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

[Erik Marklund]

Hi,

Then I'll try with dd and a big box.

Thanks for your time and help fellow scientists!

/Erik


hessb at mpip-mainz.mpg.de skrev:
> 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
>>>>
>>>> _______________________________________________
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
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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
>>
>> _______________________________________________
>> gmx-developers mailing list
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>>
>>     
>
>
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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