[gmx-users] mdrun creates pdb files!

T.A.Wassenaar at chem.rug.nl T.A.Wassenaar at chem.rug.nl
Tue Feb 3 12:00:02 CET 2004


Hi Madhuri,

The step*.pdb files indicate that your simulation crashed, is about to
crash, or should actually have crashed already. They are generated when
gromacs runs in to unrecoverable failures. It can mean several things. If
it occured just after you started the simulation there is probably
something seriously wrong in your input configuration. If you've been able
to simulate for quite a while already before the error occurs, it can be a
number of things, some more severe than others, but for that the
information you supply is too little to give any comment.

Hope it helps, cheers,

Tsjerk


 On Mon, 2 Feb 2004, Madhuri Agashe wrote:

> Hi,
> I am having a weird problem with mdrun_mpi.
> My command was:
>
> mdrun_mpi -s 3.tpr -o 3.trr -c 7.gro -e mdo1.edr
>
> But instead of creating a 7.gro as an output file, the program generated a
> .pdb file output for every step!!!
>
> I have never seen such behaviour with mdrun before.
>
> Any insights??
>
> Madhuri Agashe
>
>
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