VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sat Apr 11 2009 - 00:49:22 CDT

Hi Axel and John,

Thanks for your ideas. However, I still do not understand (or am not
convinced) why it will not work if I use the existing within command AFTER I
have wrapped the coordinates (so that the distance between any two atoms now
is the PBC based distance). I am sorry of this sounds trivial, but would be
great if you could throw some more pointers.

BTW, when will VMD 1.8.7 be released?

Regards,
Neelanjana

On Fri, Apr 10, 2009 at 7:44 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
~~~~~~~~~~~~~~~~~~~~
Neelanjana Sengupta, PhD
Physical and Materials Chemistry Division
National Chemical Laboratory
Dr. Homi Bhaba Road
Pune 411008, India
Phone: +91-20-2590 2087
Fax: +91-20-2590 2636
~~~~~~~~~~~~~~~~~~~~