[gmx-users] node decomposition' problem

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 9 22:25:56 CEST 2012

On 7/9/12 4:23 PM, Thales Kronenberger wrote:
> 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

The minimum charge group size depends on a whole host of factors:


The large size you have obtained indicates there are likely problems with the 
.mdp file, topology, or both.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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