[gmx-users] domain decomposition errors

[David van der Spoel]

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
> suggestions,
>   
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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++