[gmx-users] node decomposition' problem
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
More information about the gromacs.org_gmx-users