[gmx-users] g_rdf normalisation

Qiao Baofu qiaobf at gmail.com
Wed Mar 28 09:44:34 CEST 2007

2007/3/26, syma <syma.khalid at bioch.ox.ac.uk>:
> Hi,
> I am attempting to calculate the rdfs of the various components of my
> system
> wrt to DNA phosphate groups. However, I was wondering how I can normalise
> so
> I can compare the various rdfs? Ideally I would like to have the g(r)
> normalised in the range 0-1.

In fact, there is not flag to control the normalised range. But you can take
the range, 0-1, of rdf.xvg.
The caluclated neighbour number at dr is normalised by the ideal case at dr
(average density times the volume at dr) . For the ideal condition, the
density at the short range is the same as the average density. Therefore,

I have read on the user list that I should get three columns in the *.xvg
> output, the distance, the normalised data and the raw data, I only get two
> columns.

The default rdf.xvg will give only two columns, r and g(r)

Thanks in advance for any help.
> -Syma
> ***************************************************
> Dr Syma Khalid
> Department of Biochemistry,
> University of Oxford
> South Parks Road,
> Oxford
> OX1 3QU
> U.K.
> ***************************************************
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Sincerely yours,
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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