[gmx-users] number of DD cells

[Justin A. Lemkul]

Poojari, Chetan wrote:
> 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)
> 

I would say this further confirms Mark's suspicions.  Whatever you're doing to 
the system is causing it to rapidly collapse, a behavior that is now independent 
of the number of DD cells.

-Justin

> 
> 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.
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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