VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Tue Oct 27 2009 - 08:26:08 CDT

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Hi!

Gustavo Gust wrote:
> Using pbwithin I get more oxygen atoms around MOL than using within.
> The difference is big in some cases.
> I have to take in account the periodical boundary conditions, but using
> pbwithin or within is confusing me.

"within" will only select atoms in the primary image of the system,
"pbwithin" will also select atoms in the periodic images. It does not,
however, modify the coordinates - they will still be the coordinates of
the atom in the primary image, so if you want to compute distances, you
need to take into account the periodic boundary conditions manually.

Olaf
- --
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