[gmx-users] Mdrun box nan error

David spoel at xray.bmc.uu.se
Fri May 7 18:50:02 CEST 2004

On Fri, 2004-05-07 at 18:21, Nathalie R. Basdevant wrote:
> Dear users,
> I am running Gromacs 3.2.1 on an itanium 2 with Linux compiled with Intel
> compilers. The system that I am simulating consists of a protein in water
> box (OPLS+tip4p). I am simulating under NPT (both Berendsen baths) 300K and
> 1atm. I am running in parallel (4 processors).
> Every once in a while the simulation crashes with the following error
> messages (see below). However when I restart the simulation (tpbconv -f .trr
> -e .edr ) the simulation passes through the step that had given the error
> before without any problem, but eventually stops at a later time (varying
> between tens to hundreds of ps) with a similar error, but on a different
> atom.

what pressure coupling constants do you use? try to use at least 1 ps.
> I hope you can help me with this.
> Thanks
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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