From: Axel Kohlmeyer (
Date: Sat May 22 2010 - 10:25:06 CDT

On Sat, May 22, 2010 at 10:19 AM, Amir Hajiahmadi Farmahini
<> wrote:
> Hi,
> How can I figure out following problem to be able to generate RDF.
> I need underlying selection as my first selection in VMD to generate RDF:
> Two or more atoms at them same time have to be selected from "same molecule"
> in "one selection". To bring a very simple example: both Oxygen atoms from
> same molecule of carbon dioxide have to be selected as the first selection
> in RDF to be within a specific distance from Second selection.
> Second selection can be any atom from another molecules (Not important
> here).
> The problem is I was not able to ensure selected atoms are at the same time
> from same molecule.

the rdf code knows nothing about molecules. also, your requirements sound
very odd. can you please elaborate what property you want to calculate?

even though i am not entirely clear about what you want to do, the
most promising
route seems to be that you do a two step procedure. first extract a
set of "subtrajectories"
from your original data set that conforms to your first requirement
and then compute
the rdfs for each of those and average.

it may be possible to achieve something similar by setting the user parameter
for the oxygen atoms in question to specific numbers corresponding to your
requirements, but that can have unexpected side effects.


> Regards,
> Amir Farmahini

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