VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Fri Jun 26 2009 - 10:06:06 CDT

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Hi!

Alberto Sergio Garay wrote:
> 2) I run "pbc wrap -centersel $sel -all"
> 2') I also run "pbc wrap -centersel $sel -center origin -all" (the
> default for -center is unitcell)

Ah, I see that this is not well written in the docs. When you use
"-centersel", you will also have to choose either "-center bb" or
"-center com", otherwise the center of the box will still be the center
of the central image of the unitcell.
Otherwise, you did everything correct, I think.

> Could anyone tell me whether what I'm trying to do is posible? or I need
> a more elaborated script to do so?
> Could anyone explain me how the pbc wrap works?

pbc wrap first chooses one periodic image of the unitcell. This is
determined by the options -center, -centersel, -shiftcenter and
- -shiftcenterrel. Then, it will loop over all atoms in the selection
(-sel) and wrap them into the given box. If you have used the option
- -compound, it will also take care not to break the compounds.

Olaf
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