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

Igor Leontyev ileontyev at ucdavis.edu
Wed Mar 25 09:50:41 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?

> 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.

I try to run MD with only constrained h-bonds (constraints = hbonds) which 
allow 2fs timestep. The timestep 1fs would be needed if there will be 
vibrating (unconstrained) h-bonds. But you suggest to use constraints or it 
was a misprint? 

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