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

[David]

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?


> > 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
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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