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

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 25 09:17:28 CET 2009

Igor Leontyev wrote:
>> 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?
You can do it the way all the other programs do: only use constraints on 
bonds involving H, and reducing the timestep to 1 fs.

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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