On 27/12/2010 7:51 AM, Poojari, Chetan wrote:
Hi,
I am following umbrella sampling tutorial for my membrane protein system.
While running continuous pulling simulation (mdrun)..... under step five:
Generating Configurations of the tutorial. I get the below error.
The system ran initially but corrupted very soon with warning " The X-size of the
box (4.800448) times the triclinic skew factor (1.000000) is smaller than the number of
DD cells (4) times the smallest allowed cell size (1.200000) "
I am using 64 cores with -npme = 16. I haven't set any -dds.
My system box size is 6 x 6 x 12 nm
That's a large box deformation... 6nm to 4.8nm. I'd say your system is
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try
running on fewer processors to see whether when the DD box size is
larger whether you get other explosion symptoms.
Mark
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