[gmx-users] domain decomposition error

[nikhil damle]

Hi,

I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not upto the specified cut-off limits.

Now when i am running production MD on multiple processors it gives following error. 

There were 96 inconsistent shifts. Check your topology
There were 96 inconsistent shifts. Check your topology
There were 4 inconsistent shifts. Check your topology
There were 4 inconsistent shifts. Check your topology
There were 6 inconsistent shifts. Check your topology
There were 6 inconsistent shifts. Check your topology

-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: domdec.c, line: 5873

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 1.025 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition

Why in the very first place, it is considering box and cell size for a vacuum MD when no related parameters are input ? This error is not given if i run on single processor. What could be the possible reason ? I have checked my topology and it is proper. How should i proceed. Fast reply will be appreciated.

Regards,
Nikhil



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