[gmx-users] g_rdf
Kay Gottschalk
kay.gottschalk at weizmann.ac.il
Thu Aug 7 10:31:01 CEST 2003
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
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