Dear Batuhan,
I used iwrap=1 in my simulation, so whenever protein wanted to leave
box at one side, it appeared on the other, never really diffusing very
far from its original position. Therefore, the results are only
slightly affected by noimage option. Thank you for your feedback
though.
Kind regards,
Szymon Zaczek
2017-12-05 10:40 GMT+01:00 Batuhan Kav <bkav13.ku.edu.tr>:
> 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 Żaczek <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 - 04:00:02 PST
