[gmx-users] Re: gmx-users Digest, Vol 110, Issue 114
Raji Viswanathan
raji at yu.edu
Mon Jun 24 16:51:23 CEST 2013
I am using Red Hat Enterprise Linux 5.5
Raji
On 6/20/13 5:16 PM, "gmx-users-request at gromacs.org"
<gmx-users-request at gromacs.org> wrote:
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> 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" <vvchaban at gmail.com>
> Subject: Re: [gmx-users] System expansion
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAPXdD+bjLtfKCyL5+pXm8=aoU0DESsHVgS=7vR0Kbz=xf8914w at 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
> <o.rusche at fz-juelich.de>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
>> --
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>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 20 Jun 2013 17:57:28 +0000
> From: Raji Viswanathan <raji at yu.edu>
> Subject: [gmx-users] Error while using genion
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <B8C111F917E93F4EBB8FF5C751AA91AE431B7979 at 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." <anhphan at ou.edu>
> Subject: [gmx-users] Test Particle Insertion
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <E58C71EE258E2A4499A7F691520757935368F71C at 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 <rajesh.tnr at gmail.com>
> Subject: Re: [gmx-users] Test Particle Insertion
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAAMxdzqbGweL6TV25Fze4PVj707GqoJcPXzyc_g6Vq0=M9Lq8A at 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. <anhphan at 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
>> 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 gmx-users at gromacs.org
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>> * 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-request at gromacs.org.
>> * 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
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