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

[David van der Spoel]

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.
> 
> 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).


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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