From: Axel Kohlmeyer (
Date: Mon Sep 04 2006 - 12:14:28 CDT

On 9/4/06, Ivan Degtyarenko <> wrote:
> Dear,
> new feature in version 1.8.5 allows to plot radial distribution function.
> When one plots atom-atom rdf it is a distribution function for a pair of
> the atoms, it is clear, but what the rdf is when one selects a molecule as
> 'Selection 1' and the rest solvent molecules as 'Selection 2'? Say a case
> of a small hydrated peptide, i.e. in both selections are molecules and not
> just single atoms.


as far as VMD is concerned, a selection is nothing but a list of atoms.
the RDF programmed is the distribution function for the atoms in the
two selections. if you want an rdf between molecules, you have to
pick one atom to represent your molecule. generally speaking the RDF
is a not so well defined function otherwise (unless you have a spherical


> Thanks in advance for your reply,
> YT, Ivan Degtyarenko

Axel Kohlmeyer
  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.