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
[email protected] [email protected] http://xray.bmc.uu.se/~spoel
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