[gmx-users] mdrun -c option "did not work"

Jérôme Baffreau jerome.baffreau at umontreal.ca
Wed Jun 24 15:45:37 CEST 2009

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 

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!


From: "David van der Spoel" <spoel at xray.bmc.uu.se>
Sent: Tuesday, June 23, 2009 5:35 PM
To: "Jérôme Baffreau" <jerome.baffreau at umontreal.ca>; "Discussion list for 
GROMACS users" <gmx-users at gromacs.org>
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
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 

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