[gmx-users] location of aminoacids.dat

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 29 09:21:43 CET 2010 

On 29/12/2010 6:33 PM, delara aghaie wrote:
> Dear Justin
> many thanks for your email and your comments.
> I found aminoacids.dat in the following pat
>
> */apps/gromacs/4.0.5/share/gromacs/top*
> I connect to imerial college via vpn. they have installed several 
> gromacs versions.
> I only write
> *module load mpi* and then
> *module load gromacs*
> and then the gromacs commands become active.
>

These module files should be setting your paths correctly. You should 
also be able to choose different GROMACS versions if such are installed. 
Please consult the documentation for how the site uses modules, or ask 
the sysadmins.

> -------
> the g_msd_mpi command worked and now I have msd.xvg file and I plotted 
> it using gnuplot with this command:
> gnuplot "msd.xvg" u 1:2 w l
> now pls let me know how can I save this plot? I have written about 
> that but I am confused.
>

Note that this is a gnuplot question, not a GROMACS question. There are 
various ways to "save" a gnuplot plot, and the best approach varies with 
what you want to do next. Please have a look at some gnuplot tutorial or 
documentation material for information here.

Mark

> Thanks for your time
> Best regards
> Delara
> *
> *
>
>
> --- On *Wed, 12/22/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] location of aminoacids.dat
>     To: "Gromacs Users' List" <gmx-users at gromacs.org>
>     Date: Wednesday, December 22, 2010, 5:00 PM
>
>
>     First, please start a new thread if you are asking a new
>     question.  Hijacking an existing thread confuses the archive and
>     will likely get your question ignored by anyone not interested in
>     reading about Buckingham potentials.  I have changed the subject
>     line appropriately.
>
>     See comments below.
>
>     delara aghaie wrote:
>     > Dear Justin
>     > I hope all is well with you. I have faced a problem. I connect
>     to imperial college london from my conunty to do the simulations.
>     Today I faced an strange problem.
>     > every command wich I want to use for ex: g_msd_mpi or make_ndx_mpi
>     >  I get this fatal error:
>     > *Fatal error:
>     > Library file aminoacids.dat not found in current dir nor in
>     default directories.
>     > (You can set the directories to search with the GMXLIB path
>     variable)*
>     >  It is strange because my system is DPPC monolayer and does not
>     have nothing to do with proteins !!!
>     >
>
>     That doesn't matter.  Certain input files are required by certain
>     Gromacs tools.  In all likelihood, you simply haven't set up your
>     environment properly, but I'm not sure how that's possible.
>
>     What version of Gromacs are you using?  How was it installed?  Are
>     the Gromacs executables included in your $PATH, or do you have to
>     find them manually in order to use them (i.e., do you run
>     /path/to/gromacs/bin/grompp or just grompp)?
>
>     Also note that there is no value in compiling the entire Gromacs
>     suite with an MPI compiler.  I've seen that cause weird behavior
>     before, but I doubt it's necessarily related here.  The only
>     MPI-aware program is mdrun.
>
>     -Justin
>
>     > your help would be greatly appreciated/
>     > *Best regards*
>     > *Delara*
>     > *
>     > *
>     >
>     > --- On *Wed, 12/22/10, Justin A. Lemkul /<jalemkul at vt.edu
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>     wrote:
>     >
>     >
>     >     From: Justin A. Lemkul <jalemkul at vt.edu
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>     >     Subject: Re: [gmx-users] buckingham potentials
>     >     To: "Gromacs Users' List" <gmx-users at gromacs.org
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>     >     Date: Wednesday, December 22, 2010, 8:04 AM
>     >
>     >
>     >
>     >     sreelakshmi ramesh wrote:
>     > > Dear justin,
>     > >                    I have no clues  about rewriting a force field
>     >     so i think i can t proceed with this anymore.
>     > >
>     > > thanks a lot for your patient reply.
>     >
>     >     For the future, you will waste a lot less time (your own,
>     and that
>     >     of those who are trying to help you) if you provide a clear,
>     concise
>     >     statement of what you hope to accomplish in your very first
>     post.     You began this adventure seeking help on how to
>     (generically) use
>     >     Buckingham potentials.  What you should have asked was how
>     to use
>     >     Buckingham potentials within the Gromos force field.  Then,
>     instead
>     >     of swapping ten emails, you would have received your answer
>     in one.
>     >
>     >     -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 list gmx-users at gromacs.org
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>     >
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=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-request at gromacs.org
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
>     >
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     >     Can't post? Read 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 list gmx-users at gromacs.org
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=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-request at gromacs.org
>     <http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101229/00962d57/attachment.html>

More information about the gromacs.org_gmx-users mailing list