[gmx-users] Mdrun box nan error
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
what pressure coupling constants do you use? try to use at least 1 ps.
> I hope you can help me with this.
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
More information about the gromacs.org_gmx-users