non-cubic boxes for Periodic Boundary Conditions

From: George M. Giambasu (
Date: Mon Jun 19 2006 - 17:38:31 CDT

Dear namd users,

I was wondering if there is anyone that has some experience in
simulating non-cubic boxes with namd, for example rhombic dodecahedron
or truncated octahedron. The systems that I am interested would be a
solvated protein or nucleic acid.
I read how to define the cell vectors for those type of boxes and I made
a simple trial with a water box for RHDO. The geometry I get looks like
a prism, but I am wondering if you know how to make it look like a real
RHDO (rhombododecahedron), for exaple, the output you get from

any script, suggstions or links would be great!

thank you

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