[gmx-users] PBC dodecahedron

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 23 11:26:24 CET 2009

Hi Nahren.

> I have run my simulation for 12 ns (of a protein dimer ).. I see the box
> remain octahedron till about 5 ns after that the sides of the dodecahedron
> becomes unequal.
> i tried -pbc atom/whole etc, but does not help.
> Any advice on the issue will be truly helpful.
> regards,
> nahren
An octahedron is not the same as a dodecahedron. Besides there's noteworthy
distinction between octahedron and _truncated_ octahedron and between
dodecahedron and _rhombic_ dodecahedron.

If you use anisotropic or semi-isotropic pressure coupling, you're box may
skew and the sides from the shape resulting from using -pbc compact will not
be equal anymore. In fact, your initial _regular_ rhombic dodecahedron will
become a _general_ rhombic dodecahedron (and any unit cell can be
represented as a general rhombic dodecahedron).

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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