[gmx-users] rhombic dodecahedron - box vectors
feenstra at chem.vu.nl
Fri Jul 23 17:43:49 CEST 2004
Nuno R. L. Ferreira wrote:
> Hi all
> Perhaps its not a question to be posed here, but since MD works with
> polihedra, someone could point me out some hints about this one.
> I've done some MD sims. using a rhombic dodecahedron (xy - square) box.
> Usually I make my images or even animations within VMD soft.
> I would like to draw the 24 edges of this box type. But, since my maths is not
> so well tuned as my protein biochemistry, I need some help here.
>>From what I read, from the 3 basis vectors (defined in gmx manual) it is
> possible to get the box, by just moving this vectors in 3D space. Is this correct?
> How can I do this? Or, where can I get some math inspiration to understand this.
Altough the box type is called rhombic dodecahedron, it is actually
implemented as an triclinic box, defined by three box vectors that
span a skewered brick-like shape in space, and has 12 edges (not 24).
You can see this by converting a .gro file to .pdb using editconf, open
in rasmol and type 'set unitcell true' in rasmol. That will show you the
edges of the triclinic box (which is similar to a crystal unit-cell).
IIRC, editconf or trjconv have an hidden option to display the box edges.
Type 'editconf -h -hidden' (or trjconv...) to see it. You can select
different types of representing the box, e.g. triclinic, rectangular or compact.
A compact representation of a rhombic dodecahedral box will have 24 edges.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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