[gmx-users] location of aminoacids.dat

[delara aghaie]

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.
-------
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.
 
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>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] buckingham potentials
>     To: "Gromacs Users' List" <gmx-users at 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
> 
>     ========================================
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> 

-- ========================================

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

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