Re: [AMBER] Normalization of radial distribution function

From: Batuhan Kav <bkav13.ku.edu.tr>
Date: Tue, 5 Dec 2017 10:40:54 +0100

Dear Szymon,

Just to add one tiny point on what George said:

>> (this is true, of course, if using the minimum image convention)

As far as I know, unless you specify noimage in your rdf calculations, it will image positions of the particles to your simulation box. This is why when you go beyond a certain distance your rdf drops to zero. With noimage option, you will get different results.

Batuhan

> On 5 Dec 2017, at 09:09, Szymon ┼╗aczek <szymonzaczek.gmail.com> wrote:
>
> Dear George,
>
> thank you very much for your opinion. It seems to make sense, indeed.
>
> Kind regards,
> Szymon Zaczek
>
>
>
> 2017-12-04 16:28 GMT+01:00 George M. Giambasu <giambasu.gmail.com>:
>>> From what I understand about RDFs, if they are properly normalized,
>> their values should be very close to 1 when the distance is
>> approaching infinity.
>>
>>
>> This is true only if you compute RDFs that involve solvent particles. As
>> you approach "infinity" the solvent distribution will stop being
>> influenced by interaction with the solute and will approach their bulk
>> value, ie the normalized RDF (g(r)) will approach the value of 1.
>>
>> I think you what you obtain from your analysis is correct: as you go to
>> larger and larger distances you see zero population for the residues of
>> interest because, simply, there are no protein residues that are so far
>> away. (this is true, of course, if using the minimum image convention)
>>
>>
>> George
>>
>>
>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Dr. George M. Giambasu
>> Rutgers, The State University of New Jersey
>> 174 Frelinghuysen Road, Room 308E Piscataway,
>> NJ 08854, USA giambasu.rutgers.edu
>> www.rci.rutgers.edu/~giambasu
>> Office: 1-848-445-5223 Cell: 1-612-644-8285
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
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Received on Tue Dec 05 2017 - 02:00:02 PST
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