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

[Erik Marklund]

No. Au contraire, there probably is, but I assumed P-lincs was used 
nowadays, and that it can handle cases like this. It seems that I may 
have been wrong.

/Erik

Gerrit Groenhof skrev:
> Are you sure there are no bonded interactions between these atoms?
> Gerrit
> On 6 May 2009, at 20:46, Erik Marklund wrote:
>
>> 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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>
> -- 
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
> http://wwwuser.gwdg.de/~ggroenh/
>
> _______________________________________________
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-- 
-----------------------------------------------
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