[gmx-users] Help about 2 D periodic boundary condition

[Anton Feenstra]

David wrote:
> 
> > > As for 2D PBC, it depends on what you want in the third direction.
> > > You can for example make a two 'walls' of frozen atoms above and
> > > below your system, or perhaps simply a vacuum boundary. The system
> > > will still be treated in 3D PBC, but the third dimension will not
> > > be relevant.
> So what does it mean: not relevant?

I mean that if you have two 'walls' with enough space in between,
like:
.........
.       .
.       .
.-------.
.#######.
.#######.
.-------.
.       .
.       .
.........

where ## is your system, --- is the 'wall' and ... are the box
edges, effectively there is no interaction in the third (vertical
in my drawing) dimension, so there is no effective periodicity.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "I Used To Care, But Things Have Changed" (Bob Dylan)     |
|________|___________________________________________________________|