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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 25 08:16:56 CET 2009

Leontyev Igor wrote:
> 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?

I'd suggest updating to 4.0.4 for the copious bug fixes, one of which 
might solve your problem. I can't think of a good reason offhand why PD 
or DD should be necessary for non-PBC simulations in vacuo - try both. 
If you've still got your problem, let us know.


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