[gmx-users] g_rdf problem

[André Farias de Moura]

Hi Zhenyu,

yes, I see this behavior every time a site is buried within a large
structure, say a micelle or a lipid bilayer.

RDF profiles yield the PMF profiles between the two species, so a value
below unity stands for a repulsive region (in the thermodynamic sense, not
in the mechanical sense) and one of the reasons that it may happen is an
excluded volume region between the sites.

On Fri, Jul 31, 2015 at 3:23 AM, Zhenyu Meng <fdmm1989 at gmail.com> wrote:

> 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
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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