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 /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] buckingham potentials
To: "Gromacs Users' List" <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@gromacs.org
<http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-us...@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-requ...@gromacs.org
<http://us.mc1301.mail.yahoo.com/mc/compose?to=gmx-users-requ...@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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
