[gmx-users] non squares box

Omer Markovitch omermar at gmail.com
Sun Jun 21 11:23:58 CEST 2009

Dear All,
I would like to ask your help on the following - I want my simulation to
include a surface, and have PBC.
The surface I chose is aligned on the XY plane. However, the surface is not
a square.
The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are:
bc=ac=90 & ab=120 degrees.

I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". To
test this, I have used "trjconv -pbc nojump -center yes -boxcenter zero". My
problem is that the trjconv generates a structure where some of the surface
atoms are cut and/or overlapping...

Could you please help me? Wheres the problem?
The input PDB I use is about 2 MB in size, so it can't be attached here.

Koby Levy research group,
Weizmann Institute of Science.
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