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

Igor Leontyev ileontyev at ucdavis.edu
Wed Mar 25 09:08:54 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.
> Mark

Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations. Only
PD options is available. But PD has no flexibility to manually redistribute
particles over the nodes. As written in the manual "With PD only whole
molecules can be assigned to a processor". Does it mean that there is no way
to start PD parallel simulations of whole protein? In other words, does it
means that there is no way to run parallel simulation of protein in vacuum?

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