[gmx-users] number of DD cells

[Poojari, Chetan]

Hi Mark,

I ran on 48 processors.....the error is:

The X-size of the box (5.312040) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281)


Kind regards,
chetan


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: 27 December 2010 00:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] number of DD cells

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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