[gmx-users] how to run g_tune_pme in cluster?
Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 log but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it
Dear ALL:how to install DSSP in Gromacs4.5.7I followed someone replies mail still can not use do I do right ?DSSP website-miscellaneous-distribution-dsspold-linux distribution then get dsspcmbibut Gromacs can not recoginz this index gromacs index is do_dssp ?and DSSPagain , how to install DSSP in Gromacs ?many thanks Best Wishesli-hua -- 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] How to choose two atoms at the same time, using g_select selection.dat
On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote: e.g, I want to make an HN group of both H and N from my 2nd residue, There are multiple ways to achieve what you want with g_select. Probably the easiest is resnr 2 and name H N, or if you need the atoms in a different order (changing the order of H and N above has no effect), resnr 2 and name H N permute 2 1. You can also use plus or merge using the syntax nameH plus nameN (plus and merge are equivalent if you are merging selections with single atoms), but they are meant for more complex situations. You cannot assign the result of a plus/merge into a variable, which may be your source of confusion. - Teemu -- 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 4.5.4 on cygwin cmake
Hi I am having problems installing gromacs on cygwin using autoconf so I used cmake instead. I used the following option with cmake: cmake GMX_PREFER_STATIC_LIBS=ON ../gromacs-4.5.4 followed by make and make install. Gromacs installed finally without complaints. gromacs installs but I get the following error when I try to run the different gromacs executables: trjconv gives /usr/local/gromacs/bin/trjconv.exe: error while loading shared libraries: cyggmx/usr/local/gromacs/bin/trjconv.exe:cyggmx ana-6.dll: cannot open shared object file: No such file or directory gmxcheck gives: /usr/local/gromacs/bin/gmxcheck.exe: error while loading shared libraries: cyggm xpreprocess-6.dll: cannot open shared object file: No such file or directory Is there a way around this. I mainly need gromacs on my laptop for all the analysis routines and not to run md sims. Thanks for any and all help. Vijaya -- 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] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] how to run g_tune_pme in cluster?
hello: it can find mdrun correctly. and it is only give me the log file as I mentioned in previous thread. thank you very much On 04/26/2012 09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in log and in perf.out? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 log but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)
it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban On Thu, Apr 26, 2012 at 3:08 PM, Albert mailmd2...@gmail.com wrote: it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- 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: [gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it
You set the environment variable DSSP to the absolute path to your dssp executable. Then do_sddp can make use of it. Is that clear? Erik 26 apr 2012 kl. 09.33 skrev 李 麗花: Dear ALL: how to install DSSP in Gromacs4.5.7 I followed someone replies mail still can not use do I do right ? DSSP website-miscellaneous-distribution-dsspold-linux distribution then get dsspcmbi but Gromacs can not recoginz this index gromacs index is do_dssp ? and DSSP again , how to install DSSP in Gromacs ? many thanks Best Wishes li-hua -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] how to run g_tune_pme in cluster?
On Apr 26, 2012, at 11:37 AM, Albert wrote: hello: it can find mdrun correctly. and it is only give me the log file as I mentioned in previous thread. What files are produced by g_tune_pme? Is there a benchtest.log? Can you cat its contents? Carsten thank you very much On 04/26/2012 09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in log and in perf.out? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 log but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban -- 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] how to run g_tune_pme in cluster?
yes, here is the contents for it: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: 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 (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: 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 (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: 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 (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: 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 (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-)
[gmx-users] Force field for graphene sheet: deformation at the boundaries
Dear colleagues, I came across a puzzling behaviour when simulating graphene sheets (periodic in xy). When running a simulation of just one position restrained graphene sheet in a large vacuum slab with periodic_molecules=yes and pbc=xyz, I found a static deformation of the boundaries of the graphene sheet. On search for a more suitable force field I finally found the deletion of angle/dihedral information from the topology the best result. Why is a large graphene sheet with the same force field information for all atoms, bonds, angles and dihedrals deformed only at the border of the periodic simulation box? In case of errors in the force field I would have suspected bents all over the graphene sheet. Some information on the structure and topology preparation: The initial structure has been generated with the help of of ase.structure (https://wiki.fysik.dtu.dk/ase/epydoc/ase.structure-module.html). A 3-4 armchair nanoribbon resulted in a graphene sheet of 6 nm * 6 nm area. Afterwards I run g_x2top to obtain the topology: g_x2top -f Gl1.gro -o out.top -name Gl1 -pbc with the addition of the line C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140 in gromacs4.5.5/share/gromacs/top/oplsaa.ff/atomname2type.n2t and added position restraints in all directions for all carbon atoms (k_xyz=1000 kJ mol^-1 nm^-2). Best regards Kathleen Kathleen Kirchner PhD student Max Planck Institute for Mathematics in the Sciences (MPI f. Mathematik in den Naturwissenschaften) Inselstr. 22-26, D04103 Leipzig e-mail: kirch...@mis.mpg.de web: http://www.mis.mpg.de/scicomp/CompPhysChem/ Tel +49 341 9959 725 Fax +49 341 9959 999 -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert mailmd2...@gmail.com wrote: Hello Anirban: thanks for kind comments. How long did you mean fairly long simulation time ? does 1u ns belongs to this range? CHARMM36 ff is available in gromacs website and we can download it and put them into top directory and then it works. It is not need to make any modification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban -- 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
[gmx-users] Atom types for phosphate group in OPLS-AA force field
Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- 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] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 7:45 AM, Delmotte, Antoine wrote: Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? The problem isn't necessarily the atom types themselves (which seem to be reasonable enough from the information provided), but rather that there are no default bonded parameters for these interactions. If you look into ffnonbonded.itp, the second column is entitled bond_type and thus refers to the names used by grompp when interpreting how atoms are connected. The actual bond, angle, and dihedral parameters are in ffbonded.itp, using these names. You would have to map out what the bond_type names are for each of these and find/derive new parameters for each of the interactions that are missing. -Justin Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- 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] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert mailmd2...@gmail.com wrote: Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- 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] how to optimize the orientation of the protein in a dodecahedron
Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :) Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use: pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff amber99sb-ildn -water tip3p -ignh # set the new dodecahedron box dimensions editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro # solvate with TIP3P genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p protein.top # add ions grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o protein_ions.tpr echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top -pname NA -nname CL -np 3 grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o protein_EM.tpr mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM # to see a dodecahedron echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s protein_EM.tpr -o em_dodecahedron.xtc # measure the minimum distance from the periodic images echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi Is there any way to optimize the orientation of protein inside the dodecahedron in order to get the maximum possible mindist? Thanks in advance, Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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
[gmx-users] Re: gmx-users Digest, Vol 96, Issue 189
users gmx-users@gromacs.org Message-ID: 4f98cb52.1060...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 Please do not make unsolicited general GROMACS inquiries to private email addresses. The mailing lists exist for these kinds of purposes. On point, you cannot be helped unless you provide the command lines that you used and describe the objectives you were trying to achieve. Whatever changes you make to one of the coordinate and .top file must be matched in the other. Mark Original Message Subject:Error: coordinate file does not match with the topology file Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT) From: sonali shinde shindesonal...@yahoo.co.in Reply-To: sonali shinde shindesonal...@yahoo.co.in To: mark.abra...@anu.edu.au mark.abra...@anu.edu.au - Forwarded Message - *From:* sonali shinde shindesonal...@yahoo.co.in *To:* vini k vineetha_mand...@yahoo.co.in *Sent:* Monday, 23 April 2012 6:48 PM *Subject:* Error: coordinate file does not match with the topology file Dear Sir, I am a user of gromacs 4.0 for molecular dynamic study of a protein molecule. I have generated trajectory file before using the same commands that I use now. Recently I am suffering some problem using Gromacs , my coordinate file does not matches with the topology file.I have attached the pdb file protein, .gro and .top file . I have encountered same error a number of times with three different proteins.Please suggest the answer for the same. Thanking you. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120426/23d33012/attachment-0001.html -- Message: 6 Date: Thu, 26 Apr 2012 14:24:53 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to increase the ratio of cell size to constrain length per error message To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f98ce15.4040...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version is 4.5.3.and running my jobs on single node with 8 cores. I have two different systems which contain about 425000 atoms (protein + Lipid +SOL) one with bound ligand and another one unbound protein.I have successfully reached up to NPT equilibration run step, It is a poor idea to do equilibration with Parinello-Rahman, which is unstable when the system is not already close to equilibrium. For some reason people still do it, despite at least a post per week on this list suggesting against it, and a warning in the manual. Use Berendsen to fix the density, then equilibrate further with P-R to get the right ensemble. now I want to continue the same for production run. Without ligand I am able to run successfully But the same system with ligand is crashing with following error- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are are connected via constraints from the neighbouring cells This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs_order. I'd rather expect your system was blowing up because of the above issue. Perhaps the suggestion in the error message is not as complete as could be desired - you have so many atoms per processor that the constraint length would normally be tiny with respect to the cell size. So I think the things you have tried below are rearranging the deck chairs on the Titanic. Mark Accordingly following the suggestions given in the error I tried to solve it with Following log file and changed, 1.1. -rcon Estimated maximum distance required for p-lincs was 0.877 thus I increased it to 0.900 then it thrown another error. The initial cell size (0.877) is smaller than the cell size limit (0.900) 2 .Then I tried to increase the --dds and --rdd from original values of 1.25 and 0.623 to 1.30 and 0.670 respectively. But it does not help and ended with run crash. /*What I did was logical or I did it wrongly?*/ /*Now can anyone please suggest me the appropriate way to deal with the problem mentioned above? */ As I want the continuation of the same run without altering the output after change in the parameters (As I have to compare the output with unbound protein run thus can't afford change in output with change in parameters) I know that I need to change some of the parameters in .mdp file such as fourierspacing from 0.16 to 0.12 and on the contrary increase the pme_order from say 4 to 6. /*But as asked above by doing so the output will not or will be the exact continuation run?*/ /*How to increase the ratio
Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
Hi, And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum. Erik 26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar: Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :) Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use: pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff amber99sb-ildn -water tip3p -ignh # set the new dodecahedron box dimensions editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro # solvate with TIP3P genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p protein.top # add ions grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o protein_ions.tpr echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top -pname NA -nname CL -np 3 grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o protein_EM.tpr mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM # to see a dodecahedron echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s protein_EM.tpr -o em_dodecahedron.xtc # measure the minimum distance from the periodic images echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi Is there any way to optimize the orientation of protein inside the dodecahedron in order to get the maximum possible mindist? Thanks in advance, Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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 -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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: GPCR MD Tutorial Using GROMACS (URL)
Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? I also have another question about slecting a lipidbilayer, what is the criteria is selecting it, for instance popc, dopc or dppc? Thanks Bala S -- View this message in context: http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4930616.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] how to optimize the orientation of the protein in a dodecahedron
Hi Tsjerk and Erik, Thanks for the comments. It's strange, because I get different minimum distance for different orientations of the same protein structure using the afore-mentioned command lines. I used a single step energy minimization for speed (em_real.mdp). Below are the outputs of editconf and the last lines of the output .gro files. There are differences in the Volume (884.007 nm^3 versus 996.803 nm^3), system size, center, box vectors, box volume, and shift. What do these differences mean? Can they explain the different mindist I get? ## ## Protein Orientation 1 editconf_4.5.5 output: ## Read 17463 atoms Volume: 884.007 nm^3, corresponds to roughly 397800 electrons No velocities found system size : 9.205 8.440 11.378 (nm) diameter: 12.498 (nm) center : 6.524 6.242 9.385 (nm) box vectors : 9.205 8.440 11.378 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 884.01 (nm^3) shift : 3.226 3.508 -4.789 (nm) new center : 9.750 9.750 4.596 (nm) new box vectors : 13.000 13.000 13.000 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1553.51 (nm^3) ## Last line of the output .gro file: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time2.000 The shortest periodic distance is 1.5735 (nm) at time 2 (ps), between atoms 992 and 8506 ## ## Protein Orientation 2 editconf_4.5.5 output: ## Read 17463 atoms Volume: 996.803 nm^3, corresponds to roughly 448500 electrons No velocities found system size : 12.299 9.828 8.247 (nm) diameter: 12.498 (nm) center : 5.898 4.759 8.713 (nm) box vectors : 12.299 9.828 8.247 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 996.80 (nm^3) shift : 3.852 4.991 -4.117 (nm) new center : 9.750 9.750 4.596 (nm) new box vectors : 13.000 13.000 13.000 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1553.51 (nm^3) ## Last line of the output .gro file: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time2.000 The shortest periodic distance is 2.59235 (nm) at time 2 (ps), between atoms 3915 and 6814 Thanks in advance, Thomas On 26 April 2012 15:36, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :) Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use: pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff amber99sb-ildn -water tip3p -ignh # set the new dodecahedron box dimensions editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro # solvate with TIP3P genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p protein.top # add ions grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o protein_ions.tpr echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top -pname NA -nname CL -np 3 grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o protein_EM.tpr mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM # to see a dodecahedron echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s protein_EM.tpr -o em_dodecahedron.xtc # measure the minimum distance from the periodic images echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi Is there any way to optimize the orientation of protein inside the dodecahedron in order to get the maximum possible mindist? Thanks in advance, Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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
Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron
Hi Thomas, Apologies, you are right. I was thinking of the distance to the wall. If the protein is elongated, it will matter in the minimal distance whether the protein major radius is oriented towards a face or towards a corner. In addition, the shape of the protein plays a role. Yet it doesn't really matter for the setup of the simulation, since the rhombic dodecahedroon is built according to the radius of the system, added the distance to the wall (-d). The rhombic dodecahedron is constructed based on the inscribed sphere with that radius, such that every orientation will satisfy the minimal distance between images. For a given solute, the rhombic dodecahedron is uniquely defined, regardless the orientation, in contrast to what happens with a rectangular unit cell. I hope this clarifies things. Cheers, Tsjerk On Thu, Apr 26, 2012 at 3:57 PM, Thomas Evangelidis teva...@gmail.com wrote: Hi Tsjerk and Erik, Thanks for the comments. It's strange, because I get different minimum distance for different orientations of the same protein structure using the afore-mentioned command lines. I used a single step energy minimization for speed (em_real.mdp). Below are the outputs of editconf and the last lines of the output .gro files. There are differences in the Volume (884.007 nm^3 versus 996.803 nm^3), system size, center, box vectors, box volume, and shift. What do these differences mean? Can they explain the different mindist I get? ## ## Protein Orientation 1 editconf_4.5.5 output: ## Read 17463 atoms Volume: 884.007 nm^3, corresponds to roughly 397800 electrons No velocities found system size : 9.205 8.440 11.378 (nm) diameter : 12.498 (nm) center : 6.524 6.242 9.385 (nm) box vectors : 9.205 8.440 11.378 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 884.01 (nm^3) shift : 3.226 3.508 -4.789 (nm) new center : 9.750 9.750 4.596 (nm) new box vectors : 13.000 13.000 13.000 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1553.51 (nm^3) ## Last line of the output .gro file: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time 2.000 The shortest periodic distance is 1.5735 (nm) at time 2 (ps), between atoms 992 and 8506 ## ## Protein Orientation 2 editconf_4.5.5 output: ## Read 17463 atoms Volume: 996.803 nm^3, corresponds to roughly 448500 electrons No velocities found system size : 12.299 9.828 8.247 (nm) diameter : 12.498 (nm) center : 5.898 4.759 8.713 (nm) box vectors : 12.299 9.828 8.247 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 996.80 (nm^3) shift : 3.852 4.991 -4.117 (nm) new center : 9.750 9.750 4.596 (nm) new box vectors : 13.000 13.000 13.000 (nm) new box angles : 60.00 60.00 90.00 (degrees) new box volume :1553.51 (nm^3) ## Last line of the output .gro file: 13.0 13.0 9.19239 0.0 0.0 0.0 0.0 6.5 6.5 ## g_mindist output: Last frame 0 time 2.000 The shortest periodic distance is 2.59235 (nm) at time 2 (ps), between atoms 3915 and 6814 Thanks in advance, Thomas On 26 April 2012 15:36, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Thomas, The rhombic dodecahedron corresponds to the packing of a sphere. Consequently, the difference in the distance between periodic images over the shortest diameter and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :) Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS users, I have noticed that for constant box dimensions the minimum distance from the periodic images of a protein depends on the initial orientation of the protein, whereas the orientation of the dodecahedron relative to the x,y,z axes remains fixed. These are the command lines I use: pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff amber99sb-ildn -water tip3p -ignh # set the new dodecahedron box dimensions editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro # solvate with TIP3P genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p protein.top # add ions grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o protein_ions.tpr echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top -pname NA -nname CL -np 3 grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o protein_EM.tpr mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM # to see a dodecahedron
Re: [gmx-users] Can I equilibrate with Parinello-Rahman?
On 26/04/2012 10:47 PM, PAVAN PAYGHAN wrote: Dear Mark, Thanks a lot for the reply and highlighting the cause of error that I was facing. Still can it be possible to overcome the same error with the available facility. Unfortunately you're forcing me to guess the context for this question. If there was a way to make P-R P-couping stable for equilibration in general, then it would not have the reputation for being unstable... I gave my advice about what to do already. 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] MD simulations of covalent bound protein-ligand complex by gromacs
Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to made the topology file of the complex, do I need to change the topology file manually to add the necessary things? Thanks in advance! R.X.G. -- 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 precision energy minimization show zero pressure in gromacs 4.5.5
Hi all,
I am carrying out energy minimization on bulk polymer system (N~2) with
integrator = l-bfgs in double precision gromacs 4.5.5. I am using
tabulated force-fields for bonded, and non-bonded interactions. In the
force field, the coulombic interaction is set to zero, hence, the output is
zero in md.log file.
I used g_energy to check the energy and pressure of the system after the
minimization is finished. For some reason, the pressure output for the
system is 0 with gromacs 4.5.5. So I went back and checked the md.log file
to see if this happens during the simulation or not, and I found at time =
0, the pressure is 0.
I wanted to make sure that this has to do with gromacs version, and not how
the mdp file is configured, so I did same minimization with gromacs 4.0.7.
When using version 4.0.7 with the same input files, I get the pressure
output just fine. The potential energy at the end of simulation for both
cases are exactly the same (only difference is 4.0.7 converges at 1754
steps, and 4.5.5 converges at 2148 steps)
It is possible that I am doing (or setting) something wrong since I'm using
the same mdp file from 4.0.7 to 4.5.5. To check if I'm setting something
wrong by default, I compared the md.log output between these two versions.
It seems like there are a few new things with gromacs 4.5.5 that is missing
in 4.0.7. For example, with 4.5.5
nstcalcenergy = -1
nstcouple = -1
nstpcouple = -1
rlistlong = 1.1
I see nstcalcenergy is the frequency of energy output during calculation so
it does not affect any calculation. Also since I am not coupling my system
to thermal/pressure bath, nstcouple, nspcouple, and rlistlong does not mean
much here.
So I suppose I can repeat the calculation again with 4.0.7 instead. But
since I've already carried out lots of calculation with 4.5.5, I kind of do
not want to repeat the steps again in calculating pressure values, if
possible. If someone can help me with this, it would be great.
I am appending snippet of md.log output from 4.5.5 and 4.0.7 below as a
reference.
Greg
### md.log file 4.5.5 ###
:-) /nfs/01/cwr0351/GMX4.5.5/bin/mdrun_d (double precision) (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = l-bfgs
nsteps = 10
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm_mode= Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstcalcenergy= -1
nstenergy= 1
nstxtcout= 10
init_t = 0
delta_t = 0.003
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= TRUE
bShakeSOR= FALSE
etc = No
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 5
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]=
[gmx-users] FEP
Hello all, This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to an R-H group. Below is the orignal email. I recently tested out mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to test out that a peturbation would give you a total of 0. forcefield used was CGenFF So for procedure was that I turned the CH3 group on the left to an H with 3 dummy atoms and I turned an H and 3 dummy atoms on the right to a CH3 group, essentially mutating the molecule to another version of itself (should give you a total dG of 0 if it works). STEP 1. (uncharging everything except the -CH2 group inbetween both sides CH3-CH2-HD3) *D are dummy atoms [ atoms ] ; nr type resnr residatom cgnr chargemasstotal_charge 1CG331 1 SIM C1 1-0.27 12.0110 CG331 0.00 12.0110 2 HGA3 1 SIM H11 2 0.09 1.00800 HGA30.00 1.00800 3 HGA3 1 SIM H12 3 0.09 1.00800 HGA30.00 1.00800 4 HGA3 1 SIM H13 4 0.09 1.00800 HGA30.00 1.00800 5CG331 1 SIM C2 5-0.27 12.0110 CG331 -0.1812.0110 6 HGA3 1 SIM H21 6 0.09 7 HGA3 1 SIM H22 7 0.09 8 HGA3 1 SIM H23 8 0.09 1.00800 HGA30.00 1.00800 9 DUM 1 SIM H31 9 0.00 1.00800 10 DUM 1 SIM H3210 0.00 1.00800 11 DUM 1 SIM H3311 0.00 1.00800 STEP 2. (mutation of groups. CH3-CH2-HD3 becomes D3H-CH2-CH3) [ atoms ] ; nr type resnr residatom cgnr chargemasstotal_charge 1CG331 1 SIM C1 1 0.00 12.0110 HGA30.00 1.00800 2 HGA3 1 SIM H11 2 0.00 1.00800 DUM 0.00 1.00800 3 HGA3 1 SIM H12 3 0.00 1.00800 DUM 0.00 1.00800 4 HGA3 1 SIM H13 4 0.00 1.00800 DUM 0.001.00800 5CG331 1 SIM C2 5 -0.18 6 HGA31 SIM H21 6 0.09 7 HGA31 SIM H22 7 0.09 8 HGA31 SIM H23 8 0.00 1.00800 CG331 0.00 12.0110 9 DUM1 SIM H31 9 0.00 1.00800 HGA30.00 1.00800 10 DUM1 SIM H3210 0.00 1.00800 HGA3 0.00 1.00800 11 DUM1 SIM H3311 0.00 1.00800 HGA30.00 1.00800 STEP3. (opposite of step1) [ atoms ] ; nr type resnr residatom cgnr chargemasstotal_charge 1 HGA3 1 SIM C1 1 0.00 12.0110 HGA3 0.091.00800 2 DUM 1 SIMH11 2 0.00 1.00800 DUM0.00 1.00800 3 DUM 1 SIMH12 3 0.00 1.00800 DUM0.00 1.00800 4 DUM 1 SIMH13 4 0.00 1.00800 DUM0.00 1.00800 5CG331 1 SIM C2 5-0.18 12.0110 CG331 -0.27 12.0110 6 HGA3 1 SIM H21 6 0.09 7 HGA3 1 SIM H22 7 0.09 8CG331 1 SIM H23 8 0.00 1.00800 CG331 -0.27 12.0110 9 HGA3 1 SIM H31 9 0.00 1.00800 HGA30.09 1.00800 10 HGA3 1 SIM H3210 0.00 1.00800 HGA30.09 1.00800 11 HGA3 1 SIM H3311 0.00 1.00800 HGA30.09 1.00800 So in the end, the procedure worked using the g_bar method. I took 20 simulations for steps 1 and 3 and 50 simulations for step 2. Here are the results: Step1: -37.62 +/- 0 Step2: -0.12 +/- 0.24 Step3: 37.68 +/- 0.13 TOTAL ~ -0.06 kJ/mol which is expected My question is that I did something similar for a larger molecule (65 atoms) and someone said before that step 1 and 3 should be very small. I'm getting values in the near -20 kJ/mol for step 1 and 3. I feel it should be straightforward since I'm simply uncharging a CH3 group and I don't get why I'm getting such a large number. If it is suppose to be very small, is it safe to
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? Thanks, Antoine On 26/04/12 12:53, Justin A. Lemkul wrote: On 4/26/12 7:45 AM, Delmotte, Antoine wrote: Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? The problem isn't necessarily the atom types themselves (which seem to be reasonable enough from the information provided), but rather that there are no default bonded parameters for these interactions. If you look into ffnonbonded.itp, the second column is entitled bond_type and thus refers to the names used by grompp when interpreting how atoms are connected. The actual bond, angle, and dihedral parameters are in ffbonded.itp, using these names. You would have to map out what the bond_type names are for each of these and find/derive new parameters for each of the interactions that are missing. -Justin Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- gmx-users mailing list
Re: [gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs
On 4/26/12 10:23 AM, mirc...@sjtu.edu.cn wrote: Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to made the topology file of the complex, do I need to change the topology file manually to add the necessary things? Let pdb2gmx do all the work for you: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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] double precision energy minimization show zero pressure in gromacs 4.5.5
On 4/26/12 11:00 AM, Yongchul Chung wrote:
Hi all,
I am carrying out energy minimization on bulk polymer system (N~2) with
integrator = l-bfgs in double precision gromacs 4.5.5. I am using tabulated
force-fields for bonded, and non-bonded interactions. In the force field, the
coulombic interaction is set to zero, hence, the output is zero in md.log file.
I used g_energy to check the energy and pressure of the system after the
minimization is finished. For some reason, the pressure output for the system is
0 with gromacs 4.5.5. So I went back and checked the md.log file to see if this
happens during the simulation or not, and I found at time = 0, the pressure is
0.
I wanted to make sure that this has to do with gromacs version, and not how the
mdp file is configured, so I did same minimization with gromacs 4.0.7. When
using version 4.0.7 with the same input files, I get the pressure output just
fine. The potential energy at the end of simulation for both cases are exactly
the same (only difference is 4.0.7 converges at 1754 steps, and 4.5.5 converges
at 2148 steps)
It is possible that I am doing (or setting) something wrong since I'm using the
same mdp file from 4.0.7 to 4.5.5. To check if I'm setting something wrong by
default, I compared the md.log output between these two versions. It seems like
there are a few new things with gromacs 4.5.5 that is missing in 4.0.7. For
example, with 4.5.5
nstcalcenergy = -1
nstcouple = -1
nstpcouple = -1
rlistlong = 1.1
I see nstcalcenergy is the frequency of energy output during calculation so it
does not affect any calculation. Also since I am not coupling my system to
thermal/pressure bath, nstcouple, nspcouple, and rlistlong does not mean much
here.
So I suppose I can repeat the calculation again with 4.0.7 instead. But since
I've already carried out lots of calculation with 4.5.5, I kind of do not want
to repeat the steps again in calculating pressure values, if possible. If
someone can help me with this, it would be great.
I am appending snippet of md.log output from 4.5.5 and 4.0.7 below as a
reference.
It does not make sense to calculate pressure during EM, so Gromacs outputs it as
zero. Since there are no velocities, any reported pressure value would be
meaningless.
-Justin
Greg
### md.log file 4.5.5 ###
:-) /nfs/01/cwr0351/GMX4.5.5/bin/mdrun_d (double precision) (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = l-bfgs
nsteps = 10
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm_mode= Linear
nstlog = 1
nstxout = 1
nstvout = 1
nstfout = 1
nstcalcenergy= -1
nstenergy= 1
nstxtcout= 10
init_t = 0
delta_t = 0.003
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= TRUE
bShakeSOR= FALSE
etc = No
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 5
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -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] Atom types for phosphate group in OPLS-AA force field
Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters which have calculated for other molecules? Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote: On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -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] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 12:15 PM, Delmotte, Antoine wrote: Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters which have calculated for other molecules? There is a large database at http://virtualchemistry.org/index.php but I don't know if there will necessarily be anything similar to what you're looking for. -Justin Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote: On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -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] double precision energy minimization show zero pressure in gromacs 4.5.5
On 4/26/12 12:36 PM, Yongchul Chung wrote: Well, actually it has a meaning in the simulation that I am carrying out. Ah, I remember a discussion about this some time ago and was recalling the wrong side of it ;) What you're doing is relying on the virial to dictate the pressure then. There have been a vast amount of changes between 4.0.7 and 4.5.5 so hopefully someone who has been involved with such action will know more. It could be a sneaky bug, but I'm not stating that with 100% certainty. -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] Position Restraints
Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? Regards, Dariush -- 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] Position Restraints
On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -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] Biasing a dipole vector direction relative to the moment of inertia tensor eigenvectors
Greetings, I am trying to do electrostatics calculations for a protein system which requires knowledge of the average dipole vector for an experimental probe. I've previously obtained this average dipole vector by using umbrella sampling with WHAM over the chi_2 dihedral angle of this probe, however, it's become clear that the chi_1 orientations are important enough to the average dipole vector that being in a local min for chi_1 and biasing the single degree of freedom is not sufficient. Rather than doing the simulations for 2 DOF, it was suggested that I bias the dipole vector direction relative to the moment of inertia tensor's eigenvectors. Gromacs has a function for orientation restraints relative to the rotation matrix for each frame, however, this is presented in the context of NMR spectroscopy and observables. Would it be possible to use the orientation restraints function for umbrella sampling of dipole vector space and is there a straightforward way to interpret the biasing orientation region (which I believe is referred to as the observable in the manual) as spherical polar coordinates phi and psi? Thanks, Andrew Ritchie The University of Texas at Austin-- 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] Position Restraints
Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -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
[gmx-users] Acpype doubts
I configure Amber1.5 and installed the Acpype compatible (the tests went pretty well) BUT when I tried to submit my own job by the line acpype -i proteinname.mol2 -c user i got the message: == = | ACPYPE: AnteChamber PYthon Parser interfacE v. 2011-12-19 11:11:36Z Rev: 373 (c) 2011 AWSdS | === ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' Total time of execution: less than a second laboratorio24@laboratorio24-desktop:~/dinamicas/ATP$ it's my first time so take it easy pls ;) -- 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] Position Restraints
On 4/26/12 1:59 PM, Dariush Mohammadyani wrote: Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Then I don't understand what the problem is. You'll have to describe what you're doing in greater detail. -Justin Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-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] help about Inconsistent DD boundary staggering limits
Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 54, will try to stop all the nodes Halting parallel program mdrun on CPU 54 out of 120 Error on node 24, will try to stop all the nodes Halting parallel program mdrun on CPU 24 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 84, will try to stop all the nodes Halting parallel program mdrun on CPU 84 out of 120 gcq#359: If it weren't for bad luck, we'd have no luck at all (The Unthanks) gcq#359: If it weren't for bad luck, we'd have no luck at all (The Unthanks) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 42
Re: [gmx-users] double precision energy minimization show zero pressure in gromacs 4.5.5
I suppose I can calculate virial manually ... but thought there might be a glitch in the code when making a transition from 4.0 to 4.5. I sent an e-mail to gmx-developers. Greg On Thu, Apr 26, 2012 at 1:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 12:36 PM, Yongchul Chung wrote: Well, actually it has a meaning in the simulation that I am carrying out. Ah, I remember a discussion about this some time ago and was recalling the wrong side of it ;) What you're doing is relying on the virial to dictate the pressure then. There have been a vast amount of changes between 4.0.7 and 4.5.5 so hopefully someone who has been involved with such action will know more. It could be a sneaky bug, but I'm not stating that with 100% certainty. -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] help about Inconsistent DD boundary staggering limits
On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 54, will try to stop all the nodes Halting parallel program mdrun on CPU 54 out of 120 Error on node 24, will try to stop all the nodes Halting parallel program mdrun on CPU 24 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The
[gmx-users] gen_pairs to calculate absent 1-4 interactions in CHARMM36c FF
Dear users, In GROMACS, does CHARMM36 ff, calculate eventual 1-4 interactions that are absent from the [pairtypes] section of the ffnonbonded.itp file? I ask this because I'm converting cholesterol parameters from CHARMM36c to gmx format, and several 1-4 values are absent in the last two columns of the prm file. Does setting gen_pairs to yes in the [defaults] section in the forcefield.itp work? Thanks again, Ricardo.-- 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] help about Inconsistent DD boundary staggering limits
On 4/26/12 3:30 PM, Desheng Zheng wrote: Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? Coordinate files and topologies are largely independent of version. There was a reorganization of the force fields between 4.0.7 and 4.5, but you can easily work around such things. 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? I don't know. The easiest way to deduce the source of the problem is to do so scientifically. Turn off the electric field, does the simulation run? Eliminate other factors systematically until you arrive at the root of the problem. 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? There have been changes to the .edr format and its contents to allow for more features. -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] How to choose two atoms at the same time, using g_select selection.dat
Thanks for the reply! On Thu, Apr 26, 2012 at 3:28 AM, Teemu Murtola teemu.murt...@cbr.su.sewrote: On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote: e.g, I want to make an HN group of both H and N from my 2nd residue, There are multiple ways to achieve what you want with g_select. Probably the easiest is resnr 2 and name H N, or if you need the atoms in a different order (changing the order of H and N above has no effect), resnr 2 and name H N permute 2 1. You can also use plus or merge using the syntax nameH plus nameN (plus and merge are equivalent if you are merging selections with single atoms), but they are meant for more complex situations. You cannot assign the result of a plus/merge into a variable, which may be your source of confusion. - Teemu -- 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: [gmx-users] help about Inconsistent DD boundary staggering limits
Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? Best wishes, Desheng From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, April 26, 2012 3:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] help about Inconsistent DD boundary staggering limits On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION
RE: [gmx-users] Error in using gromacs for MD simulation
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of vineetha mandlik Sent: Tuesday, 24 April 2012 7:56 PM To: gmx-users@gromacs.org Subject: [gmx-users] Error in using gromacs for MD simulation -- Forwarded message -- From: Rossen Apostolov ros...@kth.semailto:ros...@kth.se Date: Mon, Apr 23, 2012 at 11:53 PM Subject: Re: error in using gromacs for MD simulation To: vineetha mandlik vinee2h...@gmail.commailto:vinee2h...@gmail.com Please send your questions to the mailing list gmx-users@gromacs.orgmailto:gmx-users@gromacs.org. This is the administrative mail. Rossen On 2012-04-23 17.12, vineetha mandlik wrote: Respected Sir, Thanks for your reply. I had written to you previously regarding the error in the grompp command when running the MD simulation of a protein, structure was obtaining using homology modelling approach. The error reported was : Number of coordinates in coordinate file (z_b4em.gro) does not match that of topology file (z.top). We are however not able to run the nohup command because of the above mentioned error. I m sending you the pdb,top and gro files along with a file containing the commands and output obtained. Your help in resolving this issue would be highly appreciated. Thanking you. Vineetha. -- 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: GPCR MD Tutorial Using GROMACS (URL)
Looks I got to the party late (at a conference with limited time to do emails). As a shameless self-plug, we recently published a soup-to-nuts protocol paper for GPCR + POPC + ligand in Gromacs 4.5.x and CHARMM27/36/CGenFF. Our timescales are on the order 100+ns. 20ns/day is possible on 100K atoms with around 200 xeon x5650 cores over qdr infiniband (4-order PME with 1.2nm cutoffs 0.16 fourier spacing, vdwtype switch=0.8 and h-bond LINCS with 0.002ps dt). http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract On 2012-04-26 01:40:17PM -0400, Justin A. Lemkul wrote: On 4/26/12 9:35 AM, Bala S wrote: Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? Tutorials present possible workflows. Anirban's tutorial does not significantly differ from my own (linked from his) which I happen to know has been applied to many different systems. There is nothing GPCR-specific in this new tutorial, just like there is nothing KALP-specific about mine. I also have another question about slecting a lipidbilayer, what is the criteria is selecting it, for instance popc, dopc or dppc? The choice of lipid depends on what you need to model. -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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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: GPCR MD Tutorial Using GROMACS (URL)
Hello Bala, Yes, exactly as Justin said it represents just a workflow where a GPCR protein (here B2AR) has been taken as an example. I mentioned it as a GPCR tutorial because many often inquire about GPCR MD simulations only in the forum. But it can be adapted for other membrane proteins as well. And secondly again as Justin mentioned, the choice of lipid depends upon the system you wish to replicate. Regards, Anirban On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 9:35 AM, Bala S wrote: Dear Anirban, Thanks for the tutorial you have created for the newbies like me to follow. I wonder the tutorial is only for the GPCRs not applicable for other membrane proteins? Tutorials present possible workflows. Anirban's tutorial does not significantly differ from my own (linked from his) which I happen to know has been applied to many different systems. There is nothing GPCR-specific in this new tutorial, just like there is nothing KALP-specific about mine. I also have another question about slecting a lipidbilayer, what is the criteria is selecting it, for instance popc, dopc or dppc? The choice of lipid depends on what you need to model. -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
[gmx-users] Regarding errors
Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. SURYANARAYANA SEERA, PhD student -- 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
