From: Axel Kohlmeyer (
Date: Fri Apr 10 2009 - 09:03:36 CDT

On Fri, 2009-04-10 at 17:05 +0530, Neelanjana Sengupta wrote:
> 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

this is not correct. you have to use "pbwithin" to have a version
of "within" that accounts for periodicity.


> 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

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.