[gmx-users] Reordering out.gro after mdrun_mpi

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Tue Sep 24 09:35:36 CEST 2002

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
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?
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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