[gmx-users] g_rdf problem

[Zhenyu Meng]

Hi André,
Many thanks for you big help!

2015-07-31 22:32 GMT+08:00 André Farias de Moura <moura at ufscar.br>:

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