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 <[email protected]>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 > Master's student > > Forschungszentrum Juelich GmbH > 52425 Juelich | Germany > > Building 5.8v, Room 3010 > Phone: 02461-61-9532 > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
