[gmx-users] non squares box

Omer Markovitch omermar at gmail.com
Sun Jun 21 14:34:32 CEST 2009

I prefer to keep discussions professional, Mark and Tsjerk.

Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes,
the surface is not a square and my question is how do I tell gromacs that I
have a non standard box. Please see my original post for more details:

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...

Thank you. Omer.

Koby Levy research group,
Weizmann Institute of Science.
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