VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun May 11 2008 - 13:22:18 CDT

On Sun, 11 May 2008, Neelanjana Sengupta wrote:

NS> Hi John and Axel,
NS>
NS> Thanks for the answer. Where is the 'pbcwithin' command available? (1.8.7 is
NS> not out yet, right?)

test builds (a.k.a. alpha versions) are available through the
VMD Public BioCoRE project. for details see the VMD homepage.

cheers,
  axel.

NS> -Neelanjana
NS>
NS> On Sun, May 11, 2008 at 8:54 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
NS>
NS> >
NS> > Hi,
NS> > We have a new "pbcwithin" command in the test builds of VMD 1.8.7
NS> > if you would like to try it, but the normal "within" command found
NS> > in older versions doesn't take PBC into account.
NS> >
NS> > Cheers,
NS> > John Stone
NS> > vmd_at_ks.uiuc.edu
NS> >
NS> > On Sun, May 11, 2008 at 12:04:57AM -0700, Neelanjana Sengupta wrote:
NS> > > Dear VMD users,
NS> > >
NS> > > Can anybody ascertain if the 'within' command takes into account periodic
NS> > > boundary conditions? In other words, for obtaining the atoms 'within' a
NS> > > certain distance of a selection, is the distance between the selection
NS> > and
NS> > > each atom recalculated as:
NS> > > dx=dx - cell_a*NINT(dx/cell_a), etc?
NS> > >
NS> > > This is for a dcd file where the unit cell dimensions are specified at
NS> > each
NS> > > step.
NS> > >
NS> > > Thanks,
NS> > > Neelanjana Sengupta
NS> > > --
NS> >
NS> > --
NS> > NIH Resource for Macromolecular Modeling and Bioinformatics
NS> > Beckman Institute for Advanced Science and Technology
NS> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
NS> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
NS> > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
NS> > Fax: 217-244-6078
NS> >
NS>
NS>
NS>
NS> --
NS> 

-- 
=======================================================================
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.