VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
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 (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11586.html).
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.

Thanks,
Neelanjana Sengupta