Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile

From: Bharat Manna <>
Date: Tue, 4 Sep 2018 19:05:59 +0530

Dear Daniel,

Thank you so much for your suggestion. I have got the integrated RDF values
using 'intrdf'. However, I am still confused to calculate the Coordination
Number (CN) for the first interaction shell. Do these integrated values
include the 4 * pi * density terms or do I need to separately multiply it
to the integrated rdf value for a given r?

In case it is a separate process, kindly have a look at the two data files
I have provided. From the normalized RDF profile, r(max)= 2.65 Å and
r(min)= 3.35Å for the first interaction shell. From the integrated profile,
intrdf=0.1343 (when r = 2.65Å) and intrdf=0.2611(when r=3.35Å).

So, the CN = 4 * 3.14 * 1.09 * 0.2611 = 3.57
where, density = 1.09 gm/cm^3

Is the calculation right? Please help me to understand this.

Thanking you,
Bharat Manna

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Received on Tue Sep 04 2018 - 07:00:02 PDT
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