[gmx-users] mdrun -rdd and -dds flag

manara r. (rm16g09) rm16g09 at soton.ac.uk
Thu Apr 11 12:17:54 CEST 2013

Dear gmx-users,

I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd or -dds flags (I believe), how do these value effect the simulation?

The box size is 11.5 x 11.5 x 45.

The polymer contains charged groups every repeating unit.

The error I'm getting is (note this is a test run on my home machine, not the cluster):
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 61.7923 nm
Change the number of nodes or mdrun option -rdd or -dds


Rich Manara
PhD Student
Southampton University

More information about the gromacs.org_gmx-users mailing list