advise where the performance loss comes from. Cheers, -- Szil?rd Looking at my accounting, for a single replica 52% of time is being > spent on the "Force" category with 92% of my Mflops going into NxN > Ewald Elec. + LJ [F] > > I'm wondering what I could do to reduce this bottle neck if anything. > > Thank you. > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests 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 Tue Mar 31 01:44:38 2020 From: miro.astore at gmail.com (Miro Astore) Date: Mon, 30 Mar 2020 23:44:38 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: References: Message-ID: I got up to 25-26 ns/day with my 4 replica system (same logic scaled up to 73 replicas) which I think is reasonable. Could I do better? mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 I have tried following the manual but I don't think i'm going it right I keep getting errors. If you have a minute to suggest how I could do this I would appreciate that. log file accounting: R E A L C Y C L E A N D T I M E A C C O U N T I N G On 12 MPI ranks Computing: Num Num Call Wall time Giga-Cycles Ranks Threads Count (s) total sum % ----------------------------------------------------------------------------- Domain decomp. 12 1 26702 251.490 8731.137 1.5 DD comm. load 12 1 25740 1.210 42.003 0.0 DD comm. bounds 12 1 26396 9.627 334.238 0.1 Neighbor search 12 1 25862 283.564 9844.652 1.7 Launch GPU ops. 12 1 5004002 343.309 11918.867 2.0 Comm. coord. 12 1 2476139 508.526 17654.811 3.0 Force 12 1 2502001 419.341 14558.495 2.5 Wait + Comm. F 12 1 2502001 347.752 12073.100 2.1 PME mesh 12 1 2502001 11721.893 406955.915 69.2 Wait Bonded GPU 12 1 2503 0.008 0.285 0.0 Wait GPU NB nonloc. 12 1 2502001 48.918 1698.317 0.3 Wait GPU NB local 12 1 2502001 19.475 676.141 0.1 NB X/F buffer ops. 12 1 9956280 753.489 26159.337 4.5 Write traj. 12 1 519 1.078 37.427 0.0 Update 12 1 2502001 434.272 15076.886 2.6 Constraints 12 1 2502001 701.800 24364.800 4.1 Comm. energies 12 1 125942 36.574 1269.776 0.2 Rest 1047.855 36378.988 6.2 ----------------------------------------------------------------------------- Total 16930.182 587775.176 100.0 ----------------------------------------------------------------------------- Breakdown of PME mesh computation ----------------------------------------------------------------------------- PME redist. X/F 12 1 5004002 1650.247 57292.604 9.7 PME spread 12 1 2502001 4133.126 143492.183 24.4 PME gather 12 1 2502001 2303.327 79965.968 13.6 PME 3D-FFT 12 1 5004002 2119.410 73580.828 12.5 PME 3D-FFT Comm. 12 1 5004002 918.318 31881.804 5.4 PME solve Elec 12 1 2502001 584.446 20290.548 3.5 ----------------------------------------------------------------------------- Best, Miro On Tue, Mar 31, 2020 at 9:58 AM Szil?rd P?ll wrote: > > On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote: > > > Hi everybody. I've been experimenting with REMD for my system running > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > because this is a complicated system with many DOF I'm open to being > > told this is all a silly idea). > > > > It is a bad idea, you should have at least 1 physical core per replica and > with a large system ideally more. > However, if you are going for high efficiency (aggregate ns/day per phyical > node), always put at least 2 replicas per GPU. > > > > > > My run configuration is > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > > > That is abnormal and indicates that: > - either something is wrong with the hardware mapping / assignment in your > run or; do use simply "-pin on" and let mdrun manage threads pinning (that > map-by-numa is certainly not optimal); also I advise against tweaking the > thread count and using weird numbers like 11 (just use quarter); > - your exchange overhead is very high (check the communication cost in the > log) > > If you share some log files of a standalone and a replex run, we can advise > where the performance loss comes from. > > Cheers, > -- > Szil?rd > > Looking at my accounting, for a single replica 52% of time is being > > spent on the "Force" category with 92% of my Mflops going into NxN > > Ewald Elec. + LJ [F] > > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > > > Thank you. > > -- > > Miro A. Astore (he/him) > > PhD Candidate | Computational Biophysics > > Office 434 A28 School of Physics > > University of Sydney > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe 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. -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney From m.b.abdelaal at gmail.com Tue Mar 31 02:31:35 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 31 Mar 2020 00:31:35 -0000 Subject: [gmx-users] Generating velocities Message-ID: Hello everybody, If my molecules are moving and I want to add the velocity, should I generate the velocity through the .mdp file, or should I add the velocities into my .gro file and insert the molecules? Thanks, Mohamed From m.b.abdelaal at gmail.com Tue Mar 31 02:31:35 2020 From: m.b.abdelaal at gmail.com (Mohamed Abdelaal) Date: Tue, 31 Mar 2020 00:31:35 -0000 Subject: [gmx-users] Generating velocities Message-ID: Hello everybody, If my molecules are moving and I want to add the velocity, should I generate the velocity through the .mdp file, or should I add the velocities into my .gro file and insert the molecules? Thanks, Mohamed From spoel at xray.bmc.uu.se Tue Mar 31 07:28:41 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 31 Mar 2020 05:28:41 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: Message-ID: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > Hi dear Gromacs users, > Sorry to ask again but I really appreciate the help on this subject. > > thanks. > > On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: > >> Hi, I would like to calculate the Onsager coefficient but after months of >> study, I'm not able to do that. if anybody can help me I would really >> appreciate it. I don't know if there is a specific command to do it or it >> needs a series of analyses. >> >> P.S. I attached a picture of a formula that calculates the Onsager >> coefficient from MD. >> >> sincerely, >> Sina Omrani >> I see no attachment and google does not help either. What is an Onsager coefficient? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From dallas.warren at monash.edu Tue Mar 31 08:18:35 2020 From: dallas.warren at monash.edu (Dallas Warren) Date: Tue, 31 Mar 2020 06:18:35 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> Message-ID: 3.5.9 Onsager Relations https://www.iue.tuwien.ac.at/phd/mwagner/node44.html See 3.146 and 3.147 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, 31 Mar 2020 at 16:28, David van der Spoel wrote: > Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > > Hi dear Gromacs users, > > Sorry to ask again but I really appreciate the help on this subject. > > > > thanks. > > > > On Fri, 27 Mar 2020 at 02:23, Sina Omrani > wrote: > > > >> Hi, I would like to calculate the Onsager coefficient but after > months of > >> study, I'm not able to do that. if anybody can help me I would really > >> appreciate it. I don't know if there is a specific command to do it or > it > >> needs a series of analyses. > >> > >> P.S. I attached a picture of a formula that calculates the Onsager > >> coefficient from MD. > >> > >> sincerely, > >> Sina Omrani > >> > I see no attachment and google does not help either. What is an Onsager > coefficient? > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Tue Mar 31 08:35:19 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 31 Mar 2020 06:35:19 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> Message-ID: <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> Den 2020-03-31 kl. 08:17, skrev Dallas Warren: > 3.5.9 Onsager Relations > https://www.iue.tuwien.ac.at/phd/mwagner/node44.html > > See 3.146 and 3.147 Thanks, I admit I am not familiar with this stuff, but seeing that this falls under the heading "Macroscopic Transport Models", what is the point in a microscopic simulation context? To prove or disprove or compare to the analytical relations? > > 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, 31 Mar 2020 at 16:28, David van der Spoel > wrote: > >> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: >>> Hi dear Gromacs users, >>> Sorry to ask again but I really appreciate the help on this subject. >>> >>> thanks. >>> >>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani >> wrote: >>> >>>> Hi, I would like to calculate the Onsager coefficient but after >> months of >>>> study, I'm not able to do that. if anybody can help me I would really >>>> appreciate it. I don't know if there is a specific command to do it or >> it >>>> needs a series of analyses. >>>> >>>> P.S. I attached a picture of a formula that calculates the Onsager >>>> coefficient from MD. >>>> >>>> sincerely, >>>> Sina Omrani >>>> >> I see no attachment and google does not help either. What is an Onsager >> coefficient? >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From a.mecklenfeld at tu-braunschweig.de Tue Mar 31 09:08:01 2020 From: a.mecklenfeld at tu-braunschweig.de (Andreas Mecklenfeld) Date: Tue, 31 Mar 2020 07:08:01 -0000 Subject: [gmx-users] Different force constants for different umbrella windows? Message-ID: <4cf4aa27-fd9b-dc12-d56f-9e8de0b1d236@tu-braunschweig.de> Dear GROMACS users, I've a question regarding umbrella sampling and its evaluation with gmx wham. Is it possible to use different force constants for different umbrella windows? Thanks, 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 jkozuch at zedat.fu-berlin.de Tue Mar 31 10:40:49 2020 From: jkozuch at zedat.fu-berlin.de (Jacek Artur Kozuch) Date: Tue, 31 Mar 2020 08:40:49 -0000 Subject: [gmx-users] itp file for TIP7P Message-ID: <63428.79.226.117.53.1585644047.webmail@webmail.zedat.fu-berlin.de> Dear all, I've seen the recent publication about the tip7p model (https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out in some simple MD simulations. Since I am still a pretty new Gromacs user, I didn't want to build the itp file myself and, potentially or most probably, mess up something. Is there a common github-like depository that I am missing where I could find the tip7p-parameters. If not, would be someone willing to help me in putting the itp file together - the authors haven't responded yet. Thanks in advance! Best wishes, Jacek From robert.cordina at strath.ac.uk Tue Mar 31 13:18:53 2020 From: robert.cordina at strath.ac.uk (Robert Cordina) Date: Tue, 31 Mar 2020 11:18:53 -0000 Subject: [gmx-users] Extracting information from trajectory Message-ID: Hi, I want to run numerous equilibrations of pure systems (i.e. numerous identical molecules in a box) and then extract multiple measurements (multiple bond angles, bond lengths, dihedrals etc.), and I will need to do this for all the molecules in the system once equilibrium is reached. Any suggestions as to the best approach to automate this information extraction please? Thanks in advance for your help. Best regards, Robert From pall.szilard at gmail.com Tue Mar 31 13:54:08 2020 From: pall.szilard at gmail.com (=?UTF-8?B?U3ppbMOhcmQgUMOhbGw=?=) Date: Tue, 31 Mar 2020 11:54:08 -0000 Subject: [gmx-users] replica exchange simulations performance issues. In-Reply-To: References: Message-ID: On Tue, Mar 31, 2020 at 1:45 AM Miro Astore wrote: > I got up to 25-26 ns/day with my 4 replica system (same logic scaled > up to 73 replicas) which I think is reasonable. Could I do better? > Hard to say without complete log file. Please share single run and multi run log files. > > mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir > 1 2 3 4 -replex 1000 > > I have tried following the manual but I don't think i'm going it > right I keep getting errors. If you have a minute to suggest how I > could do this I would appreciate that. > Again, the exact error messages and associated command line/log are necessary to be able to give further suggestions. -- Szil?rd > > log file accounting: > R E A L C Y C L E A N D T I M E A C C O U N T I N G > On 12 MPI ranks Computing: Num Num Call Wall time Giga-Cycles Ranks > Threads Count (s) total sum % > > ----------------------------------------------------------------------------- > Domain decomp. 12 1 26702 251.490 8731.137 1.5 > DD comm. load 12 1 25740 1.210 42.003 0.0 DD > comm. bounds 12 1 26396 9.627 334.238 0.1 > Neighbor search 12 1 25862 283.564 9844.652 1.7 > Launch GPU ops. 12 1 5004002 343.309 11918.867 2.0 > Comm. coord. 12 1 2476139 508.526 17654.811 3.0 Force 12 1 2502001 > 419.341 14558.495 2.5 > Wait + Comm. F 12 1 2502001 347.752 12073.100 2.1 > PME mesh 12 1 2502001 11721.893 406955.915 69.2 > Wait Bonded GPU 12 1 2503 0.008 0.285 0.0 > Wait GPU NB nonloc. 12 1 2502001 48.918 1698.317 0.3 > Wait GPU NB local 12 1 2502001 19.475 676.141 0.1 > NB X/F buffer ops. 12 1 9956280 753.489 26159.337 4.5 > Write traj. 12 1 519 1.078 37.427 0.0 Update 12 1 2502001 434.272 > 15076.886 2.6 > Constraints 12 1 2502001 701.800 24364.800 4.1 > Comm. energies 12 1 125942 36.574 1269.776 0.2 > Rest 1047.855 36378.988 6.2 > > ----------------------------------------------------------------------------- > Total 16930.182 587775.176 100.0 > > ----------------------------------------------------------------------------- > Breakdown of PME mesh computation > > ----------------------------------------------------------------------------- > PME redist. X/F 12 1 5004002 1650.247 57292.604 9.7 > PME spread 12 1 2502001 4133.126 143492.183 24.4 > PME gather 12 1 2502001 2303.327 79965.968 13.6 > PME 3D-FFT 12 1 5004002 2119.410 73580.828 12.5 > PME 3D-FFT Comm. 12 1 5004002 918.318 31881.804 5.4 > PME solve Elec 12 1 2502001 584.446 20290.548 3.5 > > ----------------------------------------------------------------------------- > > Best, Miro > > On Tue, Mar 31, 2020 at 9:58 AM Szil?rd P?ll > wrote: > > > > On Sun, Mar 29, 2020 at 3:56 AM Miro Astore > wrote: > > > > > Hi everybody. I've been experimenting with REMD for my system running > > > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > > > because this is a complicated system with many DOF I'm open to being > > > told this is all a silly idea). > > > > > > > It is a bad idea, you should have at least 1 physical core per replica > and > > with a large system ideally more. > > However, if you are going for high efficiency (aggregate ns/day per > phyical > > node), always put at least 2 replicas per GPU. > > > > > > > > > > My run configuration is > > > mpirun -np 4 --map-by numa gmx_mpi mdrun -cpi memb_prod1.cpt -ntomp 11 > > > -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 > > > > > > the best I can squeeze out of this is 9ns/day. In a non-replica > > > simulation I can hit 50ns/day with a single GPU and 12 cores. > > > > > > > That is abnormal and indicates that: > > - either something is wrong with the hardware mapping / assignment in > your > > run or; do use simply "-pin on" and let mdrun manage threads pinning > (that > > map-by-numa is certainly not optimal); also I advise against tweaking the > > thread count and using weird numbers like 11 (just use quarter); > > - your exchange overhead is very high (check the communication cost in > the > > log) > > > > If you share some log files of a standalone and a replex run, we can > advise > > where the performance loss comes from. > > > > Cheers, > > -- > > Szil?rd > > > > Looking at my accounting, for a single replica 52% of time is being > > > spent on the "Force" category with 92% of my Mflops going into NxN > > > Ewald Elec. + LJ [F] > > > > > > > > I'm wondering what I could do to reduce this bottle neck if anything. > > > > > > Thank you. > > > -- > > > Miro A. Astore (he/him) > > > PhD Candidate | Computational Biophysics > > > Office 434 A28 School of Physics > > > University of Sydney > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe 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. > > > > -- > Miro A. Astore (he/him) > PhD Candidate | Computational Biophysics > Office 434 A28 School of Physics > University of Sydney > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. From sinaomrani96 at gmail.com Tue Mar 31 14:19:04 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Tue, 31 Mar 2020 12:19:04 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> Message-ID: As far as I know, the Onsager coefficient is used to calculate MS diffusion coefficient that is a microscopic property. Then we can use this MS coefficient and relate it to macroscopic properties that we already have experimentally. On Tue, 31 Mar 2020 at 11:05, David van der Spoel wrote: > Den 2020-03-31 kl. 08:17, skrev Dallas Warren: > > 3.5.9 Onsager Relations > > https://www.iue.tuwien.ac.at/phd/mwagner/node44.html > > > > See 3.146 and 3.147 > > Thanks, I admit I am not familiar with this stuff, but seeing that this > falls under the heading "Macroscopic Transport Models", what is the > point in a microscopic simulation context? To prove or disprove or > compare to the analytical relations? > > > > > 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, 31 Mar 2020 at 16:28, David van der Spoel > > wrote: > > > >> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > >>> Hi dear Gromacs users, > >>> Sorry to ask again but I really appreciate the help on this subject. > >>> > >>> thanks. > >>> > >>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani > >> wrote: > >>> > >>>> Hi, I would like to calculate the Onsager coefficient but after > >> months of > >>>> study, I'm not able to do that. if anybody can help me I would really > >>>> appreciate it. I don't know if there is a specific command to do it or > >> it > >>>> needs a series of analyses. > >>>> > >>>> P.S. I attached a picture of a formula that calculates the Onsager > >>>> coefficient from MD. > >>>> > >>>> sincerely, > >>>> Sina Omrani > >>>> > >> I see no attachment and google does not help either. What is an Onsager > >> coefficient? > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Tue Mar 31 15:21:15 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 31 Mar 2020 13:21:15 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> Message-ID: <6c0f0841-e8d6-fa16-521b-76bec3b67592@xray.bmc.uu.se> Den 2020-03-31 kl. 14:11, skrev Sina Omrani: > As far as I know, the Onsager coefficient is used to calculate MS diffusion > coefficient that is a microscopic property. Then we can use this MS > coefficient and relate it to macroscopic properties that we already have > experimentally. What does MS mean? And for my curiosity, what kind of macroscopic properties are you after? As far as I know many if not most macroscopic properties can be computed directly from a simulation, but I may be wrong. > > On Tue, 31 Mar 2020 at 11:05, David van der Spoel > wrote: > >> Den 2020-03-31 kl. 08:17, skrev Dallas Warren: >>> 3.5.9 Onsager Relations >>> https://www.iue.tuwien.ac.at/phd/mwagner/node44.html >>> >>> See 3.146 and 3.147 >> >> Thanks, I admit I am not familiar with this stuff, but seeing that this >> falls under the heading "Macroscopic Transport Models", what is the >> point in a microscopic simulation context? To prove or disprove or >> compare to the analytical relations? >> >>> >>> 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, 31 Mar 2020 at 16:28, David van der Spoel >>> wrote: >>> >>>> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: >>>>> Hi dear Gromacs users, >>>>> Sorry to ask again but I really appreciate the help on this subject. >>>>> >>>>> thanks. >>>>> >>>>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani >>>> wrote: >>>>> >>>>>> Hi, I would like to calculate the Onsager coefficient but after >>>> months of >>>>>> study, I'm not able to do that. if anybody can help me I would really >>>>>> appreciate it. I don't know if there is a specific command to do it or >>>> it >>>>>> needs a series of analyses. >>>>>> >>>>>> P.S. I attached a picture of a formula that calculates the Onsager >>>>>> coefficient from MD. >>>>>> >>>>>> sincerely, >>>>>> Sina Omrani >>>>>> >>>> I see no attachment and google does not help either. What is an Onsager >>>> coefficient? >>>> >>>> -- >>>> David van der Spoel, Ph.D., Professor of Biology >>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>> http://www.icm.uu.se >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From sinaomrani96 at gmail.com Tue Mar 31 16:01:30 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Tue, 31 Mar 2020 14:01:30 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: <6c0f0841-e8d6-fa16-521b-76bec3b67592@xray.bmc.uu.se> References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> <6c0f0841-e8d6-fa16-521b-76bec3b67592@xray.bmc.uu.se> Message-ID: it is Maxwell-Stefan. I want to calculate diffusion coefficients. from EMD we can calculate the MS diffusion coefficient that it is impossible to measure experimentally (because it is based on chemical potential gradient that is hard to measure) and with the thermodynamic correction factor it could be transformed into the Fick diffusion coefficient that is experimentally measurable. Although, there are NEMD method for calculating Fick diffusion coefficient but it is not prefered for some reasons. On Tue, 31 Mar 2020 at 17:51, David van der Spoel wrote: > Den 2020-03-31 kl. 14:11, skrev Sina Omrani: > > As far as I know, the Onsager coefficient is used to calculate MS > diffusion > > coefficient that is a microscopic property. Then we can use this MS > > coefficient and relate it to macroscopic properties that we already have > > experimentally. > > What does MS mean? > > And for my curiosity, what kind of macroscopic properties are you after? > As far as I know many if not most macroscopic properties can be computed > directly from a simulation, but I may be wrong. > > > > > > On Tue, 31 Mar 2020 at 11:05, David van der Spoel > > wrote: > > > >> Den 2020-03-31 kl. 08:17, skrev Dallas Warren: > >>> 3.5.9 Onsager Relations > >>> https://www.iue.tuwien.ac.at/phd/mwagner/node44.html > >>> > >>> See 3.146 and 3.147 > >> > >> Thanks, I admit I am not familiar with this stuff, but seeing that this > >> falls under the heading "Macroscopic Transport Models", what is the > >> point in a microscopic simulation context? To prove or disprove or > >> compare to the analytical relations? > >> > >>> > >>> 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, 31 Mar 2020 at 16:28, David van der Spoel < > spoel at xray.bmc.uu.se> > >>> wrote: > >>> > >>>> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > >>>>> Hi dear Gromacs users, > >>>>> Sorry to ask again but I really appreciate the help on this subject. > >>>>> > >>>>> thanks. > >>>>> > >>>>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani > >>>> wrote: > >>>>> > >>>>>> Hi, I would like to calculate the Onsager coefficient but after > >>>> months of > >>>>>> study, I'm not able to do that. if anybody can help me I would > really > >>>>>> appreciate it. I don't know if there is a specific command to do it > or > >>>> it > >>>>>> needs a series of analyses. > >>>>>> > >>>>>> P.S. I attached a picture of a formula that calculates the Onsager > >>>>>> coefficient from MD. > >>>>>> > >>>>>> sincerely, > >>>>>> Sina Omrani > >>>>>> > >>>> I see no attachment and google does not help either. What is an > Onsager > >>>> coefficient? > >>>> > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>> http://www.icm.uu.se > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From spoel at xray.bmc.uu.se Tue Mar 31 17:03:21 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Tue, 31 Mar 2020 15:03:21 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> <6c0f0841-e8d6-fa16-521b-76bec3b67592@xray.bmc.uu.se> Message-ID: Den 2020-03-31 kl. 16:01, skrev Sina Omrani: > it is Maxwell-Stefan. > > I want to calculate diffusion coefficients. from EMD we can calculate the > MS diffusion coefficient that it is impossible to measure experimentally > (because it is based on chemical potential gradient that is hard to > measure) and with the thermodynamic correction factor it could be > transformed into the Fick diffusion coefficient that is experimentally > measurable. Although, there are NEMD method for calculating Fick diffusion > coefficient but it is not prefered for some reasons. OK, thanks, interesting. This does not look too promising: https://en.wikipedia.org/wiki/Maxwell%E2%80%93Stefan_diffusion "A major disadvantage of the Maxwell?Stefan theory is that the diffusion coefficients, with the exception of the diffusion of dilute gases, do not correspond to the Fick's diffusion coefficients and are therefore not tabulated." Long time ago I published a paper about self-diffusion in alcohol-water mixtures as a function of concentration (J Chem Phys 119 (2003) p 7308). We mention "The relation between self diffusion and mutual diffusion is not straightforward58 and has hitherto only been studied by simulation for simple Lennard-Jones particles.59". But maybe this is not relevant at all. > > On Tue, 31 Mar 2020 at 17:51, David van der Spoel > wrote: > >> Den 2020-03-31 kl. 14:11, skrev Sina Omrani: >>> As far as I know, the Onsager coefficient is used to calculate MS >> diffusion >>> coefficient that is a microscopic property. Then we can use this MS >>> coefficient and relate it to macroscopic properties that we already have >>> experimentally. >> >> What does MS mean? >> >> And for my curiosity, what kind of macroscopic properties are you after? >> As far as I know many if not most macroscopic properties can be computed >> directly from a simulation, but I may be wrong. >> >> >>> >>> On Tue, 31 Mar 2020 at 11:05, David van der Spoel >>> wrote: >>> >>>> Den 2020-03-31 kl. 08:17, skrev Dallas Warren: >>>>> 3.5.9 Onsager Relations >>>>> https://www.iue.tuwien.ac.at/phd/mwagner/node44.html >>>>> >>>>> See 3.146 and 3.147 >>>> >>>> Thanks, I admit I am not familiar with this stuff, but seeing that this >>>> falls under the heading "Macroscopic Transport Models", what is the >>>> point in a microscopic simulation context? To prove or disprove or >>>> compare to the analytical relations? >>>> >>>>> >>>>> 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, 31 Mar 2020 at 16:28, David van der Spoel < >> spoel at xray.bmc.uu.se> >>>>> wrote: >>>>> >>>>>> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: >>>>>>> Hi dear Gromacs users, >>>>>>> Sorry to ask again but I really appreciate the help on this subject. >>>>>>> >>>>>>> thanks. >>>>>>> >>>>>>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani >>>>>> wrote: >>>>>>> >>>>>>>> Hi, I would like to calculate the Onsager coefficient but after >>>>>> months of >>>>>>>> study, I'm not able to do that. if anybody can help me I would >> really >>>>>>>> appreciate it. I don't know if there is a specific command to do it >> or >>>>>> it >>>>>>>> needs a series of analyses. >>>>>>>> >>>>>>>> P.S. I attached a picture of a formula that calculates the Onsager >>>>>>>> coefficient from MD. >>>>>>>> >>>>>>>> sincerely, >>>>>>>> Sina Omrani >>>>>>>> >>>>>> I see no attachment and google does not help either. What is an >> Onsager >>>>>> coefficient? >>>>>> >>>>>> -- >>>>>> David van der Spoel, Ph.D., Professor of Biology >>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>>>> http://www.icm.uu.se >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-request at gromacs.org. >>>>>> >>>> >>>> >>>> -- >>>> David van der Spoel, Ph.D., Professor of Biology >>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>> http://www.icm.uu.se >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-request at gromacs.org. >>>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-request at gromacs.org. >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se From sinaomrani96 at gmail.com Tue Mar 31 17:35:55 2020 From: sinaomrani96 at gmail.com (Sina Omrani) Date: Tue, 31 Mar 2020 15:35:55 -0000 Subject: [gmx-users] Onsager coefficient In-Reply-To: References: <06e6e7b9-289a-370b-8e8c-65d5367431c9@xray.bmc.uu.se> <353d1cb2-b349-66f2-8ced-87bf13ca0939@xray.bmc.uu.se> <6c0f0841-e8d6-fa16-521b-76bec3b67592@xray.bmc.uu.se> Message-ID: Thanks, recently there have been studies that found a good match between MD simulations and experimental results for multicomponent systems and shows that there is a good chance for finding a relation for diffusion coefficient as a function of concentration. Self-diffusion coefficients can be used for predicting MS diffusion coefficients (like Darken equation) but I don't want to use this kind of relations. I am looking for the MS diffusion coefficient from MD to relate it to Fick's coefficient in my ternary system. On Tue, 31 Mar 2020 at 19:33, David van der Spoel wrote: > Den 2020-03-31 kl. 16:01, skrev Sina Omrani: > > it is Maxwell-Stefan. > > > > I want to calculate diffusion coefficients. from EMD we can calculate the > > MS diffusion coefficient that it is impossible to measure experimentally > > (because it is based on chemical potential gradient that is hard to > > measure) and with the thermodynamic correction factor it could be > > transformed into the Fick diffusion coefficient that is experimentally > > measurable. Although, there are NEMD method for calculating Fick > diffusion > > coefficient but it is not prefered for some reasons. > > OK, thanks, interesting. This does not look too promising: > https://en.wikipedia.org/wiki/Maxwell%E2%80%93Stefan_diffusion > "A major disadvantage of the Maxwell?Stefan theory is that the diffusion > coefficients, with the exception of the diffusion of dilute gases, do > not correspond to the Fick's diffusion coefficients and are therefore > not tabulated." > > Long time ago I published a paper about self-diffusion in alcohol-water > mixtures as a function of concentration (J Chem Phys 119 (2003) p 7308). > We mention "The relation between self diffusion and mutual diffusion is > not straightforward58 and has hitherto only been studied by simulation > for simple Lennard-Jones particles.59". But maybe this is not relevant > at all. > > > > > On Tue, 31 Mar 2020 at 17:51, David van der Spoel > > wrote: > > > >> Den 2020-03-31 kl. 14:11, skrev Sina Omrani: > >>> As far as I know, the Onsager coefficient is used to calculate MS > >> diffusion > >>> coefficient that is a microscopic property. Then we can use this MS > >>> coefficient and relate it to macroscopic properties that we already > have > >>> experimentally. > >> > >> What does MS mean? > >> > >> And for my curiosity, what kind of macroscopic properties are you after? > >> As far as I know many if not most macroscopic properties can be computed > >> directly from a simulation, but I may be wrong. > >> > >> > >>> > >>> On Tue, 31 Mar 2020 at 11:05, David van der Spoel < > spoel at xray.bmc.uu.se> > >>> wrote: > >>> > >>>> Den 2020-03-31 kl. 08:17, skrev Dallas Warren: > >>>>> 3.5.9 Onsager Relations > >>>>> https://www.iue.tuwien.ac.at/phd/mwagner/node44.html > >>>>> > >>>>> See 3.146 and 3.147 > >>>> > >>>> Thanks, I admit I am not familiar with this stuff, but seeing that > this > >>>> falls under the heading "Macroscopic Transport Models", what is the > >>>> point in a microscopic simulation context? To prove or disprove or > >>>> compare to the analytical relations? > >>>> > >>>>> > >>>>> 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, 31 Mar 2020 at 16:28, David van der Spoel < > >> spoel at xray.bmc.uu.se> > >>>>> wrote: > >>>>> > >>>>>> Den 2020-03-30 kl. 22:51, skrev Sina Omrani: > >>>>>>> Hi dear Gromacs users, > >>>>>>> Sorry to ask again but I really appreciate the help on this > subject. > >>>>>>> > >>>>>>> thanks. > >>>>>>> > >>>>>>> On Fri, 27 Mar 2020 at 02:23, Sina Omrani > >>>>>> wrote: > >>>>>>> > >>>>>>>> Hi, I would like to calculate the Onsager coefficient but > after > >>>>>> months of > >>>>>>>> study, I'm not able to do that. if anybody can help me I would > >> really > >>>>>>>> appreciate it. I don't know if there is a specific command to do > it > >> or > >>>>>> it > >>>>>>>> needs a series of analyses. > >>>>>>>> > >>>>>>>> P.S. I attached a picture of a formula that calculates the Onsager > >>>>>>>> coefficient from MD. > >>>>>>>> > >>>>>>>> sincerely, > >>>>>>>> Sina Omrani > >>>>>>>> > >>>>>> I see no attachment and google does not help either. What is an > >> Onsager > >>>>>> coefficient? > >>>>>> > >>>>>> -- > >>>>>> David van der Spoel, Ph.D., Professor of Biology > >>>>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>>>> http://www.icm.uu.se > >>>>>> -- > >>>>>> Gromacs Users mailing list > >>>>>> > >>>>>> * Please search the archive at > >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>>>> posting! > >>>>>> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>>> > >>>>>> * For (un)subscribe requests visit > >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>>> send a mail to gmx-users-request at gromacs.org. > >>>>>> > >>>> > >>>> > >>>> -- > >>>> David van der Spoel, Ph.D., Professor of Biology > >>>> Head of Department, Cell & Molecular Biology, Uppsala University. > >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >>>> http://www.icm.uu.se > >>>> -- > >>>> Gromacs Users mailing list > >>>> > >>>> * Please search the archive at > >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>>> posting! > >>>> > >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>> > >>>> * For (un)subscribe requests visit > >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>>> send a mail to gmx-users-request at gromacs.org. > >>>> > >> > >> > >> -- > >> David van der Spoel, Ph.D., Professor of Biology > >> Head of Department, Cell & Molecular Biology, Uppsala University. > >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > >> http://www.icm.uu.se > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-request at gromacs.org. > >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-request at gromacs.org. > From a.gurtovenko at googlemail.com Tue Mar 31 18:59:51 2020 From: a.gurtovenko at googlemail.com (Andrey Gurtovenko) Date: Tue, 31 Mar 2020 16:59:51 -0000 Subject: [gmx-users] 1-4 LJ interactions Message-ID: Dear All, Recently I realized that I don't fully understand what should be done in Gromacs to account for 1-4 LJ interactions. According to the manual: "gen-pairs is for pair generation. The default is ?no?, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting ?yes? generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ." http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html Therefore, I had an impression that to account for 1-4 interactions in some generic force-field, it is enough to set gen-pairs=yes. However, it turns out that this is not the case: in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the [pairs] section of the topology file of a system. Otherwise 1-4 interactions are NOT accounted for. Can someone comment on this? If I am right, maybe it is worth to clarify this point in the manual? with kind regards, Andrey Gurtovenko