[gmx-users] Reordering out.gro after mdrun_mpi

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 24 09:39:05 CEST 2002

On Tue, 2002-09-24 at 09:35, Christoph Freudenberger wrote:
> Hi there,
> After some testing I just finished my first mdrun_mpi of 'real
> system'. The .tpr was setup with this command:
> grompp -f equi_01 -c minimize -p emicl.top -o equi_01 -shuffle -sort \
>         -np 4
> the mdrun_mpi then produces an out.gro where the molecules are
> ordered in a way that does no longer match the topology.
> I suppose this is due to the -shuffle -sort options in the command
> above.
> The doc for grompp says this would not matter for setting up the
> next simulations, but when i tried it, mdrun crashed immediately,
> complaining that 1,4-interactions would be too large and that
> certain water molecules could not be settled.
> So is it nesscary to reorder the .gro file before processing the
> next run?
Yes, grompp generates a file called deshuf,ndx which you can use with
the editconf program. 
For a mere continuation run you could also use tpbconv

> Is there a tool to do so?
> best regards
> -- 
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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