[gmx-developers] Failing particle decomposition in gmx4.0.4

[David van der Spoel]

Per Larsson wrote:
> Hi!
> 
> I believe that with particle decomposition, you cannot have constraints 
> between the nodes (only implemented with domain decomp).
> 
I'm afraid Per is right. For some reason I seem to recollect that Berk 
implemented P-Lincs with PD. Then I tested it with a small protein, 
however pdb2gmx was kind enough to put the crystal waters in my topology 
automatically, such that I didn't notice them. I thus had a protein with 
water, which is split automatically over processors by putting the 
protein on one node and dividing the water over the other nodes.


> One trick around this (if you still want pd) would be to increase the 
> mass of the hydrogens somewhat, and use constraints=h-bonds, which gives 
> you local constraints only. One could of course argue whether this is 
> 100% accurate :-)
> 
Or, plan B would be to put the protein in a big box with DD.


> Cheers
> /Per
> 
> 
> 
> 6 maj 2009 kl. 20.46 skrev Erik Marklund:
> 
>> Erik Marklund skrev:
>>> Hi,
>>>
>>> I need to run a series of simulations using gromacs 4 with particle 
>>> decomposition. I constrain all bonds with LINCS and submit my job to 
>>> the cluster. Both the log-file and my mdp-file show that LINCS 
>>> constraints are indeed what is to be used, but mdrun nevertheless 
>>> quits with a fatal error and the following message:
>>>
>>> -------------------------------------------------------
>>> Program mdrun_mpi_d, VERSION 4.0.4
>>> Source code file: splitter.c, line: 130
>>>
>>> Fatal error:
>>> Shake block crossing node boundaries
>>> constraint between atoms (1467,1474)
>>> -------------------------------------------------------
>>>
>>> Shake block? Why on earth does Shake have to do with anything?! More 
>>> importantly, how can I fix this?
>>>
>>> Here's an exerpt from the log-file:
>>>  ...
>>>  nbfgscorr            = 10
>>>  ConstAlg             = Lincs
>>>  shake_tol            = 0.0001
>>>  lincs_order          = 2
>>>  lincs_warnangle      = 30
>>>  lincs_iter           = 8
>>>  bd_fric              = 0
>>>  ...
>>>
>>> I use gromacs 4.0.4 i double precision compiled from source that was 
>>> downloaded from gromacs.org, in other words no funky developer-version.
>>>
>> And here's more from the log-file:
>> ...
>> Initializing LINear Constraint Solver
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
>> LINCS: A Linear Constraint Solver for molecular simulations
>> J. Comp. Chem. 18 (1997) pp. 1463-1472
>> -------- -------- --- Thank You --- -------- --------
>>
>> The number of constraints is 1984
>> There are: 1960 Atoms
>> splitting topology...
>> There are 698 charge group borders and 1 shake borders
>> There are 698 total borders
>> Division over nodes in atoms:
>>    492     489     488     491
>> Walking down the molecule graph to make constraint-blocks
>>
>> -------------------------------------------------------
>> Program mdrun_mpi_d, VERSION 4.0.4
>> Source code file: splitter.c, line: 130
>>
>> Fatal error:
>> Shake block crossing node boundaries
>> constraint between atoms (1467,1474)
>> -------------------------------------------------------
>> ...
>>
>> -- 
>> -----------------------------------------------
>> Erik Marklund, PhD student
>> Laboratory of Molecular Biophysics,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 4537        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>>
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> 
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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