From: Axel Kohlmeyer (
Date: Wed Jun 15 2011 - 09:14:46 CDT

On Wed, Jun 15, 2011 at 9:29 AM, Rupashree Shyama Ray
<> wrote:
> Hi,
> I would like to plot rdf for a molecule solvated in water.
> The rdf should be between the O atom of the molecule with the hydrogen
> atoms(H) of water, but I should exclude the H atoms present in the molecule.
> Please tell me how to set this option in analysis of rdf in VMD.

just pick the proper selections. the rdf will be computed
between all atoms in selection one and all atoms in
selection two. the VMD selection language allows very
sophisticated constructs. please look up the details in
the VMD user's guide. the best way to "debug" a selection
is to overlay two representations: use "Lines" as a representation
for all atoms and then create a second one (e.g. Licorice or VDW)
and try out your selection string and modify it until the
proper atoms visible in the second representation.


> Thank you.
> Rupashree

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.