[gmx-users] PBC "no domain decomposition" error

jwillcox at andrew.cmu.edu jwillcox at andrew.cmu.edu
Wed May 13 23:14:53 CEST 2015

Never mind my previous message.  When I included periodicmolecule = yes in
the mdp file, I believe that took care of the problem.





I ran into an issue when simulating graphene sheets with periodic boundary
conditions.  It said:

There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 4.685 nm

I figured that was due to the apparent bond length of the carbons
connected across the box, so I set -rdd to be 0.2 nm and now the
simulation seems to be running fine.

Is the -rdd command ignoring the bonds completely for the simulation, or
still using bonds across the box edges once PBC is implemented?

Thank you!


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