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

[Gerrit Groenhof]

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/