feenstra at chem.vu.nl
Fri Aug 8 09:08:01 CEST 2003
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
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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