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On 29/12/2010 6:33 PM, delara aghaie wrote:
<blockquote cite="mid:984797.79774.qm@web130110.mail.mud.yahoo.com"
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<div>Dear Justin</div>
<div>many thanks for your email and your comments.</div>
<div> </div>
<div>I found aminoacids.dat in the following pat</div>
<div><br>
<strong>/apps/gromacs/4.0.5/share/gromacs/top</strong></div>
<div>I connect to imerial college via vpn. they have
installed several gromacs versions.</div>
<div>I only write</div>
<div><strong>module load mpi</strong> and then</div>
<div><strong>module load gromacs</strong></div>
<div>and then the gromacs commands become active.</div>
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<br>
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.<br>
<br>
<blockquote cite="mid:984797.79774.qm@web130110.mail.mud.yahoo.com"
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<div>-------</div>
<div>the g_msd_mpi command worked and now I have msd.xvg
file and I plotted it using gnuplot with this command:</div>
<div>gnuplot "msd.xvg" u 1:2 w l</div>
<div>now pls let me know how can I save this plot? I have
written about that but I am confused.</div>
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<br>
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.<br>
<br>
Mark<br>
<br>
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<div> </div>
<div>Thanks for your time</div>
<div>Best regards</div>
<div>Delara</div>
<div><strong><br>
</strong><br>
<br>
<br>
--- On <b>Wed, 12/22/10, Justin A. Lemkul <i><a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a></i></b>
wrote:<br>
</div>
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border-left: 2px solid rgb(16, 16, 255);"><br>
From: Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
Subject: Re: [gmx-users] location of aminoacids.dat<br>
To: "Gromacs Users' List" <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Wednesday, December 22, 2010, 5:00 PM<br>
<br>
<div class="plainMail"><br>
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.<br>
<br>
See comments below.<br>
<br>
delara aghaie wrote:<br>
> Dear Justin<br>
> 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.<br>
> every command wich I want to use for ex:
g_msd_mpi or make_ndx_mpi<br>
> I get this fatal error:<br>
> *Fatal error:<br>
> Library file aminoacids.dat not found in current
dir nor in default directories.<br>
> (You can set the directories to search with the
GMXLIB path variable)*<br>
> It is strange because my system is DPPC
monolayer and does not have nothing to do with
proteins !!!<br>
> <br>
<br>
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.<br>
<br>
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)?<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
> your help would be greatly appreciated/<br>
> *Best regards*<br>
> *Delara*<br>
> *<br>
> *<br>
> <br>
> --- On *Wed, 12/22/10, Justin A. Lemkul /<<a
moz-do-not-send="true"
href="http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu"
ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>/*
wrote:<br>
> <br>
> <br>
> From: Justin A. Lemkul <<a
moz-do-not-send="true"
href="http://us.mc1301.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu"
ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
> Subject: Re: [gmx-users] buckingham
potentials<br>
> To: "Gromacs Users' List" <<a
moz-do-not-send="true"
href="http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Date: Wednesday, December 22, 2010, 8:04 AM<br>
> <br>
> <br>
> <br>
> sreelakshmi ramesh wrote:<br>
> > Dear justin,<br>
> > I have no clues
about rewriting a force field<br>
> so i think i can t proceed with this anymore.<br>
> ><br>
> > thanks a lot for your patient reply.<br>
> <br>
> For the future, you will waste a lot less
time (your own, and that<br>
> of those who are trying to help you) if you
provide a clear, concise<br>
> statement of what you hope to accomplish in
your very first post. You began this adventure
seeking help on how to (generically) use<br>
> Buckingham potentials. What you should have
asked was how to use<br>
> Buckingham potentials within the Gromos force
field. Then, instead<br>
> of swapping ten emails, you would have
received your answer in one.<br>
> <br>
> -Justin<br>
> <br>
> -- ========================================<br>
> <br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]vt.edu | (540) 231-9080<br>
> <a moz-do-not-send="true"
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> <br>
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<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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