[gmx-users] Mdrun box nan error
Nathalie R. Basdevant
nrb2001 at med.cornell.edu
Fri May 7 20:03:00 CEST 2004
So I have tried your suggestion to launch the same tpr twice. The error (box
nan) is NOT reproducible. That's the only error I get, the 'atoms' thing
referred to the accompanying LINCS error.
So that leaves compiler and hardware then. I'll investigate...
> -----Original Message-----
> From: gmx-users-admin at gromacs.org
> [mailto:gmx-users-admin at gromacs.org] On Behalf Of David
> Sent: Friday, May 07, 2004 3:45 PM
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Mdrun box nan error
> 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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