Re: [gmx-users] Creating POSRES option for MDP file
On 2/27/15 8:28 PM, Agnivo Gosai wrote: Dear Users My system can be identified into 2 groups ( default ) namely DNA and Protein. To use the pull code , I want to apply pulling force on DNA and keep Protein fixed. Now, I have two itp files for my protein ( two chains,A and B). So do I need to include something like this :- ; Include Position restraint file #ifdef POSRES_P #include posre_Protein_chain_A.itp #endif and ; Include Position restraint file #ifdef POSRES_P #include posre_Protein_chain_B.itp #endif in both of the itp files for the two chains and then use -DPOSRES_P in the mdp file for the pulling simulation ? The approach is correct, provided the restraint #include statements immediately follow the [moleculetype] directives to which they apply. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GMX 5.0 compilation across different platforms
Dear All, I would like to statically compile GROMACS 5 in an Intel Xeon X3430 machine with gcc4.7 (cluster front node) BUT run it on an Intel Xeon E5-2650V2 machine (cluster compute node). Would that be possible ? And if so, how should I do it ? Haven't found it on the Installation_Instructions webpage. Thanks in advance. BR, D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX 5.0 compilation across different platforms
You need to cross-compile by selecting the SIMD support and possibly RDTSCP support. It's here: http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects -- Szilárd On Fri, Feb 27, 2015 at 2:54 PM, David McGiven davidmcgiv...@gmail.com wrote: Dear All, I would like to statically compile GROMACS 5 in an Intel Xeon X3430 machine with gcc4.7 (cluster front node) BUT run it on an Intel Xeon E5-2650V2 machine (cluster compute node). Would that be possible ? And if so, how should I do it ? Haven't found it on the Installation_Instructions webpage. Thanks in advance. BR, D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about energies in a very simple system
Hi, Thank you all for your anwsers. Let me explain the circumstances that sorround this. I'm using a developer's version of ACEMD, which grant me access to its internal data structures. When I run this version of acemd, it gives me the information of all the atoms, bonds, angles, dihedrals, exclusion list, 1-4 pairs and running parameters(cutoffs, switching mode, etc...) of the system that I'm running, with this information I can create the .gro, .top and .mdp There may be something weird in the .top file that I showed you previously in this post. If you take a look at this: [ moleculetype ] ;namenrexcl sys 0 it may look strange this nrexcl = 0 but actually it make sense because what I explained some lines above that ACEMD gives me the exclusion list, so putting this nrexcl = 0, gromacs calculates the interactions for all those pair of atoms within the cutoff radius except those that are in the exclusion list. Let me show you a pair of real cases that I've tried today. 400 WATER MOLECULES ACEMD NAMD GROMACS LJ 2540.0544 2538.2893 2538.28 COULOMB -3996.3431 -3993.6970 -3993.17 This first case is a SPE simulation of a box full of water molecules, nothing more, only 400 water molecules, as you can see, result are pretty much the same, energies are the same for the three programs (well, acemd deviates 2kj/mol in LJ and 3kj/mol in Coulomb, but this doesn't matter really) I want to highlight that water molecules don't have 1-4 pairs, only exclusions. I say this because I'm sure that the problem in the following case (actually in all cases) is caused by the 1-4 interactions. 1A1X ACEMD NAMD GROMACS BOND 201.9381 201.4818 201.809 ANGLE 1318.6907 1317.691 1317.8 DIHEDRAL 5225.9049 5222.46 5222.41 LJ 25404.8407 25391.6948 25386.68 COULOMB -219604.180 -219387.922 -231465.3 This second case is the SPE calculation of a pdb (code 1a1x) sourrounded by water. As you can see every energy term coincide between the three programs (with the logical deviation of using distinct software), but Coulomb result don't make sense in the gromacs case, it deviates more than 11000KJ/mol respect to acemd or namd. I put here the Lj and Coulomb energies in the way that g_energy gives the results: LJ(SR) = 27393.2 LJ-14= 2006.52 Coulomb(SR) = -216459 Coulomb-14 = 15006.3 Looking back to the water example, which hasn't got 1-4 interactions, I imagine that the Coulomb(SR) energy term is well calculated (in the water system coulomb energies coincide) and that the problem comes with the Coulomb-14 energy term, but this doesn't make much sense because in that case, LJ energies should also be bad... Thank you very much for your attention, any help or idea of what's going wrong would be highly appreciated. Iñigo Sáenz Universitat Pompeu Fabra 2015-02-26 2:41 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 2/24/15 3:23 PM, IÑIGO SAENZ wrote: Hi Justin, I always do the SPE as follows: grompp -f SPE.mdp -p sys.top -c sys.gro and after that I simply execute mdrun, i didn't know about the mdrun -rerun function. Now I have done: mdrun -s topol.tpr -rerun sys.gro but the energy results are the exactly the same. Start with something simpler; an actual molecule with normal bonded interactions. Equivalency of energy between GROMACS and many programs has been shown many times over, so it's certainly possible to prove. Likely there's just something weird about what you're doing with your combinations of exclusions, pairs, etc. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads
Dear Users My problem is solved and GROMACS is running successfully on multiple nodes now. The problem was that I accidentally modified a .ssh file in such a way that it broke the system's ability to spread the job among cluster nodes. This was fixed by my system administrator. Thanks Regards Agnivo Gosai Grad Student, Iowa State 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-requ...@gromacs.org.
[gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is an
I hoped that the package (gromacs_win32.zip, http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows ), with programs, which are ready to execution, will accelerate my time of study of the GROMACS program, but it appeared that I got stuck on a step GROMPP. There was an error at execution of the training example. All my attempts to understand something and to correct, replace also give mistakes. Can anybody give me useful advise? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs_win32.zip CPU version: All MS_Windows version: XP/NT/95 Libraries: Static Size: 17633280 FFTW version: 2.1.3 MPI support: no Installation prefix: customizable Comments: This is
On 2/27/15 10:21 AM, Vasiliy Znamenskiy wrote: I hoped that the package (gromacs_win32.zip, http://www.gromacs.org/Downloads/User_contributions/Gromacs_binaries/i686%2f%2fMS_Windows ), with programs, which are ready to execution, will accelerate my time of study of the GROMACS program, but it appeared that I got stuck on a step GROMPP. There was an error at execution of the training example. All my attempts to understand something and to correct, replace also give mistakes. Can anybody give me useful advise? Not if you don't provide your exact commands and error message (copy and paste from your terminal). cheers, M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error in generated Replica Exchange statistics in log file
Hello GROMACS users, I have a problem with the Replica Exchange statistics printed in log file. I ran a 25 ns Replica exchange on a cluster through a queuing system. However, due to insufficient wall time the job stopped abruptly around 24 ns and no stats were printed in the log file. I then extended the run by 1 steps using -nsteps and provided additional -cpi flag for continuation. The simulation ran without errors but the replica exchange stats that were printed in the log files of each of the replica is as follows: Replica exchange statistics Repl 10 attempts, 5 odd, 5 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl .23 .45 .57 .12 .28 .20 .82 .46 .44 .50 .07 .74 .53 .46 .44 .51 .22 .56 .24 .56 .23 .82 .30 .28 .59 .54 .34 .53 .75 .29 .62 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl1230024222043 224140324102421 412 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl .20 .40 .60 .00 .00 .40 .80 .40 .40 .40 .00 .80 .60 .40 .40 .80 .20 .80 .00 .60 .40 .80 .20 .00 .40 .80 .40 .20 .80 .20 .40 I rate of exchange attempt used was 1000, which means that the above stats somehow only take into account the last 1 steps of the simulations. Is this some bug or I did something wrong ? More importantly, is there a way to regenerate the replica exchange stats from the log file ? Regards, Abhishek Acharya Shasara Research Foundation -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella sampling Tutorial Fatal Error
Hi Dear Gromacs Users I am following umbrella sampling tutorial provided by Dr Justin Lemkul (This tutorial is not updated for Gromacs 5 However I am using Gromacs 5.0.2 and i am trying my best to use files and commands compatible with version 5) I have done all the parts up to pulling section very well http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html but at the stage that I want to generate pull.tpr file it gives me a fatal Error: Fatal error: Group pull_group1 required by grompp was undefined. I Checked spelling of Chain_A that i named, utilizing mgx make_ndx command at previous step Any advice or guidance would be greatly appreciated Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University 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-requ...@gromacs.org.
[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error
Excuse me that I forgot to attach the complete Error page: nima@nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr GROMACS:gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2014, 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 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr NOTE 1 [file md_pull.mdp, line 62]: md_pull.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'optimize_fft' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR: pull-coord1-groups should have 2 components Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# WARNING 1 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group0' in parameter file WARNING 2 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group1' in parameter file WARNING 3 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_rate1' in parameter file WARNING 4 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_k1' in parameter file NOTE 2 [file md_pull.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. NOTE 3 [file md_pull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 4 [file md_pull.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Setting the LD random seed to 1032180820 Generated 165 of the 1596 non-bonded 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 3 bonded neighbours molecule type 'Protein_chain_E' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet The center of mass of the position restraint coord's is 3.265 2.171 2.977 The center of mass of the position restraint coord's is 3.265 2.171 2.977 --- Program gmx, VERSION 5.0.2 Source code file: /home/nima/Documents/Gromacs-Program/gromacs-5.0.2/src/gromacs/gmxpreprocess/readpull.c, line: 257 Fatal error: Group pull_group1 required by grompp was undefined. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. = -- Forwarded message -- From: Nima Soltani nima@gmail.com Date: Sat, Feb 28, 2015 at 3:34 AM Subject: Umbrella sampling Tutorial Fatal Error To: gmx-us...@gromacs.org Hi Dear Gromacs Users I am following umbrella sampling tutorial provided by Dr Justin Lemkul (This tutorial is not updated for Gromacs 5 However I am using Gromacs
Re: [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error
Hi, Did you check the parameters in .mdp file for pulling simulation?! I think you have to define this pulling group in .mdp file that you use in grompp. On Fri, Feb 27, 2015 at 7:16 PM, Nima Soltani nima@gmail.com wrote: Excuse me that I forgot to attach the complete Error page: nima@nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr GROMACS:gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2014, 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 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr NOTE 1 [file md_pull.mdp, line 62]: md_pull.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'optimize_fft' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR: pull-coord1-groups should have 2 components Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# WARNING 1 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group0' in parameter file WARNING 2 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group1' in parameter file WARNING 3 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_rate1' in parameter file WARNING 4 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_k1' in parameter file NOTE 2 [file md_pull.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. NOTE 3 [file md_pull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 4 [file md_pull.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Setting the LD random seed to 1032180820 Generated 165 of the 1596 non-bonded 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 3 bonded neighbours molecule type 'Protein_chain_E' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet The center of mass of the position restraint coord's is 3.265 2.171 2.977 The center of mass of the position restraint coord's is 3.265 2.171 2.977 --- Program gmx, VERSION 5.0.2 Source code file: /home/nima/Documents/Gromacs-Program/gromacs-5.0.2/src/gromacs/gmxpreprocess/readpull.c, line: 257 Fatal error: Group pull_group1 required by grompp was undefined. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. = -- Forwarded
Re: [gmx-users] Problems Running Gromacs v-5.0.4
Thank you for your reply. Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, February 27, 2015 5:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problems Running Gromacs v-5.0.4 On 2/27/15 4:01 PM, Stephen P. Molnar wrote: The original of this message was sent on 2/18. To date it has greeted freeted with thundering silence. I would really appreciate an answer, even if no solution is readily apparent. I have compiled and installed Gromacs v-5.0.4 (rather than using the version bundled with the distribution() in RoboLinux 7.81. without any warning or error messages. However, I have encountered problems running gmxdemo. Although I get the message Display variable is set I see a flash, but the window does not stay open. However, I do get the final display of the box and the simulation. Probably my first question is how are you running gmxdemo? It was removed from the source code in 2012...before version even the release of 4.6-beta1. The second problem probably involves permissions. If I run the demo as the superuser, (RoboLinux does not allow the enablement of the root during the installation) The demo runs to completion without problems, other that the one of the vanishing window. Running gmxdemo as the superuser generated 39 files (including gmxdemo and cpeptide.pdb) while running as a user generates 23 files. Depends on where GROMACS is installed and what you've done to get gmxdemo running. FWIW, it was removed because it wasn't useful and no one wanted to maintain it. If it's not working, the solution is to find better tutorial material, as suggested in README.tutor :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] about source code of the old version of GROAMCS (1.0 to 2.0)
On Fri, Feb 27, 2015 at 7:16 AM, Man Hoang Viet mhv...@ifpan.edu.pl wrote: Dear GROMACS team, I am looking for source code of the old version (v1.0 to v2.0) of GROMACS, which is not available for downloading on GROMACS home page. Could you please share them to me? I didn't find them on the ftp server in a brief excursion through the accumulated junk. However release-2-0 is tagged in the git repo, and the initial commit is (I think) release 1.6. If you really need 1.0 for some reason, then you should contact the original authors directly. Mark Thank you very much, Yours sincerely, Viet Man -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error
On 2/27/15 7:16 PM, Nima Soltani wrote: Excuse me that I forgot to attach the complete Error page: nima@nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr GROMACS:gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman 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) 2001-2014, 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 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy -o pull.tpr NOTE 1 [file md_pull.mdp, line 62]: md_pull.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'optimize_fft' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR: pull-coord1-groups should have 2 components Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# WARNING 1 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group0' in parameter file WARNING 2 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_group1' in parameter file WARNING 3 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_rate1' in parameter file WARNING 4 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_k1' in parameter file The simple answer is you have not translated the options properly. Refer to: http://manual.gromacs.org/online/mdp_opt.html#pull I have been somewhat hesitant to update the tutorial for 5.0 because of all the changes, and the tutorial is linked directly to one of my papers. I have been considering what to do for some time. I don't intend to update the tutorial for a while at least, just because I don't have the time to make the changes and verify its accuracy, so please just ask questions via the list. -Justin NOTE 2 [file md_pull.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. NOTE 3 [file md_pull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 4 [file md_pull.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Setting the LD random seed to 1032180820 Generated 165 of the 1596 non-bonded 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 3 bonded neighbours molecule type 'Protein_chain_E' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Removing all charge groups because cutoff-scheme=Verlet The center of mass of the position restraint coord's is 3.265 2.171 2.977 The center of mass of the position restraint coord's is 3.265 2.171 2.977 --- Program gmx, VERSION 5.0.2 Source code file: /home/nima/Documents/Gromacs-Program/gromacs-5.0.2/src/gromacs/gmxpreprocess/readpull.c, line: 257 Fatal error: Group pull_group1 required by grompp was undefined. For more information and tips for troubleshooting, please check the GROMACS website at
[gmx-users] Creating POSRES option for MDP file
Dear Users My system can be identified into 2 groups ( default ) namely DNA and Protein. To use the pull code , I want to apply pulling force on DNA and keep Protein fixed. Now, I have two itp files for my protein ( two chains,A and B). So do I need to include something like this :- ; Include Position restraint file #ifdef POSRES_P #include posre_Protein_chain_A.itp #endif and ; Include Position restraint file #ifdef POSRES_P #include posre_Protein_chain_B.itp #endif in both of the itp files for the two chains and then use -DPOSRES_P in the mdp file for the pulling simulation ? Or there is some other method ? Thanks Regards Agnivo Gosai Grad Student, Iowa State 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-requ...@gromacs.org.
Re: [gmx-users] GPU low performance
I report the changes made to improve the performance of a molecular dynamics on a protein of 1925 running on GPU INVIDIA K20 Tesla : a.. To limit the number of cores used in the calculation (option -pin on) and to have a better performance: gmx_mpi mdrun ... -ntomp 16 -pin on where ntomp is the number of OpenMP threads a.. clock frequency using the NVDIA management tool is been increased from the default 705 MHz to 758 MHz. a.. to reduce runtime to calculate energies every step in mdp file: nstcalcenergy option = -1 The actual performance is about 7ns /day against 2ns/day without these changes. Carmen - Original Message - From: Szilárd Páll pall.szil...@gmail.com To: Carmen Di Giovanni cdigi...@unina.it Cc: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Friday, February 20, 2015 1:25 AM Subject: Re: [gmx-users] GPU low performance Please consult the manual an wiki. -- Szilárd On Thu, Feb 19, 2015 at 6:44 PM, Carmen Di Giovanni cdigi...@unina.it wrote: Szilard, about: Fatal error 1) Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The error is quite clearly explains that you're trying to use mdrun's built-in thread-MPI parallelization, but you have a binary that does not support it. Use the MPI launching syntax instead. Can you help me about the MPI launching syntax? What is the suitable command ? A previous poster has already pointed you to the Acceleration and parallelization page which, I believe describes the matter in detail. 2) Have you looked at the the performance table at the end of the log? You are wasting a large amount of runtime calculating energies every step and this overhead comes in multiple places in the code - one of them being the non-timed code parts which typically take 3%. As can I reduce runtime to calculate the energies every step? I must to modify something in mdp file ? This is discussed throughly in the manual, you should be looking for the nstcalcenergy option. Thank you in advance Carmen -- Carmen Di Giovanni, PhD Dept. of Pharmaceutical and Toxicological Chemistry Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it Quoting Szilárd Páll pall.szil...@gmail.com: On Thu, Feb 19, 2015 at 11:32 AM, Carmen Di Giovanni cdigi...@unina.it wrote: Dear Szilárd, 1) the output of command nvidia-smi -ac 2600,758 is [root@localhost test_gpu]# nvidia-smi -ac 2600,758 Applications clocks set to (MEM 2600, SM 758) for GPU :03:00.0 Warning: persistence mode is disabled on this device. This settings will go back to default as soon as driver unloads (e.g. last application like nvidia-smi or cuda application terminates). Run with [--help | -h] switch to get more information on how to enable persistence mode. run nvidia-smi -pm 1 if you want to avoid that. Setting applications clocks is not supported for GPU :82:00.0. Treating as warning and moving on. All done. 2) I decreased nlists to 20 However when I do the command: gmx_mpi mdrun -deffnm nvt -ntmpi 8 -gpu_id give me a fatal error: GROMACS: gmx mdrun, VERSION 5.0 Executable: /opt/SW/gromacs-5.0/build/mpi-cuda/bin/gmx_mpi Library dir: /opt/SW/gromacs-5.0/share/top Command line: gmx_mpi mdrun -deffnm nvt -ntmpi 8 -gpu_id Back Off! I just backed up nvt.log to ./#nvt.log.8# Reading file nvt.tpr, VERSION 5.0 (single precision) Changing nstlist from 10 to 40, rlist from 1 to 1.097 --- Program gmx_mpi, VERSION 5.0 Source code file: /opt/SW/gromacs-5.0/src/programs/mdrun/runner.c, line: 876 Fatal error: Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- The error is quite clearly explains that you're trying to use mdrun's built-in thread-MPI parallelization, but you have a binary that does not support it. Use the MPI launching syntax instead. Halting program gmx_mpi gcq#223: Jesus Not Only Saves, He Also Frequently Makes Backups. (Myron Bradshaw) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
Re: [gmx-users] GTX980 performance
Szilárd thank you for the useful adivices about the configuration of the new server machine. I report the changes made to improve the performance of a molecular dynamics on a protein of 1925 running on GPU INVIDIA K20 Tesla : a.. To limit the number of cores used in the calculation (option -pin on) and to have a better performance: gmx_mpi mdrun ... -ntomp 16 -pin on where ntomp is the number of OpenMP threads a.. clock frequency using the NVDIA management tool is been increased from the default 705 MHz to 758 MHz. a.. to reduce runtime to calculate energies every step in mdp file: nstcalcenergy option = -1 The actual performance is about 7ns /day against 2ns/day without these changes. Carmen - Original Message - From: Szilárd Páll pall.szil...@gmail.com To: Carmen Di Giovanni cdigi...@unina.it Cc: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Thursday, February 26, 2015 2:37 PM Subject: Re: GTX980 performance On Wed, Feb 25, 2015 at 1:21 PM, Carmen Di Giovanni cdigi...@unina.it wrote: A special thank you to Szilárd Páll for the good advices in GPU low performance discussion. The perfomance calculation is much improved after its suggestions. I'm glad it helped. Could you post the changes you made to your mdp/command line and the results these gave? It would allow others to learn from it. Dear GROMACS users and developers, we are thinking to buy a new tyan server machine with these features: SERVER SYSTEM TYAN FT48 - Tower/Rack,Dual Xeon ,8xSATA N. 2 CPU INTEL XEON E5-2620 2.0Ghz - 6 CORE 15MCache LGA2011 N. 4 Scheda Video Nvidia GTX980, 4GB GDDR5,PCIE 3.0 , 2DVI, HD N. 4 DDR3 8 GB 1600 Mhz HARD DISK 1 TB SATA 3 WD I known that the GTX980 offer good performance for GROMACS 5.0 What are your views about this ? That CPU-GPU combination will give heavily CPU-bound GROMACS runs, those GTX 980s are 1.5-2x faster than what you can use with those CPUs - conversely, if you'd get 6-core 3 GHz CPUs, you'll see a huge, nearly 50% improvement in performance. This will change in the futur, but at least with GROMACS v5.1 and earlier, the performance on this machine won't be much higher than with a single fast CPU and one GTX 980. For better performance with GROMACS, consider getting better CPUs in this machine or for the same (or less) money get two workstations with i7 4930K or 4960X CPUs. -- Szilárd Thank you in advance Carmen Carmen Di Giovanni, PhD Postdoctoral Researcher Dept. of Pharmacy Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GTX980 performance
Szilárd thank you for the useful adivices about the configuration of the new server machine. I report the changes made to improve the performance of a molecular dynamics on a protein of 1925 running on GPU INVIDIA K20 Tesla : a.. To limit the number of cores used in the calculation (option -pin on) and to have a better performance: gmx_mpi mdrun ... -ntomp 16 -pin on where ntomp is the number of OpenMP threads a.. clock frequency using the NVDIA management tool is been increased from the default 705 MHz to 758 MHz. a.. to reduce runtime to calculate energies every step in mdp file: nstcalcenergy option = -1 The actual performance is about 7ns /day against 2ns/day without these changes. Carmen - Original Message - From: Szilárd Páll pall.szil...@gmail.com To: Carmen Di Giovanni cdigi...@unina.it Cc: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Thursday, February 26, 2015 2:37 PM Subject: Re: GTX980 performance On Wed, Feb 25, 2015 at 1:21 PM, Carmen Di Giovanni cdigi...@unina.it wrote: A special thank you to Szilárd Páll for the good advices in GPU low performance discussion. The perfomance calculation is much improved after its suggestions. I'm glad it helped. Could you post the changes you made to your mdp/command line and the results these gave? It would allow others to learn from it. Dear GROMACS users and developers, we are thinking to buy a new tyan server machine with these features: SERVER SYSTEM TYAN FT48 - Tower/Rack,Dual Xeon ,8xSATA N. 2 CPU INTEL XEON E5-2620 2.0Ghz - 6 CORE 15MCache LGA2011 N. 4 Scheda Video Nvidia GTX980, 4GB GDDR5,PCIE 3.0 , 2DVI, HD N. 4 DDR3 8 GB 1600 Mhz HARD DISK 1 TB SATA 3 WD I known that the GTX980 offer good performance for GROMACS 5.0 What are your views about this ? That CPU-GPU combination will give heavily CPU-bound GROMACS runs, those GTX 980s are 1.5-2x faster than what you can use with those CPUs - conversely, if you'd get 6-core 3 GHz CPUs, you'll see a huge, nearly 50% improvement in performance. This will change in the futur, but at least with GROMACS v5.1 and earlier, the performance on this machine won't be much higher than with a single fast CPU and one GTX 980. For better performance with GROMACS, consider getting better CPUs in this machine or for the same (or less) money get two workstations with i7 4930K or 4960X CPUs. -- Szilárd Thank you in advance Carmen Carmen Di Giovanni, PhD Postdoctoral Researcher Dept. of Pharmacy Drug Discovery Lab University of Naples Federico II Via D. Montesano, 49 80131 Naples Tel.: ++39 081 678623 Fax: ++39 081 678100 Email: cdigi...@unina.it -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS
On 2/26/15 5:39 PM, Thomas Lipscomb wrote: Dear gmx-users, Ok I understand. My specific question is how do I do these two tasks: 1. What do I need to change about the KALP15 with DPPC tutorial (again substituting maximin 3 for KALP15) so that when I repeat it I get better data, because some parts of the tutorial are just for practice and not for better data, eg. the 1 nanosecond simulation time. Increased time and probably a better force field. I strongly recommend CHARMM36. 2. What is your general advice about how to simulate several maximin 3 at once interacting with the membrane? Eg., If I put the maximin 3 somewhat close to each other on or in the membrane at the initial conditions, will they diffuse around enough during the simulation that they can aggregate, or is the diffusion so low that I need to put the maximin 3 in one of the five possible aggregates at the initial conditions of the simulation? To help you answer this question please see the diagram below that shows the five possible ways that maximin 3 may aggregate. I doubt you'll ever see dynamics on that scale in atomistic simulations happening spontaneously. Consider multiple starting/assembly states and perhaps consider coarse graining. -Justin The diagram linked below visualizes all of the five possible ways maximin 3 might be acting to disrupt the membrane and have antimicrobial activity. The red part of the peptide represents a hydrophilic surface and the blue part represents a hydrophobic surface. The cylindrical shape of the peptide represents the maximin 3 being an alpha-helix. http://imgur.com/y4yw0Mq Image was taken from: Tryptophan- and arginine-rich antimicrobial peptides: Structures and mechanisms of action Thank you. Sincerely, Thomas On 2/24/15 10:18 PM, Thomas Lipscomb wrote: Dear gmx-users, Ok Justin here is the information you asked for: My questions were rhetorical. I honestly don't have time to through all of this and tell you how to do a thesis project :) If you have specific questions about using GROMACS to carry out specific tasks, that's the main purpose of this list. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in generated Replica Exchange statistics in log file
On Fri, Feb 27, 2015 at 12:07 PM, Abhi Acharya abhi117acha...@gmail.com wrote: Hello GROMACS users, I have a problem with the Replica Exchange statistics printed in log file. I ran a 25 ns Replica exchange on a cluster through a queuing system. However, due to insufficient wall time the job stopped abruptly around 24 ns and no stats were printed in the log file. I then extended the run by 1 steps using -nsteps and provided additional -cpi flag for continuation. The simulation ran without errors but the replica exchange stats that were printed in the log files of each of the replica is as follows: Replica exchange statistics Repl 10 attempts, 5 odd, 5 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl .23 .45 .57 .12 .28 .20 .82 .46 .44 .50 .07 .74 .53 .46 .44 .51 .22 .56 .24 .56 .23 .82 .30 .28 .59 .54 .34 .53 .75 .29 .62 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl1230024222043 224140324102421 412 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Repl .20 .40 .60 .00 .00 .40 .80 .40 .40 .40 .00 .80 .60 .40 .40 .80 .20 .80 .00 .60 .40 .80 .20 .00 .40 .80 .40 .20 .80 .20 .40 I rate of exchange attempt used was 1000, which means that the above stats somehow only take into account the last 1 steps of the simulations. Is This is normal. The subsequent mdrun will not read from the old .log file, and the data is not in the checkpoint. this some bug or I did something wrong ? More importantly, is there a way to regenerate the replica exchange stats from the log file ? Not without writing a custom script to parse the per-exchange information. Mark Regards, Abhishek Acharya Shasara Research Foundation -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding RDF calculations
On 2/27/15 2:00 AM, soumadwip ghosh wrote: Dear users, I have a query about some reviews one a paper which I submitted recently. It deals with the binding of molecular ions with double stranded DNA segments. My questions are- 1. Is it customary to take into account The centre-of -mass for DNA grooves or backbones while calculating RDF? Without that being taken into account, what kind of artifacts are to be seen? Dealing with RDFs or occupancies around DNA is extremely challenging. Normal RDF lack sensitivity and do not fully describe the behavior of ions around DNA, especially given the asymmetry between major and minor grooves. See, for instance, dx.doi.org/10.1021/ja0629460 2. Why is it necessary to show the running co-ordination number up to the first solvation shell? I have calculated the excess cordination number for each ions in DNA up to half of the box length using the Kirkwood-Buff integrals. But I think there is a confusion between running coordination and the excess coordination number. They state that if a coordination number 3. They have asked about the CHARMM 27 force field being outdated now..How is this true? Yes. There are specific improvements in CHARMM36 for DNA and RNA, with a reparametrization of some important backbone torsions in DNA that have implications for sampling substates of B-DNA and correct sugar puckering. -Justin Please help me out in addressing the reviews. Thanks for your help in advance. P.S: I did not take the center-of-mass of molecular ions into account. I dont think it is wrong for a small molecule.. Regards Soumadwip Ghosh Research Fellow IITB, Mumbai India -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Re : Re : GROMACS 4.6.7 not running on more than 16 MPI threads
The following problem is still there : Number of CPUs detected (16) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! The above message is always there and I am not sure about how to set it. Even when I set OpenMP threads manually it shows. I ran my system using only MPI with automatic PME node selection. I found that for nodes = 16 and ppn = 16 there was issue with domain decomposition. Message from standard output and error files of job script :- There is no domain decomposition for 224 nodes that is compatible with the given box and a minimum cell size of 1.08875 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... Largest charge group radii for Van der Waals: 0.039, 0.039 nm Largest charge group radii for Coulomb: 0.078, 0.078 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 64x64x128, spacing 0.117 0.117 0.117 The log file was incomplete as the simulation crashed. Then I fiddled with the node numbers and found that for nodes = 10 and ppn = 16 mdrun_mpi could successfully work. This is part of the log file : Average load imbalance: 36.5 % Part of the total run time spent waiting due to load imbalance: 8.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 3 % Z 17 % Average PME mesh/force load: 0.847 Part of the total run time spent waiting due to PP/PME imbalance: 1.4 % NOTE: 8.7 % of the available CPU time was lost due to load imbalance in the domain decomposition. Core t (s) Wall t (s)(%) Time: 212092.050 1347.16715743.6 (ns/day)(hour/ns) Performance: 32.0670.748 .. Then I set OpenMP threads = 8 and this is what happened. ( I had to use Verlet cutoff scheme ) Number of CPUs detected (16) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Reading file pull1.tpr, VERSION 4.6.7 (double precision) The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 8 (and the command-line setting agreed with that) Will use 144 particle-particle and 16 PME only nodes This is a guess, check the performance at the end of the log file Using 160 MPI processes Using 8 OpenMP threads per MPI process .. .. NOTE: 9.9 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. NOTE: 11 % of the run time was spent in domain decomposition, 9 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) Core t (s) Wall t (s)(%) Time: 319188.130 2019.34915806.5 33:39 (ns/day)(hour/ns) Performance: 21.3931.122 So , I have bad performance. Now I am using only MPI for running the jobs. Any suggestions on performance improvement ? Thanks Regards Agnivo Gosai Grad Student, Iowa State 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-requ...@gromacs.org.
Re: [gmx-users] Re : GROMACS 4.6.7 not running on more than 16 MPI threads
Good to hear! However, are you sure the Number of CPUs detected (16) does not match the number reported by OpenMP (1) message was also solved by the same? You should try to make this go away by telling your MPI what threads/rank count you want, otherwise you *may* experience performance loss. -- Szilárd On Fri, Feb 27, 2015 at 7:25 PM, Agnivo Gosai agnivogromac...@gmail.com wrote: Dear Users My problem is solved and GROMACS is running successfully on multiple nodes now. The problem was that I accidentally modified a .ssh file in such a way that it broke the system's ability to spread the job among cluster nodes. This was fixed by my system administrator. Thanks Regards Agnivo Gosai Grad Student, Iowa State 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-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problems Running Gromacs v-5.0.4
On 2/27/15 4:01 PM, Stephen P. Molnar wrote: The original of this message was sent on 2/18. To date it has greeted freeted with thundering silence. I would really appreciate an answer, even if no solution is readily apparent. I have compiled and installed Gromacs v-5.0.4 (rather than using the version bundled with the distribution() in RoboLinux 7.81. without any warning or error messages. However, I have encountered problems running gmxdemo. Although I get the message Display variable is set I see a flash, but the window does not stay open. However, I do get the final display of the box and the simulation. Probably my first question is how are you running gmxdemo? It was removed from the source code in 2012...before version even the release of 4.6-beta1. The second problem probably involves permissions. If I run the demo as the superuser, (RoboLinux does not allow the enablement of the root during the installation) The demo runs to completion without problems, other that the one of the vanishing window. Running gmxdemo as the superuser generated 39 files (including gmxdemo and cpeptide.pdb) while running as a user generates 23 files. Depends on where GROMACS is installed and what you've done to get gmxdemo running. FWIW, it was removed because it wasn't useful and no one wanted to maintain it. If it's not working, the solution is to find better tutorial material, as suggested in README.tutor :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
