Re: [AMBER] Calculating density during Radial distribution analysis

From: Jason Swails <>
Date: Mon, 12 Jan 2015 08:18:11 -0500

> On Jan 11, 2015, at 3:45 PM, Sylvester Tumusiime <> wrote:
> Dear Amber members,
> I would like to find out how critical it is to include the "volume" keyword
> when calculating radial distribution function (RDF). Will omitting the
> volume keyword thereby not determining the system actual density
> significantly affect the accuracy of the observed data obtained after
> running radial? Should i include it anyway since it can only improve the
> accuracy of my data?

The ‘volume’ keyword only affects how the radial distribution function is normalized. If you omit ‘volume’, then the RDF is normalized by the experimental particle density (0.033456 mols/Ang^3). If “volume” is given, then the density normalization is computed basically as the number of particles selected divided by the average volume of the unit cell for the whole trajectory.

The *shape* of the RDF will look identical, but the asymptotic limit of the RDF will change. I believe that if you include the “volume” keyword, the asymptotic limit of a water RDF will approach 1 (i.e., the RDF will be relative to “bulk” solvent).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 12 2015 - 05:30:04 PST
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