[gmx-users] problem in mdrun

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 28 17:07:58 CET 2012

kumud agarwal wrote:
> Hi
> During mdrun I got the following
> Program mdrun, VERSION 4.5.5
> Source code file: domdec.c, line: 6005
> Fatal error:
> Domain decomposition does not support simple neighbor searching, use 
> grid searching or use particle decomposition
> What is the problem here?

You've set "nstype = simple" in the .mdp file, and as the error says, you can't 
do that when invoking the DD algorithm.  If you need simple neighbor searching, 
use the (slower) particle decomposition (mdrun -pd), otherwise set "nstype = 
grid" to be compatible with DD.



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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