[gmx-users] error: triclinic skew factor - number of DD cells

Berk Hess gmx3 at hotmail.com
Tue Nov 18 10:05:09 CET 2008


This errors means that one of your box dimensions has shrunk by more than 20%
or a skewness change caused such an effects.
Normally you would have to lower the -dds option of mdrun.

But the skew_fac I determined from your box is 0.73, i.e. twice as high.
Therefore I guess you are using 4.0, which has a "bug".
In 4.0.2 skew_fac has been corrected.
Due to your "extreme" box shape, the effect of the bug isa factor of 2
(for normal rhombic dodehedra the effect is less than 20%
So switching to 4.0.2 will solve your problem and will also reduce 
the communication load by a factor of 2.


Date: Mon, 17 Nov 2008 18:58:59 +0000
From: lastexile7gr at yahoo.de
Subject: RE: [gmx-users] error: triclinic skew factor - number of DD cells
To: gmx-users at gromacs.org


when I start the simulation my box vectors are the following :
16.89660   2.61581   2.07800   0.00000   0.00000  -0.43665   0.00000   0.00000   0.00000

and with the command (the final written step was at 40487):
trjconv -f traj.trr -dump 40487 -o out.gro

I got these box vectors:
22.35607   1.93762   2.21866   0.00000   0.00000  -1.78430   0.00000   0.11905   0.05522

Thank you,

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