[gmx-users] center of dodecahedron

[Tsjerk Wassenaar]

Oh, what a wonderful PBC confusion :)

Actually, it is in the center of the triclinic cell corresponding to a
rhombic dodecahedron, but it is not in the center of the rectangular brick
representation of that, which is the default output representation. The
rhombic dodechahedron does not have an easy center, as it does not have an
easy origin. When using trjconv -ur compact, a rhombic dodecahedron is
drawn with the center of the triclinic cell as its center, but does that
make it the real rhombic dodecahedron center? The tiling is translation
invariant...

The triclinic representation of a rhombic dodecahedron is not a rectangular
brick.

Cheers,

Tsjerk



On Sun, Jan 26, 2014 at 4:11 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Jan 26, 2014 9:30 AM, "Mahboobeh Eslami" <mahboobeh.eslami at yahoo.com>
> wrote:
> >
> > hi GMX users
> > i simulate protein ligand complex in dodecahedron box
> > when i use following command
> >
> > editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c
> > My complex is not located in the center of box,
> >
> > How do I put the complex  in the center of box?
>
> It is in the center of the dodecahedral cell, but not in the triclinic
> representation of that cell, which is the default output representation.
> See
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditionsfor
> info and suggestions on using trjconv to get the visual confirmation
> you seek.
>
> Mark
>
> > thanks for your's help
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.