Hi,
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.
Berk
Date: Mon, 17 Nov 2008 18:58:59 +0000
From: [EMAIL PROTECTED]
Subject: RE: [gmx-users] error: triclinic skew factor - number of DD cells
To: gmx-users@gromacs.org
Hello,
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,
Nikos
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