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

[hessb at mpip-mainz.mpg.de]

Hi,

I have also seen this error recently.
I think I have not implemented P-LINCS for PD.
I will soon implement DD for vacuum.
But putting is in a big enough box will make it work with DD.

Berk

> 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
>
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