[gmx-users] rdf doesn't tend to unity

Tue Sep 13 13:10:30 CEST 2005

Hi Ester,

if your polymer chains are not water-soluble, i.e., they
aggregate in solution, then the water molecules do not
have too much room arond the polymer. in other words,
there is an excluded volume where water is not likely to
be found because the system is micro-heterogeneous. if it
happens to be so, g(r) would converge to unity only at
"VERY" large distances, several tens or even hundreds
of nanometers.

I hope it helps,

Andre'

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

    Dr. Andre' Farias de Moura

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

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

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

        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

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

On Tue, 13 Sep 2005, Ester Chiessi wrote:

>
> ----- Original Message -----
> From: "David" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Monday, September 12, 2005 7:22 PM
> Subject: Re: [gmx-users] rdf doesn't tend to unity
>
>
> > On Mon, 2005-09-12 at 17:30 +0200, Ester Chiessi wrote:
> >> ----- Original Message -----
> >> From: "David" <spoel at xray.bmc.uu.se>
> >> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >> Sent: Monday, September 12, 2005 2:06 PM
> >> Subject: Re: [gmx-users] rdf doesn't tend to unity
> >>
> >>
> >>
> >> Thanks for your answer.
> >>
> >> > On Mon, 2005-09-12 at 13:31 +0200, Ester Chiessi wrote:
> >> >> Hi.
> >> >>
> >> >> I calculated the MD of a polymeric network in SPC water. I was very
> >> >> surprised when I found that the rdf between the oxygen atoms of the
> >> >> polymer
> >> >> and the water oxygen atoms doesn't reach the value of 1 at high r
> >> >> values.
> >> >> The g(r) remains lower than unity and tends to 0.87.
> >> >> I could expect a value higher than 1, eventually for inhomogeneity,
> >> >> but
> >> >> not
> >> >> lower.
> >> > Test whether the integral (4 pi r^2 g(r)) goes to #Ow
> >> The number of polymer oxygens is 611.
> >> OW number is 8773.
> >> The box is cubic with size of 6.707 nm.
> >> The integral in the 0-3.3535 nm distance interval results 136.16 nm^3.
> > It should go to 8773, did you include the terms above in the integral?
>
> I calculated the integral of    (4 pi r^2 g(r))  with r from 0 to 3.3535 nm
> and the result was 136.16 nm^3.
>
> If you multiply this value for #OW and divide for the box volume, you obtain
> a number of oxygens (3959)  lower than that you can estimate (4593) by
> considering a sphere of water with radius 3.3535 and density equal to the
> water average density in the box.
>
> The ratio 3959/4593 is 0.86, the limiting value of g(r). If it is not a
> chance, what could it mean?
>
>
> >
> >
> >> > Test whether the RDF goes to distances longer than half the shortest
> >> > box
> >> > length
> >> g(r) is given from 0 to 3.3535 nm
> >> >>
> >> >> Can this result have a physical meaning or is it an artifact?
> >> >>
> >> >> If there is a lower density at long distances, respect to the average
> >> >> density in the system, it should be some r interval where g(r) becomes
> >> >> higher than unity. Is it correct?
> >> >>
> >> >> I used pbc=full for the trajectory calculation, as polymer chains are
> >> >> covalenty linked to their periodic images.
> >> >>
> >> >> Thanks in advance for any suggestion or comment.
> >> >>
> >> >> Ester
> >> >>
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> >> > David.
> >> > ________________________________________________________________________
> >> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >> > Dept. of Cell and Molecular Biology, Uppsala University.
> >> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >> > phone:  46 18 471 4205          fax: 46 18 511 755
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> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
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