[gmx-users] gromacs query

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 20:22:14 CET 2011

Anushree Tripathi wrote:
> I m using gromacs 4.5.3 version and trying to simulate a protein in 
> liquid media but I found problem in eqilibration step especially when I 
> give following command:
> mdrun -deffnm nvt
> .After giving this command it is showing error,i.e.,
> There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.02659 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition.
> What should I do now.Please suggest me.I tried above options also.

I don't see any reason why a normal protein in water simulation should require 
such a huge minimum cell size.  See here for more:


Likely you have something wrong in the topology, .mdp file, or both.



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


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