[gmx-users] no domain decomposition

Chetan Mahajan chetanvm10 at gmail.com
Wed Jun 25 12:25:56 CEST 2014


I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
my system. I am getting following error:

Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 1.81239 nm
Change the number of nodes or mdrun option -rdd

 Following is an excerpt of log file:

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163
  multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163
Minimum cell size due to bonded interactions: 1.812 nm
Using 0 separate PME nodes, as there are too few total
 nodes for efficient splitting
Optimizing the DD grid for 16 cells with a minimum initial size of 1.812 nm
The maximum allowed number of cells is: X 1 Y 1 Z 6

*I tried decreasing number of nodes from 48 to 16, but this error appears
always. 2161 and 2163 atoms mentioned in log file excerpt above are formate
atoms each of which is in a different charge group. I can't put them in
same charge group, since they are different energy groups as we can see. *

*Any suggestions how to interpret log file excerpt or what more can be


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