I am using Red Hat Enterprise Linux 5.5 Raji
On 6/20/13 5:16 PM, "[email protected]" <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: System expansion (Dr. Vitaly Chaban) > 2. Error while using genion (Raji Viswanathan) > 3. Test Particle Insertion (Phan, Anh T.) > 4. Re: Test Particle Insertion (Naga Rajesh Tummala) > 5. Decouple (Hari Pandey) > 6. Re: Error while using genion (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Jun 2013 18:12:16 +0200 > From: "Dr. Vitaly Chaban" <[email protected]> > Subject: Re: [gmx-users] System expansion > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAPXdD+bjLtfKCyL5+pXm8=aoU0DESsHVgS=7vR0Kbz=xf89...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Oliver - > > Hmmmmmm. 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 > <[email protected]>wrote: > >> 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<https://www.dropbox.c >> om/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<https://www.dropbox.c >> om/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 list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.or >> g/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Sea >> rch>before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support >> /Mailing_Lists> >> > > > ------------------------------ > > Message: 2 > Date: Thu, 20 Jun 2013 17:57:28 +0000 > From: Raji Viswanathan <[email protected]> > Subject: [gmx-users] Error while using genion > To: "[email protected]" <[email protected]> > Message-ID: > <b8c111f917e93f4ebb8ff5c751aa91ae431b7...@aewexcpm14.yuad.uds.yu.edu> > Content-Type: text/plain; charset="iso-8859-1" > > 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, P?r 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 > ------------------------------------------------------------ > -s ion.tpr Input Run input file: tpr tpb tpa > -table table.xvg Input, Opt. xvgr/xmgr file > -n index.ndx Input, Opt. Index file > -o fws-b4em.gro Output Structure file: gro g96 pdb etc. > -g ion.log Output Log file > -pot pot.pdb Output, Opt. Protein data bank file > -p fws.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 > -nice int 19 Set the nicelevel > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none > -np int 0 Number of positive ions > -pname string NA Name of the positive ion > -pq int 1 Charge of the positive ion > -nn int 0 Number of negative ions > -nname string CL Name of the negative ion > -nq int -1 Charge of the negative ion > -rmin real 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 > -seed int 1993 Seed for random number generator > -scale real 0.001 Scaling factor for the potential for -pot > -conc real 0.15 Specify 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) has 35 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 > Group 10 ( Prot-Masses) has 495 elements > Group 11 ( non-Protein) has 12171 elements > Group 12 ( Water) has 12171 elements > Group 13 ( SOL) has 12171 elements > Group 14 ( 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 > > > ------------------------------ > > Message: 3 > Date: Thu, 20 Jun 2013 19:08:43 +0000 > From: "Phan, Anh T." <[email protected]> > Subject: [gmx-users] Test Particle Insertion > To: "[email protected]" <[email protected]> > Message-ID: > <e58c71ee258e2a4499a7f691520757935368f...@it-osmium.sooner.net.ou.edu> > Content-Type: text/plain; charset="us-ascii" > > 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 > 26734SOL HW145745 21.969 6.253 3.019 > 26734SOL HW245746 21.886 6.188 2.895 > 26735SOL OW45747 15.155 7.211 2.853 > 26735SOL HW145748 15.220 7.265 2.801 > 26735SOL HW245749 15.204 7.151 2.916 > 26736SOL OW45750 24.606 4.896 3.053 > 26736SOL HW145751 24.594 4.972 2.989 > 26736SOL HW245752 24.532 4.896 3.120 > 26737INS X45752 1.000 1.000 1.000 ( 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 > > > ------------------------------ > > Message: 4 > Date: Thu, 20 Jun 2013 15:47:47 -0400 > From: Naga Rajesh Tummala <[email protected]> > Subject: Re: [gmx-users] Test Particle Insertion > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAAMxdzqbGweL6TV25Fze4PVj707GqoJcPXzyc_g6Vq0=m9l...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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. <[email protected]> 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 >> 26734SOL HW145745 21.969 6.253 3.019 >> 26734SOL HW245746 21.886 6.188 2.895 >> 26735SOL OW45747 15.155 7.211 2.853 >> 26735SOL HW145748 15.220 7.265 2.801 >> 26735SOL HW245749 15.204 7.151 2.916 >> 26736SOL OW45750 24.606 4.896 3.053 >> 26736SOL HW145751 24.594 4.972 2.989 >> 26736SOL HW245752 24.532 4.896 3.120 >> 26737INS X45752 1.000 1.000 1.000 ( 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 list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > Raji Viswanathan Professor of Chemistry Yeshiva College 2495 Amsterdam Avenue New York, NY 10033 Phone: 212-960-5443 Fax: 212-960-0035 -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
