[gmx-users] domain decomposition errors
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 26 21:10:50 CET 2009
pedro alberto valiente flores wrote:
> Hi gromacs users:
> I' am trying to run a MD simulation of PlmII+Inhibitor system in cubic
> box (59002 atoms) with gromacs 4.0.5 on 8 processors, but my simulation
> crashes. In attach are files.tgz which contains the log
> (PlmII+PepstatinA_free.log) and error files (BSA.err.%j). However, I can
> run the simulation without problems in 2 processors (PlmII
> +PepstatinA_equilibration.log). Can I fix this error setting domain
> decomposition parameters of mdrun. I going to appreciate any
Have you played with the -dd flag?
E.g. -dd 2 2 2?
Please don't attach files but describe your problem concise but clear.
David van der Spoel, PhD, Professor of Biology
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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