From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 17 2010 - 17:13:23 CDT

On Mon, May 17, 2010 at 6:05 PM, martin klvana
<martin.mk.klvana_at_gmail.com> wrote:
> What is the mathematical formula for RDF calculation & normalization
> used in VMD?

it is the plain textbook version, i.e. a regular spherical volume
integral over the average particle density and corrected for
finite size effects (so that it levels out at exactly 1.0).

for non-periodic systems, the normalization is arbitrary
and i just use the average number density of bulk water.
that should be all explained in the documentation.

perhaps it would be easier if you explain what the real
problem is that you want to solve, or the inconsistencies
that you see, instead of me playing 20 questions with you.

thanks,
   axel.

>
> 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.
>>
>

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