From: David A Case <>
Date: Mon, 18 Jul 2016 15:56:03 -0400

On Mon, Jul 18, 2016, Mahmood Jasim wrote:
> Definitely a silly question for many but I could not find the answer in the
> mailing list not in the manuals. I wanted to know what RDF actually
> measures? Is the result the number of water molecules as a function of
> distance or is the density of water as a function of distance? and do we
> need to perform normalization if the solvent was water?
> My objective is the distribution of water around a key atom in the protein,
> so my solventmask is water and my solutemask is the protein atom.

I think the manual is about as clear as I could be here:

"The RDF is calculated from the histogram of the number of particles found as
a function of distance R, normalized by the expected number of particles at
that distance"

If the solvent is water (as in your case), cpptraj automatically does
the proper normalization (see the "rdf" command in the Manual). There are
options to use other methods of normalization, but they are not needed for
your use case.


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Received on Mon Jul 18 2016 - 13:00:03 PDT
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