VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 16 2010 - 14:01:26 CDT

On Sun, May 16, 2010 at 1:39 PM, martin klvana
<martin.mk.klvana_at_gmail.com> wrote:
> Hi everybody - I have two questions about RDF:
>
> * How exactly are the values of g(r) calculated?

a histogram of all atom pair distances between both
selections is being compiled and then normalized.

> * When I calculate RDF for water molecules around a protein atom, is
> it then possible to quantify how many water molecules are, on average,
> located within various distances from the selected atom?

this can be inferred from the number integral which is
effectively the integral over the histogram bins.

cheers,
     axel.

> Thanks,
> martin
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.