[gmx-users] domain decomposition error

Moeed lecielll at googlemail.com
Thu Feb 17 17:17:05 CET 2011

Hello Justin,

I am running in parallel but this error comes up with 8, 7, 6, 5, 4 and even
3 number of processors. I read about domain decomposition on the website and
tried less number of processors, as just mentioned. My understanting after
reading about the error is that parallel simulation is not working with a
small system as mine! but there are 11000 atoms in there and I am doing FE
stuff... I dont see why this is considered as small simulation!
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 5.70044 nm
Change the number of nodes or mdrun option -rdd or -dds
Also I checked the manual for  the options below but I have no clue what
value to set for my system.

-rdd         real   0       The maximum distance for bonded interactions
                            DD (nm), 0 is determine from initial coordinates

-dds         real   0.8     Minimum allowed dlb scaling of the DD cell size


BTW: About mdp setting for electrostatics, I have set zero charges to all
atoms so there is no electrostatics term ( I have only C and H). Thats why I
commented out ;coulombtype         =  PME
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