[gmx-users] Ion positioning 2

[Anton Feenstra]

Lieven Buts wrote:
> 
> I was starting to wonder about the shape of the water box :-).
> I still don't completely understand this "stacking with shifts"
> but I'll look into it.

You seem to have rasmol installed (the screen output betrays it...).
In rasmol you can visualize the triclinic box by the command 
# set unitcell true
Do this with the 'brick-shaped' water box, and if you like also with
the 'compact' version. This usually gives some understanding... ;-)

The point here is that all of the box shapes (brick, triclinic and
dodecahedral) must be able to stack to fill a three-dimensional
space (otherwise, you cannot have PBC). This directly means that
these shapes must on some level be interchangable. If you still
understand what I am saying, you might want to have a look at the
'full monty' of all this in the thesis of Henk Bekker:
http://www.ub.rug.nl/eldoc/dis/science/h.bekker/
(Chapter 3 deals with box shapes).


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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