[gmx-users] mdrun creates pdb files!

[Madhuri Agashe]

Yes, that does help.

But I cannot figure out what the problem might be. Here are some more inputs
on my system: 
It consists of an methyl terminated SAM surface with a protein fragment
adsorbing to it. The main aim of the simulation is to study the adsorption
behavior.
After solvating the system, I ran the genion command to replace some solvent
atoms by charged NA/CL ions.
Then an mdrun was run for energy minimization. Now this did say at the end
of the run that the system did not converge in 40 steps. Could that be the
problem with the mdrun failure later?

The generation of pdb files occurred immediately after starting the
simulation. How can I check for the correctness of the input configuration?

I really appreciate your help!!
Thanks,
madhuri


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] On
Behalf Of T.A.Wassenaar at chem.rug.nl
Sent: Monday, February 02, 2004 10:28 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdrun creates pdb files!


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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