[gmx-users] node decomposition' problem

Thales Kronenberger kronenberger7 at gmail.com
Mon Jul 9 22:23:09 CEST 2012

I'm trying to run a kinase (what means that I had ATP - large charged
group) energy minimization and then MD.

But when I put my protein together with its ligands I gotcha the
follow error message:

"There is no domain decomposition for 6 nodes that is compatible with
the given box and a minimum cell size of 6.47943 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition"

I read about in gromacs forums and I can force the thing's running
with the option nt 1 (one node...).

My problem is that I still want to run in parallel. Is it still that
possible for my system or I'm doomed to the 1 core simulation

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