[gmx-users] Mdrun box nan error

[Nathalie R. Basdevant]

David,
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...
Thank you
-- 
Nathalie Basdevant 

> -----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.
> ______________________________________________________________
> __________
> 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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