[gmx-users] g_rdf problem

André Farias de Moura moura at ufscar.br
Mon Jul 27 17:06:51 CEST 2015

RDF may behave just like that (slowly growing from 0 to 1 without peaks),
meaning that you have a pair of sites without significant structure besides
the excluded volume in the region where RDF < 1.

for instance, we observed that behavior for the water distribution around
the hydrophobic atoms inside a micelle:

J. Phys. Chem. B, 2013, 117 (24), pp 7324–7334
*DOI: *10.1021/jp312840y

On Mon, Jul 27, 2015 at 10:49 AM, Zhenyu Meng <fdmm1989 at gmail.com> wrote:

> Dear all,
> I used g_rdf to calculate the RDF and sometimes I got a strange curve in
> which the RDF increase slowly from 0 to 1 and no peak appears.
> According to my knowledge, it's opposite to the definition of RDF cause the
> RDF is the rate of density at certain r by the average density, so the
> integration of the function divided by the range of domain should be 1.
> While for a RDF which is less than 1 in most of its domain the final
> average of the function value should be less than 1.
> I wonder why this is so? Or maybe I think wrongly for the definition of
> RDF?
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
> --
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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