[gmx-users] double and single precision
Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] double and single precision
Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] double and single precision
On 20/02/2012 7:19 PM, Edvin Erdtman wrote: Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? We should probably put in a check to prevent this occurring (and an environment variable to override it?). I expect you can get the first part back through using eneconv -e and the above environment variable. I can't think of a way to access the second (and subsequent) parts without writing new code - but perhaps that code should exist anyway, emitting a warning that a change of precision was detected. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Sv: Re: [gmx-users] double and single precision
Hi So the best I can do now is to recreate the first part, and rerun new the simulations? /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS 2012-02-20 kl. 09:26, skrev Mark Abraham mark.abra...@anu.edu.au : On 20/02/2012 7:19 PM, Edvin Erdtman wrote: Hi I have been running GMX in double precision and by mistake an extension of a run in single precision was written to the same files. When I run for example gmxcheck or g_energy I get the following error after the program has scanned through the double part: Fatal error: Energy header magic number mismatch, this is not a GROMACS edr file If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can I do something to divide the file into a double and a single part? We should probably put in a check to prevent this occurring (and an environment variable to override it?). I expect you can get the first part back through using eneconv -e and the above environment variable. I can't think of a way to access the second (and subsequent) parts without writing new code - but perhaps that code should exist anyway, emitting a warning that a change of precision was detected. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Sv: Re: [gmx-users] double and single precision
On 20/02/2012 7:29 PM, Edvin Erdtman wrote: Hi So the best I can do now is to recreate the first part, and rerun new the simulations? If you have a full frame (positions+velocities+maybe energies, or a checkpoint file) then I expect so. Save your crossbreed files in case someone has a better idea. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs-GPU benchmark test killed after exhausting the memory
Hi, I have Gromacs- GPU version 4.5.5 and GTX 580. I run dhfr-solv-PME benchmark test (see below) and my run is killed after couple of hours when it exhausts all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What do I do wrong? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] FW: Gromacs-GPU benchmark test killed after exhausting the memory
Sorry, I forgot to enclose the command line and output mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -deffnm md :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun-gpu (-: Option Filename Type Description -s md.tpr InputRun input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi md.cpt Input, Opt. Checkpoint file -cpo md.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb etc. -e md.edr Output Energy file -g md.log Output Log file -dhdlmd.xvg Output, Opt. xvgr/xmgr file -field md.xvg Output, Opt. xvgr/xmgr file -table md.xvg Input, Opt. xvgr/xmgr file -tablep md.xvg Input, Opt. xvgr/xmgr file -tableb md.xvg Input, Opt. xvgr/xmgr file -rerun md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi md.xvg Output, Opt. xvgr/xmgr file -tpidmd.xvg Output, Opt. xvgr/xmgr file -ei md.edi Input, Opt. ED sampling input -eo md.edo Output, Opt. ED sampling output -j md.gct Input, Opt. General coupling stuff -jo md.gct Output, Opt. General coupling stuff -ffout md.xvg Output, Opt. xvgr/xmgr file -devout md.xvg Output, Opt. xvgr/xmgr file -runav md.xvg Output, Opt. xvgr/xmgr file -px md.xvg Output, Opt. xvgr/xmgr file -pf md.xvg Output, Opt. xvgr/xmgr file -mtx md.mtx Output, Opt. Hessian matrix -dn md.ndx Output, Opt. Index file -multidirmd Input, Opt., Mult. Run directory Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string md Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names -maxhreal -1 Terminate after 0.99
[gmx-users] problems with martinize.py
Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and the dssp file with the second structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the pdb structure as input, I get the following error message that I really don't understand. INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize.py, line 2037, in module for title,atoms,box in frameIterator(inStream): File ./martinize.py, line 1303, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize.py, line 1290, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' Can anyone help me on that? Thanks -- Francesca -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Sv: Re: [gmx-users] double and single precision
Hi again How do I set the env.var. GMX_ENX_NO_FATAL? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS 2012-02-20 kl. 09:38, skrev Mark Abraham mark.abra...@anu.edu.au : On 20/02/2012 7:29 PM, Edvin Erdtman wrote: Hi So the best I can do now is to recreate the first part, and rerun new the simulations? If you have a full frame (positions+velocities+maybe energies, or a checkpoint file) then I expect so. Save your crossbreed files in case someone has a better idea. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Sv: Re: [gmx-users] double and single precision
On 20/02/2012 9:13 PM, Edvin Erdtman wrote: Hi again How do I set the env.var. GMX_ENX_NO_FATAL? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. http://en.wikipedia.org/wiki/Environment_variable#Getting_and_setting_environment_variables Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water radial distribution function
Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water radial distribution function
On 20/02/2012 10:40 PM, Nidhi Katyal wrote: Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. Please read g_rdf -h, try things out and ask a focussed question. :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta. Cheers, Tsjerk On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini francesca.vitalin...@gmail.com wrote: Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and the dssp file with the second structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the pdb structure as input, I get the following error message that I really don't understand. INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize.py, line 2037, in module for title,atoms,box in frameIterator(inStream): File ./martinize.py, line 1303, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize.py, line 1290, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' Can anyone help me on that? Thanks -- Francesca -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone were my input file is very simply Protein in water 2410 1ALA N1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102 1ALA H12 1.409 1.866 1.338 0.8590 -0.1748 1.1978 1ALA H23 1.547 1.948 1.296 2.0372 -1.4201 0.8359 1ALA H34 1.483 1.837 1.194 1.8924 -0.0993 -0.5621 1ALA CA5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955 1ALA CB6 1.625 1.781 1.480 0.3554 -0.5405 0.4275 1ALA C7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917 1ALA O8 1.407 1.624 1.268 -0.0033 0.4302 0.1378 2GLU N9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921 2GLUOE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469 2GLUOE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621 2.91477 2.91477 2.91477 Can you help me on that? Thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta. Cheers, Tsjerk On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini francesca.vitalin...@gmail.com wrote: Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and the dssp file with the second structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the pdb structure as input, I get the following error message that I really don't understand. INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize.py, line 2037, in module for title,atoms,box in frameIterator(inStream): File ./martinize.py, line 1303, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize.py, line 1290, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' Can anyone help me on that? Thanks -- Francesca -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] problems with martinize.py
Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheers, Tsjerk On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone were my input file is very simply Protein in water 2410 1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102 1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978 1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359 1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621 1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955 1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275 1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917 1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378 2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921 2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469 2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621 2.91477 2.91477 2.91477 Can you help me on that? Thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta. Cheers, Tsjerk On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini francesca.vitalin...@gmail.com wrote: Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and the dssp file with the second structure downloaded from http://swift.cmbi.ru.nl/gv/dssp using the pdb structure as input, I get the following error message that I really don't understand. INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize.py, line 2037, in module for title,atoms,box in frameIterator(inStream): File ./martinize.py, line 1303, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize.py, line 1290, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), ,
Re: [gmx-users] problems with martinize.py
I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheers, Tsjerk On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone were my input file is very simply Protein in water 2410 1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102 1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978 1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359 1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621 1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955 1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275 1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917 1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378 2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921 2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469 2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621 2.91477 2.91477 2.91477 Can you help me on that? Thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta. Cheers, Tsjerk On Mon, Feb 20, 2012 at 10:43 AM, francesca vitalini francesca.vitalin...@gmail.com wrote: Hi all, I'm trying to coarsegrain my structure using the script martinize.py and using my gro file as inmput and
[gmx-users] Molecular Dynamics basics...
Hi GROMACS users, I am a very novice to GROMACS.. .. My question may be very simple but very important to me..!!! These may be very basics... 1. What is the meaning of comm_mode and nstcomm.. I read the manual but unable to digest it..so please explain in more detail along with its effect on system.. 2. When I am want to study self assembly of protein what should my comm_mode -linear or angular or none ?? 3. what is the meaning of emtol in minimisation proces?? Should I take emtol value more or less to come to minimum energy state ??? the structure on which I am working is not having any crystal or NMR structure , so I need the maximum energy minimised structure 4. When I am doing energy minimisation the gromacs shows (potential energy= -2.07) conjugate gradient step wise to small or no change in energy . converged to machine precision in 15881 step but dindn´t reach to the requested Fmax10 What should to do?? or the structure I get is energy minimised or not..??? please give me your valuable advice..These help me a lot Thank you in advace !!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheers, Tsjerk On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' I have used the command line ./martinize-1.0.py -f npt_strip_wat.gro -o frag_npt_cg_pdb.top -x frag_npt_cg_pdb.gro -v -p backbone were my input file is very simply Protein in water 2410 1ALA N 1 1.497 1.862 1.290 0.1206 -0.3069 -0.2102 1ALA H1 2 1.409 1.866 1.338 0.8590 -0.1748 1.1978 1ALA H2 3 1.547 1.948 1.296 2.0372 -1.4201 0.8359 1ALA H3 4 1.483 1.837 1.194 1.8924 -0.0993 -0.5621 1ALA CA 5 1.585 1.753 1.335 -0.1231 -0.2165 0.4955 1ALA CB 6 1.625 1.781 1.480 0.3554 -0.5405 0.4275 1ALA C 7 1.517 1.617 1.323 0.1234 -0.2807 -0.1917 1ALA O 8 1.407 1.624 1.268 -0.0033 0.4302 0.1378 2GLU N 9 1.566 1.515 1.393 -0.2655 -0.2542 0.1191 2GLU H 10 1.655 1.536 1.434 0.1561 0.1079 -0.9482 2GLU CA 11 1.501 1.384 1.402 0.3096 -0.5394 0.1823 2GLU CB 12 1.601 1.272 1.427 0.7527 -0.2033 -0.0775 2GLU CG 13 1.694 1.280 1.548 -0.0279 0.1789 0.5017 2GLU CD 14 1.779 1.405 1.571 0.4664 -0.1532 0.4921 2GLU OE1 15 1.882 1.412 1.500 0.2904 -0.0189 0.2469 2GLU OE2 16 1.740 1.489 1.654 0.2746 0.1001 0.1509 2GLU C 17 1.378 1.355 1.489 0.5085 -0.1385 0.5964 2GLU O 18 1.352 1.237 1.510 0.3837 -0.1792 0.2200 3GLU N 19 1.307 1.458 1.535 -0.1887 -0.4392 0.2009 3GLU H 20 1.315 1.547 1.489 -1.1961 0.1298 1.0835 3GLU CA 21 1.180 1.436 1.604 -0.3118 -0.2722 0.0307 3GLU CB 22 1.192 1.426 1.757 -0.3397 0.1329 0.0602 3GLU C 23 1.066 1.533 1.572 -0.3117 -0.4554 -0.5274 3GLU O1 24 1.072 1.606 1.471 0.0488 0.2651 0.0047 3GLU O2 25 0.965 1.542 1.646 -0.1745 -0.2606 -0.3621 2.91477 2.91477 2.91477 Can you help me on that? Thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was
Re: [gmx-users] problems with martinize.py
Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheers, Tsjerk On Mon, Feb 20, 2012 at 1:57 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I was using the one available from the tutorial but now I have downloaded the new one and it gives me still an error message like INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File
Re: [gmx-users] Molecular Dynamics basics...
On 21/02/2012 12:11 AM, prashant kurkute wrote: Hi GROMACS users, I am a very novice to GROMACS.. .. My question may be very simple but very important to me..!!! These may be very basics... 1. What is the meaning of comm_mode and nstcomm.. I read the manual but unable to digest it..so please explain in more detail along with its effect on system.. http://en.wikipedia.org/wiki/Flying_ice_cube 2. When I am want to study self assembly of protein what should my comm_mode -linear or angular or none ?? You choose based on the above. 3. what is the meaning of emtol in minimisation proces?? Should I take emtol value more or less to come to minimum energy state ??? What's not clear in manual section 7.3.5? the structure on which I am working is not having any crystal or NMR structure , so I need the maximum energy minimised structure 4. When I am doing energy minimisation the gromacs shows (potential energy= -2.07) conjugate gradient step wise to small or no change in energy . converged to machine precision in 15881 step but dindn´t reach to the requested Fmax10 You are minimizing a noisy function (cutoffs), so oscillation or apparent stagnation near a stationary point can occur. See manual 3.10 What should to do?? or the structure I get is energy minimised or not..??? That depends what you want to do with it next. For MD, it's probably fine. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]), I(a[:5]), , 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) ValueError: invalid literal for int() with base 10: '2.' 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, The problem is that the second line of your gro file indicates there are 2410 atoms in the file, while there are only 25. Did you manually remove water? In that case you have to update the number of atoms in the second line. The error message should be more explanatory though. Cheers, Tsjerk On Mon, Feb 20, 2012 at
Re: [gmx-users] problems with martinize.py
Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a GRO file. Chains will be labeled consecutively. Traceback (most recent call last): File ./martinize-1.0.py, line 2306, in module for title,atoms,box in frameIterator(inStream): File ./martinize-1.0.py, line 1183, in groFrameIterator atoms = [groAtom(streamIterator.next()) for i in range(natoms)] File ./martinize-1.0.py, line 1170, in groAtom return (S(a[10:15]), S(a[5:10]),
Re: [gmx-users] Umbrella_pull_simulation
shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: I've changed that but it is still complaining... INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used
[gmx-users] Re: gmx-users Digest, Vol 94, Issue 119
HI GROMACS users, Thank you mark for your advice.. As per these link http://en.wikipedia.org/wiki/Flying_ice_cube such as those using explicitly represented solvent under periodic boundary conditions - only the translational motion should be removed. Although it does not produce a perfectly continuous trajectory, periodic reassignment of velocities as in the Andersen thermostat method also minimize the problem.. So I have to use the comm_mode linear when explicit solvent is used, is it right?? If I used Nose - Hoover thermostat Is then comm_mode is needed to use..? (AS per your link ..More conservatively, the rate of velocity rescaling can be reduced, the scale factor computed over a time-averaged sample of instantaneous temperatures, or an alternative means of thermostatting such as the Nosé-Hoover thermostat can be used.) Thank you a lot in advance On Mon, Feb 20, 2012 at 7:20 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: problems with martinize.py (francesca vitalini) 2. Re: Molecular Dynamics basics... (Mark Abraham) 3. Re: problems with martinize.py (Tsjerk Wassenaar) -- Message: 1 Date: Mon, 20 Feb 2012 14:34:45 +0100 From: francesca vitalini francesca.vitalin...@gmail.com Subject: Re: [gmx-users] problems with martinize.py To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caprcf+k1x4qy20azmicvzkeibncl3kai-0x147vpprr+aga...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining.
Re: [gmx-users] problems with martinize.py
Hi Francesca, The output is written in .pdb format. That's also stated in the help. Cheers, Tsjerk On Mon, Feb 20, 2012 at 4:05 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL 1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try converting your structure to PDB and use that for coarsegraining. Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:08 PM, francesca vitalini
Re: [gmx-users] problems with martinize.py
On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL This looks like a PDB file. If you load cg.gro into VMD it will recognize it as GRO file, but you provide the wrong format. Rename cg.gro to cg.pdb and it should be loaded successfully into VMD. /Flo Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try
Re: [gmx-users] problems with martinize.py
Thanks Tsjerk, Florian, However I need the .gro file for the reverse transformation and I cannot simply obtain it through pdb2gmx as it won't recognize the atoms Fatal error: Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms while sorting atoms. . Any help with that? Thanks a lot 2012/2/20 Dommert Florian domm...@icp.uni-stuttgart.de: On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL 1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL This looks like a PDB file. If you load cg.gro into VMD it will recognize it as GRO file, but you provide the wrong format. Rename cg.gro to cg.pdb and it should be loaded successfully into VMD. /Flo Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARK THIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3
Re: [gmx-users] problems with martinize.py
francesca vitalini wrote: Thanks Tsjerk, Florian, However I need the .gro file for the reverse transformation and I cannot simply obtain it through pdb2gmx as it won't recognize the atoms Use editconf to convert between .pdb and .gro (as well as other formats). pdb2gmx is for producing topologies, not interconverting coordinate files. -Justin Fatal error: Atom BB in residue ALA 1 was not found in rtp entry ALA with 8 atoms while sorting atoms. . Any help with that? Thanks a lot 2012/2/20 Dommert Florian domm...@icp.uni-stuttgart.de: On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL This looks like a PDB file. If you load cg.gro into VMD it will recognize it as GRO file, but you provide the wrong format. Rename cg.gro to cg.pdb and it should be loaded successfully into VMD. /Flo Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00
Re: [gmx-users] Problem with simulation of Protein-DNA complex
Hi Tsjerk, I have checked and re-checked the structure and it seems fine. I also made sure to minimise the starting structure really well after pdb2gmx. Although it did not achive required precision, but machine precision instead. Also, the problem starts with the NVT, before that everythings seems to work fine. Could there be any other source of error? I am not able to figure it out. Many Thanks. Quoting Tsjerk Wassenaar tsje...@gmail.com: Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, rar...@ens-cachan.fr wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina lina.lastn...@gmail.com: On Thu, Feb 9, 2012 at 8:44 PM, rarora@ens-cachan.f... Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-... Rohit Arora Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR 8113) Ecole Normale Supérieure, Cachan France Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Scaling/performance on Gromacs 4
Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Scaling/performance on Gromacs 4
Hi Sara, my guess is that 1500 steps are not at all sufficient for a benchmark on 64 cores. The dynamic load balancing will need more time to adapt the domain sizes for optimal balance. It is also important that you reset the timers when the load is balanced (to get clean performance numbers); you might want to use the -resethway switch for that. g_tune_pme will help you find the performance optimum on any number of nodes, from 4.5 on it is included in Gromacs. Carsten Am Feb 20, 2012 um 5:12 PM schrieb Sara Campos: Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Lennard-Jones Parameters in ffnonbonded.itp
Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this parameters in the ffnonbonded.itp file in the section [ pairtypes ] and I have to give following informations: ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS in example CP1 CP1 1 0.338541512893 0.04184 Now here is a section of information given in the charmm documentation. !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! HN1 0.0 -0.04600.2245 HN2 0.0 -0.04600.2245 The question is: How to adopt the values in the charmm force field for the basic atom types in gromacs? I do not really know what I have to write in the [ pairtypes ] section in gromacs. Thank you for helping me Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. Shahid Nayeem On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem msnay...@gmail.com wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists profile.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp
On 21/02/2012 4:36 AM, Lara Bunte wrote: Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this parameters in the ffnonbonded.itp file in the section [ pairtypes ] and I have to give following informations: ; i j funcsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS in example CP1 CP1 1 0.338541512893 0.04184 Now here is a section of information given in the charmm documentation. !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! HN1 0.0 -0.04600.2245 HN2 0.0 -0.04600.2245 Sometimes CHARMM has special values for 1-4 interactions of some atom types (in the last two columns) and sometimes not. CHARMM computes the actual interaction parameters in the program. GROMACS has pre-computed these in the [ pairtypes ] according to the combination rule. IIRC there's some redundant entries where neither atom type has special 1-4 interactions. See manual 4.1.1 and 5.3.2 for how GROMACS needs these computations to work. The question is: How to adopt the values in the charmm force field for the basic atom types in gromacs? I do not really know what I have to write in the [ pairtypes ] section in gromacs. What's wrong with the existing contents of $GMXLIB/share/top/charmm27.ff/ffnonbonded.itp? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 18, 2012 5:29 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp
A quick answer to this is, there's two sets of tables based on equations I know of off hand for LJ's and calculating the other such LJ parameters from these. In one it uses the epsilon/ sigma and the other a table of either the 9-6 or the 6-12. The later two you can look up either on the European or US standards data base on the web or in a CRC book. The former, you have to do a conversion, although for your force field you might have to do a back conversion if you look up say the 6-12. I would trust A professor more with this though...and getting the proper equations. With the equation you have listed below it would be strait forward plug and paste and then a calculator...either you have one or the other portions of the equation. I assume the 4 epsilon is from the normal equation, and the sigma as well for a 12-6 equation. All of these are on wiki though as well. Hope thats not too confusing. Stephan Watkins Original-Nachricht Datum: Mon, 20 Feb 2012 17:36:07 + (GMT) Von: Lara Bunte lara.bu...@yahoo.de An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp Hello I use a charmm force field in gromacs. I almost finished my parametrization except for Lennard-Jones parameters. For this parameters I want to adopt the values in the charmm force field for the basic atom types. In gromacs I have to put this parameters in the ffnonbonded.itp file in the section [ pairtypes ] and I have to give following informations: ; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS in example CP1 CP1 1 0.338541512893 0.04184 Now here is a section of information given in the charmm documentation. !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! HN1 0.0 -0.04600.2245 HN2 0.0 -0.04600.2245 The question is: How to adopt the values in the charmm force field for the basic atom types in gromacs? I do not really know what I have to write in the [ pairtypes ] section in gromacs. Thank you for helping me Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Umbrella Pulling
Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? My mdp file: title = Umbrella pulling simulation define = -DPOSRES_L ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 0.5ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG182 pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns pull_k1 = 200 ; kJ mol^-1 nm^-2 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin My mdp file: title = Umbrella pulling simulation define = -DPOSRES_L ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 0.5ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG182 pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns pull_k1 = 200 ; kJ mol^-1 nm^-2 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. They're not terrible, but could be better. The PMF profile is a little rough and there are some regions of the reaction coordinate with little sampling. Maybe your simulations need to be longer and/or you need to exclude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering). -Justin Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Interchain Disulfide Bond
Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that I am following are: pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -f PDB -o GRO -p TOP However this step DOES NOT generate interchain disulfide bond. So, I tried to generate .top file using: pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -f PDB -o GRO -p TOP When asked for merging chains, I say y The above step generates correct disulfide bonds and termii; however when I use grompp -f min_run.mdp -c solvate.gro -p VAK.top –o min1.tpr I get the error: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1346 Fatal error: Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence, physically this cmap torsion is not required. I will appreciate your suggestions in helping me resolve this issue. Thanks, Neeraj -- View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488594p4488594.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Interchain Disulfide Bond
Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that I am following are: pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -f PDB -o GRO -p TOP However this step DOES NOT generate interchain disulfide bond. So, I tried to generate .top file using: pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -f PDB -o GRO -p TOP When asked for merging chains, I say y The above step generates correct disulfide bonds and termii; however when I use grompp -f min_run.mdp -c GRO -p TOP –o TPR I get the error: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1346 Fatal error: Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence, physically this cmap torsion is not required. I will appreciate your suggestions in helping me resolve this issue. Thanks, Neeraj -- View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488616p4488616.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze -ee
dina dusti wrote: Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! The warnings indicate that the error estimates are not reliable. It's all to do with the autocorrelation time. Some quantities converge faster than others. The appendix of the cited paper in g_analyze -h explains the entire derivation and what each term means. -Justin Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina *From:* Justin A. Lemkul jalem...@vt.edu *To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 18, 2012 5:29 PM *Subject:* Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, February 20, 2012 11:07 PM Subject: Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Justin, Thank you very much from your response. OK, but is it important? Because these warnings are appeared some where, not for all of calculations. For example, these are appeared for gyrate.xvg and not for moment.xvg! The warnings indicate that the error estimates are not reliable. It's all to do with the autocorrelation time. Some quantities converge faster than others. The appendix of the cited paper in g_analyze -h explains the entire derivation and what each term means. -Justin Thank you again from your help and excuse me from my delay for thank from you. Best Regards Dina *From:* Justin A. Lemkul jalem...@vt.edu *To:* dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, February 18, 2012 5:29 PM *Subject:* Re: [gmx-users] g_analyze -ee dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do g_analyze -f .xvg -av -ee error.xvg , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the statistics might be bad invalid fit: e.e. 0.285911 a 0.995985 tau1 1434.16 tau2 1.41932e+09 Will fix tau2 at the total time: 864000 Set 2: err.est. 0.00859257 a 0.995692 tau1 1432.7 tau2 864000 Set 3: err.est. 0.00527967 a 0.588024 tau1 804.83 tau2 3603.55 a fitted parameter is negative invalid fit: e.e. 0.00421461 a 1.08722 tau1 1672.3 tau2 6955.25 Will fix tau2 at the total time: 864000 a fitted parameter is negative invalid fit: e.e. -nan a 1.00449 tau1 1455.53 tau2 864000 Will use a single exponential fit for set 4 Set 4: err.est. 0.00453113 a 1 tau1 1400.34 tau2 0 Please help me. Thanks in advance from your response. It likely means the data are poorly converged. Refer to the paper cited in g_analyze -h regarding the error calculation for details and a complete description of the error estimate method. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? Steven My mdp file: title = Umbrella pulling simulation define = -DPOSRES_L ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 0.5ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG182 pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns pull_k1 = 200 ; kJ mol^-1 nm^-2 -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? By changing pull_k1. I thought that's what you meant you had already done, but I can see now that my interpretation wasn't correct. Understand the SMD is a non-equilibrium, path-dependent process. I don't know what you're pulling from what, but if the interactions are slightly different along the dissociation pathway, the forces are different because the path is different. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? By changing pull_k1. I thought that's what you meant you had already done, but I can see now that my interpretation wasn't correct. Understand the SMD is a non-equilibrium, path-dependent process. I don't know what you're pulling from what, but if the interactions are slightly different along the dissociation pathway, the forces are different because the path is different. -Justin I used exactly the same mdp file with the same parameters - the same same pull_k1 as well and I obtained different plots. The starting configuration is also the same. I pull a ligand away from the protein. Would you obtain from two normal MD or SMD simulations with the same starting configuration different results? Steven -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? By changing pull_k1. I thought that's what you meant you had already done, but I can see now that my interpretation wasn't correct. Understand the SMD is a non-equilibrium, path-dependent process. I don't know what you're pulling from what, but if the interactions are slightly different along the dissociation pathway, the forces are different because the path is different. -Justin I used exactly the same mdp file with the same parameters - the same same pull_k1 as well and I obtained different plots. The starting configuration is also the same. I pull a ligand away from the protein. Would you obtain from two normal MD or SMD simulations with the same starting configuration different results? Yes, it's quite possible. MD is a chaotic process. http://www.gromacs.org/Documentation/Terminology/Reproducibility http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? By changing pull_k1. I thought that's what you meant you had already done, but I can see now that my interpretation wasn't correct. Understand the SMD is a non-equilibrium, path-dependent process. I don't know what you're pulling from what, but if the interactions are slightly different along the dissociation pathway, the forces are different because the path is different. -Justin I used exactly the same mdp file with the same parameters - the same same pull_k1 as well and I obtained different plots. The starting configuration is also the same. I pull a ligand away from the protein. Would you obtain from two normal MD or SMD simulations with the same starting configuration different results? Yes, it's quite possible. MD is a chaotic process. http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility http://www.gromacs.org/**Documentation/How-tos/** Extending_Simulations#Exact_**vs_binary_identical_**continuationhttp://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation -Justin Like in a real experiment :) In this case it is required to run a lot of simulations with the same parameters to be able to exract desired values? Thank you Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Pulling
Steven Neumann wrote: On Mon, Feb 20, 2012 at 8:07 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Feb 20, 2012 at 7:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I run a pulling of my ligand away from my protein with the same mdp file and I obtained two different plots - Force vs time (The breaking point occured at different times with different force). Can you please explain? If you change the stiffness of the spring, you change the magnitude of the applied force. Thus, the behavior you see will occur either faster or slower, depending on the strength of the spring. -Justin So how can I change the stiffness of my spring? By changing pull_k1. I thought that's what you meant you had already done, but I can see now that my interpretation wasn't correct. Understand the SMD is a non-equilibrium, path-dependent process. I don't know what you're pulling from what, but if the interactions are slightly different along the dissociation pathway, the forces are different because the path is different. -Justin I used exactly the same mdp file with the same parameters - the same same pull_k1 as well and I obtained different plots. The starting configuration is also the same. I pull a ligand away from the protein. Would you obtain from two normal MD or SMD simulations with the same starting configuration different results? Yes, it's quite possible. MD is a chaotic process. http://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility http://www.gromacs.org/__Documentation/How-tos/__Extending_Simulations#Exact___vs_binary_identical___continuation http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation -Justin Like in a real experiment :) In this case it is required to run a lot of simulations with the same parameters to be able to exract desired values? Thank you Justin It depends on what you hope to demonstrate. For instance, if you want to try to extract equilibrium thermodynamic information from SMD (which is inherently a non-equilibrium method), look into work by Jarzynski. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Scaling/performance on Gromacs 4
Poor scaling with MPI on many-core machines can also be due uneven job distributions across cores or jobs being wastefully swapped between cores. You might be able to fix this with some esoteric configuration options of mpirun (--bind-to-core worked for me with openMPI), but the surest option is to switch to gromacs 4.5 and run using thread-level parallelisation, bypassing MPI entirely. From: Sara Campos srrcam...@gmail.com To: gmx-users@gromacs.org Sent: Monday, 20 February 2012, 17:12 Subject: [gmx-users] Scaling/performance on Gromacs 4 Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] T-coupling problem?
Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do grompp, it gives me this error: == Fatal error: 14623 atoms are not part of any of the T-Coupling groups == What I did is I first made .ndx file that include the protein atoms. Then, I wrote this in the comand: grompp -f .mdp -c -.gro -n .ndx -p .top -o --.tpr -.mdp: I include the freeze option in this file. -.ndx: This includes the group that I want to freeze. 1841: the total number of protein atoms. 116100: the total nuber of system atoms. Could you please tell me what to do? Thanks, Talal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] T-coupling problem?
Talal Alotaibi wrote: Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do grompp, it gives me this error: == Fatal error: 14623 atoms are not part of any of the T-Coupling groups == What I did is I first made .ndx file that include the protein atoms. Then, I wrote this in the comand: grompp -f .mdp -c -.gro -n .ndx -p .top -o --.tpr -.mdp: I include the freeze option in this file. -.ndx: This includes the group that I want to freeze. 1841: the total number of protein atoms. 116100: the total nuber of system atoms. Could you please tell me what to do? You haven't included some large part of your system in the temperature coupling section. All elements of the system have to be under the control of a thermostat. Do not confusing the freezing method with something related to temperature; they are separate concepts. If you need further help, post your full .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Scaling/performance on Gromacs 4
On 21/02/2012 8:11 AM, Floris Buelens wrote: Poor scaling with MPI on many-core machines can also be due uneven job distributions across cores or jobs being wastefully swapped between cores. You might be able to fix this with some esoteric configuration options of mpirun (--bind-to-core worked for me with openMPI), but the surest option is to switch to gromacs 4.5 and run using thread-level parallelisation, bypassing MPI entirely. That can avoid problems arising from MPI performance, but not those arising from PP-vs-PME load balance, or intra-PP load balance. The end of the .log files will suggest if these latter effects are strong contributors. Carsten's suggested solution is one good one. Mark *From:* Sara Campos srrcam...@gmail.com *To:* gmx-users@gromacs.org *Sent:* Monday, 20 February 2012, 17:12 *Subject:* [gmx-users] Scaling/performance on Gromacs 4 Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] T-coupling problem?
On 21/02/2012 8:39 AM, Talal Alotaibi wrote: Hi, I am trying to freeze the protein during equilibruim. I made the energy minimization with no freezing. but when I freeze the protein and try to do grompp, it gives me this error: A more sound protocol for preparation for MD probably involves the use of position restraints, rather than frozen atoms. See various tutorials for examples. == Fatal error: 14623 atoms are not part of any of the T-Coupling groups == What I did is I first made .ndx file that include the protein atoms. Then, I wrote this in the comand: grompp -f .mdp -c -.gro -n .ndx -p .top -o --.tpr Copying and pasting actual command lines is preferred by those who might give feedback. They want to see what actually happened, not what you think happened. -.mdp: I include the freeze option in this file. -.ndx: This includes the group that I want to freeze. 1841: the total number of protein atoms. 116100: the total nuber of system atoms. 116100 14623. Some part of your report is badly wrong. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interchain Disulfide Bond
On 21/02/2012 6:20 AM, jneeraj wrote: Hello, I am trying to perform a MD simulation of a protein consisting of two chains. These two chains are connected via single disulfide bond. These two chains are separated by TER record in the input pdb file. I am using charmm27 force-field. The steps that I am following are: pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -fPDB -oGRO -pTOP However this step DOES NOT generate interchain disulfide bond. So, I tried to generate .top file using: pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -fPDB -o GRO -pTOP When asked for merging chains, I say y -merge and -chainsep do different things. You need separated chains that are merged into the same moleculetype, because the specbond.dat mechanism requires that the atoms be in the same [moleculetype]. Check out pdb2gmx -h and choose a suitable combination of -merge and -chainsep. The above step generates correct disulfide bonds and termii; however when I use I don't think all your termini would be correct, and the subsequent error suggests that. Mark grompp -f min_run.mdp -cGRO -pTOP –oTPR I get the error: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1346 Fatal error: Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence, physically this cmap torsion is not required. I will appreciate your suggestions in helping me resolve this issue. Thanks, Neeraj -- View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488616p4488616.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] [solved] Using CHARMM force fields in Gromacs, pt. 2
@Peter C. Lai: I did like you suggested and now the two forcefields work in tandem as expected. @Mark Abraham: Thank you for the explanation. Best. Jernej Zidar On Mon, Feb 20, 2012 at 15:27, gmx-users-requ...@gromacs.org wrote: There's no need to patch the forcefields.dat file because Gromacs will first look for the forcefields in /opt/share/gromacs/top/ and later in the local directory. oh ok. I added an entry anyway because I liked having the main charmm36 one grouped with the charmm36cgen one in the menu.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Interchain Disulfide Bond
Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f pdb -o gro -p top $grompp -f mdp -c gro -p top -o tpr and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27 force field instead of amber99sb, I get the following error from grompp: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1346 Fatal error: Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 So I believe this error is specific to charmm27 force-field. Any thoughts ? Thanks neeraj -- View this message in context: http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-tp4488616p4489663.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Interchain Disulfide Bond
On 21/02/2012 12:33 PM, jneeraj wrote: Thank you Mark for you prompt response. I tried: $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -fpdb -ogro -ptop $grompp -fmdp -cgro -ptop -otpr and it works perfectly, i.e. it correctly creates interchain disulfide bond. However, when I use charmm27 force field instead of amber99sb, I get the following error from grompp: Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1346 Fatal error: Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 So I believe this error is specific to charmm27 force-field. Any thoughts ? Because those are the atoms across the 1-C 2-N region, that suggests that the mechanism that adds CMAP to the backbone is not interacting correctly with the -merge mechanism. Please open a new issue on Redmine http://redmine.gromacs.org http://redmine.gromacs.org/ and attach files that will reproduce the problem. If my guess is correct, the fix should be straightforward. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella_pull_simulation
Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it. Shahid Nayeem On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows. ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= YN Y pull_vec1 = 0.75 0 1 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence. They're not terrible, but could be better. The PMF profile is a little rough and there are some regions of the reaction coordinate with little sampling. Maybe your simulations need to be longer and/or you need to exclude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering). -Justin Shahid Nayeem On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: shahid nayeem wrote: Thanks Justin I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation. chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier. Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists profile.xvg Description:
