[gmx-users] Domain decomposition configuration

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 9 21:39:18 CET 2011

Denny Frost wrote:
> I am trying to start a run using domain decomposition on a 5x5x10 nm box 
> with about 26,000 atoms in it.  I've tried running 8-16 pp nodes, but 
> gromacs always throws an error saying that there is no domain 
> decomposition compatible with this box and a minimum cell size of 6.728 
> nm.  I've tried many values for -dds and a few dd vectors, but with no 
> luck.  Does anyone know to get domain decomposition working on a 
> rectangular system like this?

Not without significantly more information.  Please post:

1. Your Gromacs version
2. Any DD-related information that is printed to either the log file or stdout
3. Your .mdp file



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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