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

[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