[gmx-users] Mdrun box nan error

David spoel at xray.bmc.uu.se
Fri May 7 19:44:01 CEST 2004

On Fri, 2004-05-07 at 19:04, Nathalie R. Basdevant wrote:
> David-
> Thanks fir your reply. I am using 1ps for pressure coupling should I use a
> larger constant .e.g 5-10ps?
1 ps should work for Berendsen coupling. 
I don't really know what could cause this. Have you tried to run the
same tpr file twice, to see if the problem is reproducible? If it is
reproducible it might be a gromacs problem, if not then it could be a
hardware problem (e.g. flaky memory chips). Compiler problems tend to be
reproducible as well (but not always).

Is it always the same problem? You write about box nans but also about
"other atoms"?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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