VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 10 2009 - 09:14:00 CDT
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Hi,
I should also add that the "pbwithin" selection is only found
in VMD 1.8.7, so you'll want to try one of the new test versions
to take advantage of this.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Fri, Apr 10, 2009 at 10:03:36AM -0400, Axel Kohlmeyer wrote:
> 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
> > (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
>
> this is not correct. you have to use "pbwithin" to have a version
> of "within" that accounts for periodicity.
>
> cheers,
> axel.
>
> > 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 akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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.
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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