From: Axel Kohlmeyer (
Date: Mon Jun 27 2011 - 09:08:35 CDT

On Mon, Jun 27, 2011 at 2:15 AM, divya nayar <> wrote:
> Hi,
> I want to calculate the protein-water (oxygen) RDF from the VMD GUI Plugin
> of RDF.  I give "protein" in selection 1 and "name OH2" in selection 2. The
> keyword "protein" over here means that the center of mass of protein will be
> taken into consideration or it will take any heavy atom of protein because
> in Tcl script if "protein" keyword is given in any selection ,it means any
> heavy atom of protein.

please think about this for a bit and see the inconsistency.
atom selections _always_ select atoms that match the
selection criterion. thus protein _has_ to select all atoms
that match the "protein" macro (which is based on pdb file
standards and common use heuristics and _do_ include
hydrogen atoms. it basically matches everything that has
it connected to a protein backbone and has the same resid)

how should a program determine whether you mean that
you want to address the center of mass of all atoms in
one case and all individual atoms in the second?

> Somebody please clear my doubt as to what exactly is taken as selection in
> VMD RDF if "protein" is written.
> Morevover, from where can I obtain the in-built tcl script for calculation
> of RDF that  VMD uses?

you cannot. RDF calculation can be very time consuming and thus
has been implemented as (multi-threaded) c++ code and as GPU
accelerated CUDA code. you can find it in the VMD source code
in Measure.C,, and MeasureRDF.C


> Thanks,
> Divya

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