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

Igor Leontyev ileontyev at ucdavis.edu
Wed Mar 25 11:41:01 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?
> This is subject to discussion, see e.g. gromacs manual. Actually, with all
> bonds constrained 2 fs is already a large time step, and with only bonds
> containing H constrained 1 fs is also quite large. A further discussion
> can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p.
> 116).

Thank you for the reference. The subject is what I would like to know in
more details. Regarding the problem that "Shake block crossing node
boundaries", the "-load" option implemented in gromacs-3.3.3 seems to remain
the most computationally efficient due to the larger, at least technically,
2fs timestep.

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