[gmx-users] Polymer in periodic boundary conditions again

[Anton Feenstra]

Ester Chiessi wrote:
> 
[...]
> 
> 1) When I prepare the polimer inside the box, should the last atom of the chain be
> the periodically correspondent of the first? If so, should first and last atom
> touch opposite faces of the box, in the right orientation?
> Till now, I built my chain as (for example) : A-B-A-B-A-B
> and not : A-B-A-B-A-B-A, as I'm describing in this question.

You want A-B-A-B-A-B. THat way, the last B will again be connected
to an A (which just happens to be the first one again).


> 2) During the minimizations, should I have to apply the periodic boundary
> conditions?

Definitely.


-- 
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   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "You Will Be Surprised At What Resides In Your Inside"    |
|        | (Arrested Development)                                    |
|________|__