Re: [AMBER] Normalization of radial distribution function

From: George M. Giambasu <>
Date: Mon, 04 Dec 2017 10:28:33 -0500

>From what I understand about RDFs, if they are properly normalized,
their values should be very close to 1 when the distance is
approaching infinity.

This is true only if you compute RDFs that involve solvent particles. As
you approach "infinity" the solvent distribution will stop being
influenced by interaction with the solute and will approach their bulk
value, ie the normalized RDF (g(r)) will approach the value of 1.

I think you what you obtain from your analysis is correct: as you go to
larger and larger distances you see zero population for the residues of
interest because, simply, there are no protein residues that are so far
away. (this is true, of course, if using the minimum image convention)


Dr. George M. Giambasu
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Room 308E Piscataway,
NJ 08854, USA
Office: 1-848-445-5223 Cell: 1-612-644-8285
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Received on Mon Dec 04 2017 - 07:30:03 PST
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