From: Neelanjana Sengupta (
Date: Fri Apr 10 2009 - 06:35:19 CDT

Hi VMD community,

VMD 1.8.6 does not invoke periodic oundary conditions in the 'within'
keyword (
However, if one uses the pbcwrap tool from the pbctools plugin to re-write a
trajectory with the coordinates wrapped, then the results obtained with
'within' should be accurate, right? The reason I am bringing this up is
because when I do the above and compare with results obtained rigorously
(ie. by taking each atom pair and re-calculating their distance based on
PBC), I do not get a perfect match. Some comments would be appreciated.

Neelanjana Sengupta