[gmx-users] g_rdf problem

[Zhenyu Meng]

Hi André,
Thanks for your paper, so in your opnion the particle C may be kept out of
a sphere (like the micelles in your paper, for example)?

2015-07-27 23:06 GMT+08:00 André Farias de Moura <moura at ufscar.br>:

> 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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-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University