[gmx-users] number of DD cells

[Mark Abraham]

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