Re: [AMBER] Calculating density during Radial distribution analysis

From: Daniel Roe <>
Date: Mon, 12 Jan 2015 08:40:49 -0700


Just to add on to Jason's answer, the default behavior (i.e. when
'volume' is not specified) is to normalize to the density of water
(1.0 g/mL, 0.033456 molecules/Ang^3). If you happen to be calculating
the RDF for water all this means is at larger values of distance your
RDF should become ~1.0. If you aren't calculating an RDF for water you
can either specify a density with the 'density' keyword, or use the
'volume' keyword, which as Jason mentioned normalizes to a density
calculated from the number of particles and the average volume. It has
nothing to do with improving accuracy - just normalization.


On Sun, Jan 11, 2015 at 1:45 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?
> Thank you,
> Silver
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jan 12 2015 - 08:00:02 PST
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