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

Erik Marklund erikm at xray.bmc.uu.se
Wed May 6 20:34:29 CEST 2009


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.

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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