VMD-L Mailing List

From: martin klvana (martin.mk.klvana_at_gmail.com)
Date: Mon May 17 2010 - 17:05:03 CDT

What is the mathematical formula for RDF calculation & normalization
used in VMD?

Thanks,
martin

On 16 May 2010 14:01, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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.
>