[gmx-developers] GB Dom Decomp problem

[David van der Spoel]

Hi,

I'm running a long GV simulation on 8 cores, and after tens of 
nanoseconds it crashes with this error:

Program mdrun, VERSION 4.5-beta1-20100730-f9ac35b
Source code file: /scratch/spoel/GG/gromacs/src/mdlib/domdec.c, line: 2629

Fatal error:
Step 83099555: The domain decomposition grid has shifted too much in the 
Y-direction around cell 1 0 0

Original output is:

Making 3D domain decomposition 2 x 2 x 2
starting mdrun 'Generated by trjconv : MPRA t= 2000.00000'
100000000 steps, 200000.0 ps (continuing from step 82508605, 165017.2 ps).
step 82508605, will finish Tue Aug 10 16:01:41 2010

Simulations run with angular comm removed, so the protein should not 
move away from the center of the box.

Can this be prevented?


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se