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

[David van der Spoel]

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
> 
> 
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-- 
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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