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: [email protected]
[[email protected]] On Behalf Of Mark Abraham
[[email protected]] 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 -- gmx-users mailing list [email protected]
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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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