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