From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 11 2008 - 13:12:48 CDT

Hi,
  You can try out the VMD 1.8.7 test versions if you like, they are
available here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, May 11, 2008 at 10:35:35AM -0700, Neelanjana Sengupta wrote:
> Hi John and Axel,
>
> Thanks for the answer. Where is the 'pbcwithin' command available? (1.8.7 is
> not out yet, right?)
> -Neelanjana
>
> On Sun, May 11, 2008 at 8:54 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > We have a new "pbcwithin" command in the test builds of VMD 1.8.7
> > if you would like to try it, but the normal "within" command found
> > in older versions doesn't take PBC into account.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, May 11, 2008 at 12:04:57AM -0700, Neelanjana Sengupta wrote:
> > > Dear VMD users,
> > >
> > > Can anybody ascertain if the 'within' command takes into account periodic
> > > boundary conditions? In other words, for obtaining the atoms 'within' a
> > > certain distance of a selection, is the distance between the selection
> > and
> > > each atom recalculated as:
> > > dx=dx - cell_a*NINT(dx/cell_a), etc?
> > >
> > > This is for a dcd file where the unit cell dimensions are specified at
> > each
> > > step.
> > >
> > > Thanks,
> > > Neelanjana Sengupta
> > > --
> >
> > --
> > 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
> >
>
>
>
> --

-- 
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