[gmx-users] about truncated octahedral periodic box

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 3 13:47:47 CEST 2007

Hi Rui Li,

There is no center in an infinite periodic lattice...
But what will be used as the center in gromacs is the center of the
rectangular brick, which can be derived from the lattice vectors (also
for a truncated octahedron). See chapter 3 of the manual.
By the way.., a rhombic dodecahedron is smaller than a truncated
octahedron and more spherical like (the best packing of a sphere).



On 7/3/07, Rui Li <moonfine at mail.sdu.edu.cn> wrote:
> Dear all,
>  I use a truncated octahedral periodic box. After I use genbox to add water
> molecules, I find the protein is not at the center of the water box. I don't know
> why it will depart the center.
> Thank you in advance.
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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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