[gmx-users] Smallest allowed cell size

Matthew Hoopes mihoopes at ucdavis.edu
Thu Oct 23 01:52:59 CEST 2008


I received the following error

Program mdrun, VERSION 4.0
Source code file: domdec.c, line: 2933

Fatal error:
Step 10: The X-size (-32.295326) times the triclinic skew factor (1.000000)
is smaller than the smallest allowed cell size (1.200000) for domain
decomposition grid cell 0 0 0

under the following conditions

GROMACS 4.0 installed on a Cray XT4 at nics.utk.edu

#PBS -l walltime=12:00:00,size=16
aprun -n 16 mdrun -maxh 29.5

The system has 84272 atoms in a box that is approx. 10x10x10. It works with
8 processors but I would think that this is fine divided up between 16

Any suggestions for understanding this error message would be appreciated.


Matthew Hoopes
Biophysics Graduate Group
University of California, Davis

mihoopes at ucdavis.edu

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