Thank you for your answer David.
Actually no my run did not finish normally the first time (it has been
stopped after 7 days because of the time limitation on the cluster it was
running on). So I started it again (I ran the same command and added the
option "-append yes") and this time the calculation finished normally, but
when I look at the md.log file it looks like the second run did not add
anything since it stops in the middle of a line (in the middle of a word
actually!)...
Maybe I just did not use the correct command to start this calculation
again, that would explain the end of the md.log and the "no-generation" of
the final structure.
What option(s) should I use with trjconv? Actually I already tried to use
this command, but it generated a 200 MB pdb file which was not my aim!
Jerome
--------------------------------------------------
From: "David van der Spoel" <[email protected]>
Sent: Tuesday, June 23, 2009 5:35 PM
To: "Jérôme Baffreau" <[email protected]>; "Discussion list for
GROMACS users" <[email protected]>
Subject: Re: [gmx-users] mdrun -c option "did not work"
Jérôme Baffreau wrote:
Hello everyone,
this is my very first post on GROMACS mailing list, so please apologize
if my question seems very simple.
Here is my problem... I ran a calculation using GROMACS 4.0.3 and this
command line:
mpirun -np 32 mdrun -s prot_md.tpr -c prot_md.gro -g md.log -e md.edr -o
prot_md.trr -deffnm md -nov
I think everything went well, but the prot_md.gro (final structure) file
has NOT been generated so I'm wondering if there's a way to generate it
from tpr, trr ou xct output files?
Yes, use trjconv.
Did your run finish normally otherwise? Check your md.log, it should have
performance statistics at the bottom of the file. You should also consider
upgrading to 4.0.5, in particular if the problem does not go away...
Thanks a lot,
Jerome B.
**********************************************
Jerome Baffreau, PhD
Stagiaire postdoctoral - Postdoctoral fellow
Departement de Biochimie - Biochemistry Department
Universite de Montreal
Montreal, QC
Canada
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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