[gmx-users] How to avoid the error: "Shake block crossing node boundaries"

Leontyev Igor ileontyev at ucdavis.edu
Wed Mar 25 08:59:05 CET 2009

I just switched from the version 3.3 to 4.0. It turned out that the 4.0 
version does not allow to run a parallel simulation of my protein in vacuum. 
The protein consists of 2 chains and 4 separated (no bonds with chains) 
co-factors. For vacuum simulation 'pbc=no' which makes to use particle 
decomposition option "-pd" of mdrun. In this case the automatic particle 
distribution over the nodes leads to the error:
"Fatal error:
Shake block crossing node boundaries
constraint between atoms (11191,11193)"

In the previous version 3.3 I used manual balancing with the "-load" option 
to avoid the problem. In the current version 4.0 I did not find anything 
similar for the particle decomposition. Is there a way to run parallel 
simulations of the protein in vacuum?

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