[gmx-users] rdf doesn't tend to unity
spoel at xray.bmc.uu.se
Tue Sep 13 16:36:25 CEST 2005
> >> >> 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?
It's correct. Do you have a cluster of polymer surrounded by water?
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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