[gmx-users] g_rdf

[Kay Gottschalk]

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.
Cheers,
Kay.

On Thursday, August 7, 2003, at 10:50 AM, Christoph Freudenberger wrote:

> christoph.freudenberger at chemie.uni-ulm.de
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel