[gmx-users] Simulation crashes (Gromacs 4.0.5)

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 20 06:59:12 CEST 2009

Baudilio Tejerina wrote:
> Hello:
> I'm trying to run a simulation that crashes with the message below.
> At this point, I'm not a the level of being able to interpret the error 
> so, I'm uncertain whether is caused by an ill-conditioned model ( input 
> ) or an actual bug in the code.

There's a third hypothesis - the domain decomposition (DD) algorithm 
requires various parameters that you can give to mdrun to make it cope 
better with atypical simulation systems. You can experiment with them.

To help further, we'd have to know more about your simulation system, 
equilibration protocol, execution environment and mdrun command line.


> I would enormously appreciate if someone can give me a hands with this.
> Sincerely,
> Baudilio
> -------------------------------------------------------
> Program mdrun_mpi_d, VERSION 4.0.5
> Source code file: domdec.c, line: 2592
> Fatal error:
> The X-size of the box (9.999306) times the triclinic skew factor 
> (1.000000) is smaller than the number of DD cells (4) times the smallest 
> allowed cell size (2.500000)
> -------------------------------------------------------
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