[gmx-users] System expansion

Dr. Vitaly Chaban vvchaban at gmail.com
Thu Jun 20 18:12:16 CEST 2013

Hi Oliver -

Hmmmmmm. Did you try to start from (a little bit) different configurations
on the problematic machine? Or re-install gromacs there, perhaps?

Dr. Vitaly Chaban

On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
<o.rusche at fz-juelich.de>wrote:

> Dear Gromacs users,
> I experience a very strange problem.
> I have a well equilibrated system consisting of a protein, a ligand, ions
> and water. On most machines I run my simulations on, everything is just
> fine. Except for one compute cluster, where the system undergoes an extreme
> expansion when I use the md-vv integrator for an NPT-simulation. To give
> you an impression I uploaded a short video showing the first 100
> picoseconds of the run to my Dropbox:
> https://www.dropbox.com/s/**d1ef94bbns0hasr/explode.mpg<https://www.dropbox.com/s/d1ef94bbns0hasr/explode.mpg>
> The system expands so heavily that it consists mainly of vacuum.
> If I switch the integrator from md-vv to md, everything is fine again.
> The same simulation (same .mdp file, same starting positions and
> velocities from previous simulation) runs fine with the md-vv integrator on
> our GPU-cluster.
> The .mdp file can be downloaded here:
> https://www.dropbox.com/s/**k9it6eiqb259o59/explode.mdp<https://www.dropbox.com/s/k9it6eiqb259o59/explode.mdp>
> I have no idea if it is me who is doing something wrond, a bug in Gromacs,
> a problem with the cluster or something else.
> Any suggestions and ideas are appreciated.
> Regards,
> Oliver
> --
> Oliver Schillinger
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> Forschungszentrum Juelich GmbH
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