[gmx-users] A confusion about domain decomposition

Amir Marcovitz amarcovitz at gmail.com
Sun Jun 20 13:34:19 CEST 2010

Hi all,

I'm trying to run a parallel Job for a system of dummy atoms that arranged
as 2 surface (each is 6X6 atom surface- with bonds that i defined between
the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with
salt, minimized and equlibrated fine.

however, when trying to execute parallel Job i get the following domain
decomposition error:
Program mdrun, VERSION 4.0.7
Source code file: domdec.c, line: 5888*
*Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 3.37646 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
i read the relevant paragraphs on the manual regarding domain decomposition
, but remained confused.
my question is How do you think i should solve it, and what are the thumb
rules for the use of the -rdd and -dds flags? (i think that i did not quit
understood from the manual how are the 2 flags relate to the parameters of
my system)

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100620/7c42a515/attachment.html>

More information about the gromacs.org_gmx-users mailing list