[gmx-users] g_rdf calculations for monolayer

[Andre Farias de Moura]

Hi David and Sriprajak,

rdf may be normalized if you take into account the effects of
inhomogeneity, see for instance:

Ahlstrom and Berendsen, J. Phys. Chem. 1993, 97, 13691-13702.

I hope it helps.

Andre'

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    Dr. Andre' Farias de Moura

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  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil

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        Endereco Atual

    Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
    Universidade de Sao Paulo
    Sao Carlos - SP - Brasil
    Telefone: 55-16-3373-8055

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On Sun, 21 Aug 2005, David wrote:

> On Sun, 2005-08-21 at 01:04 -0700, Sriprajak Krongsuk wrote:
> > Dear Users
> >   I have some problem about g_rdf  calculation for monolayer system.
> > My system is porphyrazine monolayer at air-water interface. I tried to
> > calculate the rdf for water around the center of mass of porphyrazine,
> > but the result is still not nomalized. I mean it does not goes to 1 at
> > the long distance.
> > My questions are that
> > (1) Can I use g_rdf for calculating such a system
> yes
> > (2) If I can, how should I do to get normalized rdf?
> problem is that your system is not homogeneous. If you can come up with
> the equation how to do the normalization it can be implemented.
>
>
> >
> > Best wish,
> >
> >
> > Mr. Sriprajak Krongsuk
> > Physics Department
> > Faculty of Science
> > Mahidol University
> > Bangkok, Thailand 10400
> >
> > E-Mail: sriprajak at hotmail.com
> >             sprajakk at yahoo.com
> > Tel.      01-2620095
> >     ^^^   ^^^
> >
> >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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