spoel at xray.bmc.uu.se
Fri Aug 8 09:22:00 CEST 2003
On Thu, 2003-08-07 at 17:39, Anton Feenstra wrote:
> Kay Gottschalk wrote:
> > Hi Christoph,
> > danke fuer das Angebot! I'd like to try it. But perhaps I should restate
> > my problem to make it (even more:)) clear: The relative probability of
> > finding a water water molecule at a given distance r is (approximately
> > as stated in the manual)
> > g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water in a
> > sperical shell (4*pi*r^2*dr), normalized by the water density rho.
> > However, this is only true for symmetrical systems. The problem in my
> > case is that the protein excludes water from certain regions, thus I
> > have a assymetrical system. Therefore, the spherical shell is not the
> > correct volume over which to normalize the function.
> Hmm, I'm not sure actually how it is implemented. It could be either as a
> distribution function, which is normalized to an integral of 1, or it is
> normalized to a bulk density (i.e. at 'infinite' or 'large' distances) of 1,
> which is taken from your actual distribution, not an 'external' reference
> value. In any case, there is no normalization to a 'reference' average water
> density (which would also be pressure & temperature dependent, and water
> model dependent as well).
> In either case, I believe three columns are written in the output (.xvg)
> file, first the distance, then the normalized rdf and finally the 'raw'
> numbers (if not, it would be straightforward to add to the source code).
> If you type 'xmgrace -nxy rdf.xvg', you will see all available plots in
> the file.
I don't think there is any reason to renormalize, the normalization is
done based on the number of water molecules (oxygens) in the
computational box, and since your site of interest is partially occluded
by protein the number of bound water molecules will not be the same as
for a particle in solution.
Try to take the integral of the RDF (using Int 4 pi r^2 g(r) from 0 to
the first minimum), that will give you the average number of hydrogen
bonded water molecules.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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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