VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 11 2009 - 09:36:08 CDT

Hi,
  Test versions of VMD 1.8.7 are already available now. I will
release a new beta version this week. You can already download the
alpha versions by following the instructions here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 11, 2009 at 11:19:22AM +0530, Neelanjana Sengupta wrote:
[...]
> 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
> ~~~~~~~~~~~~~~~~~~~~ 

-- 
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