[gmx-users] domain decomposition

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sun Apr 3 17:51:27 CEST 2011

Dear All

I have a file which contains afew residues (noncontinuous),
When I use mdrun on a computer(4 cpu) I am facing with the following Error:

Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 3.28697 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition

it is relating to domain decomposition,
Besides I checked either restraining residues and not restraining.But it
dosn't differed

I changed the number of nodes to 1 but it didn't work!
mpirun   -np  1  mdrun   -v   -deffnm  EM

Besides I looked in the log file and the important part of it was:

Initializing Domain Decomposition on 4 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: 2.988 nm, LJ-14, atoms 922 943
  multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943
Minimum cell size due to bonded interactions: 3.287 nm
Using 0 separate PME nodes
Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm
The maximum allowed number of cells is: X 1 Y 1 Z 1

please let me know how can I solve this problem.
Thanks in advance
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