[gmx-users] atomtype names case INsensitive?
Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- 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] Distance travelled from time 0
Hi guys, What is the best way of calculating how far a residue has traveled from its starting position during a simulations? Thanks Natalie -- 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] atomtype names case INsensitive?
Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- 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] atomtype names case INsensitive?
Hi, GROMACS is indeed case insensitive when it comes to atomtypes. I had the same problem a while ago. The simplest way to deal with it is just to add a letter at the end of your atomtypes. 2013/6/20 Mark Abraham mark.j.abra...@gmail.com Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- 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] atomtype names case INsensitive?
Thanks Mark and Baptiste, yes its case insensitive for atomtype names. I have changed all names and its working now :-) regards, On Thu, Jun 20, 2013 at 2:55 PM, Baptiste Demoulin bat.demou...@gmail.comwrote: Hi, GROMACS is indeed case insensitive when it comes to atomtypes. I had the same problem a while ago. The simplest way to deal with it is just to add a letter at the end of your atomtypes. 2013/6/20 Mark Abraham mark.j.abra...@gmail.com Probably Mark On Jun 20, 2013 11:42 AM, gromacs query gromacsqu...@gmail.com wrote: Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atomtypes.atp are modified with all the atomtype names with lowercases thinking that it will avoid over riding and mixing of parameters (as some of angles and dihedrals are common). for example (there are many) WARNING 4 [file A.top, line 342]: Overriding Ryckaert-Bell. parameters. showing old and new values. The old values are from modified oplsaa.ff/ffbonded.itp in which I have already used lowercase atometype names. Using gmxdump I can see system B is using modified oplsaa.ff. So does this mean Gromacs is case insensitive as I get warning even I used lowercase letters? regards, -- 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 -- 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] Distance travelled from time 0
Hi Natalie, You might want to look into g_rmsf, used to calculate the root mean squared fluctuation of atoms or residues. sample usage: g_rmsf -f trajectory.xtc -s struc_mass.tpr -oq rmsf.pdb -o rmsf.xvg Additional commands of interest: -res (when true, calculates residues as a whole) -b (first read frame) -e (last read frame) For more information see the guide: http://manual.gromacs.org/current/online/g_rmsf.html Cheers, Parker On Thu, Jun 20, 2013 at 5:50 AM, Natalie Stephenson natalie.stephen...@manchester.ac.uk wrote: Hi guys, What is the best way of calculating how far a residue has traveled from its starting position during a simulations? Thanks Natalie -- 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] Distance travelled from time 0
Hi, g_rmsf doesn't do distances. To answer the question, you can use g_rms with -fit none and a suitable index group. Does depend a bit on what you mean with distance. The distance traveled by a residue could well mean the average distance for all particles in the residue, which is what you'll get with g_rms. Cheers, Tsjerk On Thu, Jun 20, 2013 at 2:44 PM, Parker de Waal parker.dewaa...@kzoo.eduwrote: Hi Natalie, You might want to look into g_rmsf, used to calculate the root mean squared fluctuation of atoms or residues. sample usage: g_rmsf -f trajectory.xtc -s struc_mass.tpr -oq rmsf.pdb -o rmsf.xvg Additional commands of interest: -res (when true, calculates residues as a whole) -b (first read frame) -e (last read frame) For more information see the guide: http://manual.gromacs.org/current/online/g_rmsf.html Cheers, Parker On Thu, Jun 20, 2013 at 5:50 AM, Natalie Stephenson natalie.stephen...@manchester.ac.uk wrote: Hi guys, What is the best way of calculating how far a residue has traveled from its starting position during a simulations? Thanks Natalie -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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: Membrane Runs Crashing
Justin Lemkul wrote What was the outcome of EM before this? What if you try NVT before NPT? Have you tried reducing the timestep or the value of nstlist? I would try everything with ref_p = 1.0 instead of zero to make sure you can get a normal setup to work. -Justin The membrane I am using is pre-equilibrated at 325 K and zero surface tension according to the Martini website, so I felt like energy minimization was unnecessary. I have tried reducing the value of nstlist, but to no avail. I have not tried reducing the time step as this time step seems to be on the lower side of what is acceptable for Martini parameters already. -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Runs-Crashing-tp5009264p5009309.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] System expansion
Dear Gromacs users, I experience a very strange problem. I have a well equilibrated system consisting of a protein, a ligand, ions and water. On most machines I run my simulations on, everything is just fine. Except for one compute cluster, where the system undergoes an extreme expansion when I use the md-vv integrator for an NPT-simulation. To give you an impression I uploaded a short video showing the first 100 picoseconds of the run to my Dropbox: https://www.dropbox.com/s/d1ef94bbns0hasr/explode.mpg The system expands so heavily that it consists mainly of vacuum. If I switch the integrator from md-vv to md, everything is fine again. The same simulation (same .mdp file, same starting positions and velocities from previous simulation) runs fine with the md-vv integrator on our GPU-cluster. The .mdp file can be downloaded here: https://www.dropbox.com/s/k9it6eiqb259o59/explode.mdp I have no idea if it is me who is doing something wrond, a bug in Gromacs, a problem with the cluster or something else. Any suggestions and ideas are appreciated. Regards, Oliver -- Oliver Schillinger Master's student Forschungszentrum Juelich GmbH 52425 Juelich | Germany Building 5.8v, Room 3010 Phone: 02461-61-9532 Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] System expansion
Hi Oliver - Hmm. Did you try to start from (a little bit) different configurations on the problematic machine? Or re-install gromacs there, perhaps? Dr. Vitaly Chaban On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger o.rus...@fz-juelich.dewrote: Dear Gromacs users, I experience a very strange problem. I have a well equilibrated system consisting of a protein, a ligand, ions and water. On most machines I run my simulations on, everything is just fine. Except for one compute cluster, where the system undergoes an extreme expansion when I use the md-vv integrator for an NPT-simulation. To give you an impression I uploaded a short video showing the first 100 picoseconds of the run to my Dropbox: https://www.dropbox.com/s/**d1ef94bbns0hasr/explode.mpghttps://www.dropbox.com/s/d1ef94bbns0hasr/explode.mpg The system expands so heavily that it consists mainly of vacuum. If I switch the integrator from md-vv to md, everything is fine again. The same simulation (same .mdp file, same starting positions and velocities from previous simulation) runs fine with the md-vv integrator on our GPU-cluster. The .mdp file can be downloaded here: https://www.dropbox.com/s/**k9it6eiqb259o59/explode.mdphttps://www.dropbox.com/s/k9it6eiqb259o59/explode.mdp I have no idea if it is me who is doing something wrond, a bug in Gromacs, a problem with the cluster or something else. Any suggestions and ideas are appreciated. Regards, Oliver -- Oliver Schillinger Master's student Forschungszentrum Juelich GmbH 52425 Juelich | Germany Building 5.8v, Room 3010 Phone: 02461-61-9532 Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Error while using genion
I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin peptide. I was going through the steps in the tutorial but got stuck with the genion command. When I am prompted to select a group, I get the error that it is not found. I tried many different ways of specifying this but still get the same error. I would appreciate your help. I am enclosing the output below: GROtesk MACabre and Sinister :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) genion (-: Option Filename Type Description -sion.tpr InputRun input file: tpr tpb tpa -tabletable.xvg Input, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file -o fws-b4em.gro Output Structure file: gro g96 pdb etc. -gion.log Output Log file -potpot.pdb Output, Opt. Protein data bank file -pfws.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int0 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -[no]random bool yes Use random placement of ions instead of based on potential. The rmin option should still work -seedint1993Seed for random number generator -scale real 0.001 Scaling factor for the potential for -pot -concreal 0.15Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options. -[no]neutral bool yes This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. Reading file ion.tpr, VERSION 4.5.5 (single precision) Using a coulomb cut-off of 1 nm Will try to add 12 NA ions and 14 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 12666 elements Group 1 (Protein) has 495 elements Group 2 ( Protein-H) has 257 elements Group 3 (C-alpha) has35 elements Group 4 ( Backbone) has 105 elements Group 5 ( MainChain) has 141 elements Group 6 ( MainChain+Cb) has 171 elements Group 7 (MainChain+H) has 176 elements Group 8 ( SideChain) has 319 elements Group 9 (SideChain-H) has 116 elements Group10 (Prot-Masses) has 495 elements Group11 (non-Protein) has 12171 elements Group12 ( Water) has 12171 elements Group13 (SOL) has 12171 elements Group14 ( non-Water) has 495 elements Select a group: 13 bash: 13: command not found [9]+ Stopped genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g ion.log -- 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] Test Particle Insertion
Dear GMX Users, My name is Anh Phan, a PhD student at University of Oklahoma. I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs. In this method, I will insert this gas molecule at a random position in each configuration of the system. With Gromacs, I see I can use tpi (integrator = tpi). I know I have to add this gas molecule in the topology (topol.top) Also, it is indicated in the manual that insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. That is what I desire. The question I would like to ask is whether I have to add the specified coordinate of gas molecule in the .gro file at the beginning of running simulation. For example, in the initial.gro file . 26734SOL OW45744 21.969 6.237 2.921 26734SOLHW145745 21.969 6.253 3.019 26734SOLHW245746 21.886 6.188 2.895 26735SOL OW45747 15.155 7.211 2.853 26735SOLHW145748 15.220 7.265 2.801 26735SOLHW245749 15.204 7.151 2.916 26736SOL OW45750 24.606 4.896 3.053 26736SOLHW145751 24.594 4.972 2.989 26736SOLHW245752 24.532 4.896 3.120 26737INS X457521.0001.0001.000 ( Do I have to add this line in the initial.gro file) The command lines grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr -maxwarn 2 mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg I am looking forward to receiving your reply. Thank you for your help. Sincerely, Anh -- 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] Test Particle Insertion
As far as I know it should not be included. Make a tpr file new .top and input file and run the mdrun with -rerun option as described here. http://manual.gromacs.org/online/mdp_opt.html#run; Cheers, Rajesh On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T. anhp...@ou.edu wrote: Dear GMX Users, My name is Anh Phan, a PhD student at University of Oklahoma. I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs. In this method, I will insert this gas molecule at a random position in each configuration of the system. With Gromacs, I see I can use tpi (integrator = tpi). I know I have to add this gas molecule in the topology (topol.top) Also, it is indicated in the manual that insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. That is what I desire. The question I would like to ask is whether I have to add the specified coordinate of gas molecule in the .gro file at the beginning of running simulation. For example, in the initial.gro file . 26734SOL OW45744 21.969 6.237 2.921 26734SOLHW145745 21.969 6.253 3.019 26734SOLHW245746 21.886 6.188 2.895 26735SOL OW45747 15.155 7.211 2.853 26735SOLHW145748 15.220 7.265 2.801 26735SOLHW245749 15.204 7.151 2.916 26736SOL OW45750 24.606 4.896 3.053 26736SOLHW145751 24.594 4.972 2.989 26736SOLHW245752 24.532 4.896 3.120 26737INS X457521.0001.0001.000 ( Do I have to add this line in the initial.gro file) The command lines grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr -maxwarn 2 mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg I am looking forward to receiving your reply. Thank you for your help. Sincerely, Anh -- 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 -- Naga Rajesh Tummala, PhD Post-Doctoral Researcher, School of Chemistry and Biochemistry, Georgia Institute of Technology -- 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] Decouple
Hi , How do I solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for B. Gromacs display error, what is temperature for B. How do aI decouple part B thanks for help Hari -- 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] Error while using genion
On 6/20/13 1:57 PM, Raji Viswanathan wrote: I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin peptide. I was going through the steps in the tutorial but got stuck with the genion command. When I am prompted to select a group, I get the error that it is not found. I tried many different ways of specifying this but still get the same error. I would appreciate your help. I am enclosing the output below: GROtesk MACabre and Sinister :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) genion (-: Option Filename Type Description -sion.tpr InputRun input file: tpr tpb tpa -tabletable.xvg Input, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file -o fws-b4em.gro Output Structure file: gro g96 pdb etc. -gion.log Output Log file -potpot.pdb Output, Opt. Protein data bank file -pfws.top In/Out, Opt! Topology file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int0 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -[no]random bool yes Use random placement of ions instead of based on potential. The rmin option should still work -seedint1993Seed for random number generator -scale real 0.001 Scaling factor for the potential for -pot -concreal 0.15Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options. -[no]neutral bool yes This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. Reading file ion.tpr, VERSION 4.5.5 (single precision) Using a coulomb cut-off of 1 nm Will try to add 12 NA ions and 14 CL ions. Select a continuous group of solvent molecules Group 0 ( System) has 12666 elements Group 1 (Protein) has 495 elements Group 2 ( Protein-H) has 257 elements Group 3 (C-alpha) has35 elements Group 4 ( Backbone) has 105 elements Group 5 ( MainChain) has 141 elements Group 6 ( MainChain+Cb) has 171 elements Group 7 (MainChain+H) has 176 elements Group 8 ( SideChain) has 319 elements Group 9 (SideChain-H) has 116 elements Group10 (Prot-Masses) has 495 elements Group11 (non-Protein) has 12171 elements Group12 ( Water) has 12171 elements Group13 (SOL) has 12171 elements Group14 ( non-Water) has 495 elements Select a group: 13 bash: 13: command not found [9]+ Stopped genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g ion.log Your shell is interpreting your selection as a command rather than an input file stream. What OS are you running? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist
Re: [gmx-users] Decouple
On 6/20/13 5:01 PM, Hari Pandey wrote: Hi , How do I solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for B. Gromacs display error, what is temperature for B. How do aI decouple part B Per the manual: tau-t: [ps] time constant for coupling (one for each group in tc-grps), -1 means no temperature coupling -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Test Particle Insertion
Dear Anh, You need to construct a .tpr file for the mdrun -rerun with: - a .gro file with the ligand to be inserted at the end, which _must_ be geometrically centered at 0,0,0 ; - a matching .top file (which means with the ligand topology appropriately inserted) ; - a .mdp file with the specific parameters for the tpi algorithm . Since you happen to have a single particle to insert, that particle's coordinates should be 0,0,0 in the .gro file from grompp (your initial.gro). Best, João On Thu, Jun 20, 2013 at 8:08 PM, Phan, Anh T. anhp...@ou.edu wrote: Dear GMX Users, My name is Anh Phan, a PhD student at University of Oklahoma. I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs. In this method, I will insert this gas molecule at a random position in each configuration of the system. With Gromacs, I see I can use tpi (integrator = tpi). I know I have to add this gas molecule in the topology (topol.top) Also, it is indicated in the manual that insertions are performed nsteps times in each frame at random locations and with random orientiations of the molecule. That is what I desire. The question I would like to ask is whether I have to add the specified coordinate of gas molecule in the .gro file at the beginning of running simulation. For example, in the initial.gro file . 26734SOL OW45744 21.969 6.237 2.921 26734SOLHW145745 21.969 6.253 3.019 26734SOLHW245746 21.886 6.188 2.895 26735SOL OW45747 15.155 7.211 2.853 26735SOLHW145748 15.220 7.265 2.801 26735SOLHW245749 15.204 7.151 2.916 26736SOL OW45750 24.606 4.896 3.053 26736SOLHW145751 24.594 4.972 2.989 26736SOLHW245752 24.532 4.896 3.120 26737INS X457521.0001.0001.000 ( Do I have to add this line in the initial.gro file) The command lines grompp -f input.mdp -c initial.gro -p topol.top -n index.ndx -o tpi.tpr -maxwarn 2 mdrun -s tpi.tpr -rerun md.trr -x traj.xtc -c final.gro -e init3.ener -g init3.log -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg I am looking forward to receiving your reply. Thank you for your help. Sincerely, Anh -- 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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] Decouple
Please keep the discussion on the gmx-users mailing list; I am not a private tutor. Comments embedded below. On 6/20/13 8:35 PM, Hari Pandey wrote: Hi Justin, Thanks for last help. I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps, temperature of A and C should be constant (i.e reach up to steady state) and B may not be. for that My NVT.mdp is: ; simulation at 300K and 2 ps is on constraints =all-bonds integrator =md dt =0.001 ; ps nsteps =10 ; total 100 ps nstcomm =10 nstxout =1000 nstxtcout =0 nstvout =0 nstfout =0 nstenergy =100 nstlist =100 This value of nstlist is much too large. ns_type =grid rlist =0.5 coulombtype =pme rcoulomb=0.5 vdwtype =cut-off rvdw=0.5 Unless you are using some custom force field that requires 0.5-nm cutoffs, these values are incorrect. pme_order =4 ewald_rtol =1e-5 optimize_fft=yes DispCorr=no ;Brendsen tempereture coupling is on Tcoupl = nose-hoover Nose-Hoover is a poor choice for initial equilibration, especially when generating velocities. tau_t =0.001 -1 0.001 Setting tau_t = dt is a bad idea and grompp should have warned you about this. tc-grps =A B C ref_t =750 300 350 ;pressure coupling is on Pcoupl =no Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =yes gen_temp=750 300 350 gen_seed=-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on Tcoupl =nose-hoover tau_t =1 -1 1 tc-grps =NCALPHA MIDDLE NCNN ref_t =750 300 350 ;pressure coupling is on Pcoupl =Berendsen Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =1 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no gen_temp=750 300 350 gen_seed=-1 MY NVE.mdp is: ( here all output control parameters also) tc-grps = A B C ref_t =750 300 300 energygrps = NCALPHA MIDDLE NCNN tcoupl = nose-hoover tau-t = 1 -1 1 If you're using thermostats, you're not simulating in an NVE ensemble. ;pressure coupling is on Pcoupl =no ;Pcoupltype =isotropic ;tau_p =0.5 ;compressibility =1e-5 ;ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no ; gen_temp=750 300 350 ; gen_seed=-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg But the system do not get equilibrated and A, B has not steady state temperature after time even 100 ps. please help me, where I did wrong You have numerous issues, listed above. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] (no subject)
Hi all gromacs users I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps, temperature of A and C should be constant (i.e reach up to steady state) and B may not be. for that My NVT.mdp is: ; simulation at 300K and 2 ps is on constraints =all-bonds integrator =md dt =0.001 ; ps nsteps =10 ; total 100 ps nstcomm =10 nstxout =1000 nstxtcout =0 nstvout =0 nstfout =0 nstenergy =100 nstlist =100 ns_type =grid rlist =0.5 coulombtype =pme rcoulomb =0.5 vdwtype =cut-off rvdw =0.5 pme_order =4 ewald_rtol =1e-5 optimize_fft =yes DispCorr =no ;Brendsen tempereture coupling is on Tcoupl = nose-hoover tau_t =0.001 -1 0.001 tc-grps =A B C ref_t =750 300 350 ;pressure coupling is on Pcoupl =no Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =yes gen_temp =750 300 350 gen_seed =-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on Tcoupl =nose-hoover tau_t =1 -1 1 tc-grps =NCALPHA MIDDLE NCNN ref_t =750 300 350 ;pressure coupling is on Pcoupl =Berendsen Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =1 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no gen_temp =750 300 350 gen_seed =-1 MY NVE.mdp is: ( here all output control parameters also) tc-grps = A B C ref_t =750 300 300 energygrps = NCALPHA MIDDLE NCNN tcoupl = nose-hoover tau-t = 1 -1 1 ;pressure coupling is on Pcoupl =no ;Pcoupltype =isotropic ;tau_p =0.5 ;compressibility =1e-5 ;ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no ; gen_temp =750 300 350 ; gen_seed =-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg But the system do not get equilibrated and A, B has not steady state temperature after time even 100 ps. please help me, where I did wrong Thanks for your help -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] (no subject)
On 6/20/13 11:11 PM, Hari Pandey wrote: Hi all gromacs users I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps, temperature of A and C should be constant (i.e reach up to steady state) and B may not be. for that My NVT.mdp is: ; simulation at 300K and 2 ps is on constraints =all-bonds integrator =md dt =0.001 ; ps nsteps =10 ; total 100 ps nstcomm =10 nstxout =1000 nstxtcout =0 nstvout =0 nstfout =0 nstenergy =100 nstlist =100 ns_type =grid rlist =0.5 coulombtype =pme rcoulomb=0.5 vdwtype =cut-off rvdw=0.5 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes DispCorr=no ;Brendsen tempereture coupling is on Tcoupl = nose-hoover tau_t =0.001 -1 0.001 tc-grps =A B C ref_t =750 300 350 ;pressure coupling is on Pcoupl =no Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =yes gen_temp=750 300 350 gen_seed=-1 MY NPT.mdp is: ( here all output control parameters also) ;Brendsen tempereture coupling is on Tcoupl =nose-hoover tau_t =1 -1 1 tc-grps =NCALPHA MIDDLE NCNN ref_t =750 300 350 ;pressure coupling is on Pcoupl =Berendsen Pcoupltype =isotropic tau_p =0.5 compressibility =1e-5 ref_p =1 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no gen_temp=750 300 350 gen_seed=-1 MY NVE.mdp is: ( here all output control parameters also) tc-grps = A B C ref_t =750 300 300 energygrps = NCALPHA MIDDLE NCNN tcoupl = nose-hoover tau-t = 1 -1 1 ;pressure coupling is on Pcoupl =no ;Pcoupltype =isotropic ;tau_p =0.5 ;compressibility =1e-5 ;ref_p =0.5 ;generate velocities at 300 k i.e. at room tempereture gen_vel =no ; gen_temp=750 300 350 ; gen_seed=-1 What I did is: pdb2gmx - argnew.pdb -o fws.pdb -p fws.top; editconf -f fws.pdb -bt dodecahedron -o fws.pdb -d 1.0; grompp-f em.mdp -c fws.pdb -p fws.top -n index.ndx -o em.tpr -maxwarn 5; mdrun -deffnm em -v; grompp -f nvt.mdp -c em.gro -p fws.top -n index.ndx -o nvt.tpr -maxwarn 5; mdrun -deffnm nvt -v; grompp -f npt.mdp -c nvt.gro -p fws.top -n index.ndx -o npt.tpr -maxwarn 5; mdrun -deffnm npt -v grompp -f nve.mdp -c npt.gro -p fws.top -n index.ndx -o nve.tpr -maxwarn 5; mdrun -deffnm nve -v; g_energy -f nve.edr -s nve.tpr -o F1.xvg But the system do not get equilibrated and A, B has not steady state temperature after time even 100 ps. please help me, where I did wrong See my previous reply: http://lists.gromacs.org/pipermail/gmx-users/2013-June/082392.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
