Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ?

From: Matias Machado <>
Date: Sun, 16 Sep 2018 11:50:47 -0300 (UYT)

Dear Bharat,

According to the RDF definition [], the integral of the RDF up to a given distance gives you the average number of particles into that range...

In general, the first coordination shell is defined from 0 to the first minimum after the first peak in the RDF (which is ~3 to 3.5A in your plot)

In case of complex molecules like glucose and acetate you should be careful on how to calculate the RDF to get the information you are looking for... for example, these three RDFs definitions may have different meanings in terms of coordination numbers:

+ Any atom of glucose to any atom of acetate
+ a given atom of glucose to a given atom of acetate
+ The closest atom of glucose to the closest atom of acetate



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Bharat Manna" <>
Enviados: Jueves, 13 de Septiembre 2018 15:48:48
Asunto: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ?

Dear AMBER users,

I am trying to find the coordination number of glucose with its surrounding
acetate solvent molecules within the first interaction shell of glucose. I
have obtained both the normalized RDF profile of and integrated rdf profile
from cpptraj. Is there anyway to calculate the coordination number directly
from these data? I have provided both the data files here.

Bharat Manna.

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Received on Sun Sep 16 2018 - 08:00:02 PDT
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