# Re: [AMBER] Radial distribution function of waters

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 5 Jun 2018 09:05:34 -0400

It's the combined (think of it as averaged) RDF of each atom in the
mask. If you want the geometric center of the mask you have to use the
respectively).

One minor point - to get the correct normalization, typically what you
want is to have the first mask be the one with many atoms (in this
case the water), and the second to have fewer atoms (solute).

Hope this helps,

-Dan

On Tue, Jun 5, 2018 at 8:53 AM, <diego.soler.uam.es> wrote:
> Thank you so much! That worked for me. One more quick question. If
> in the first mask (:XXX.YYY, in Olsson's message) I put two or more
> atoms, the output is just a single RDF. What is reference/origin of
> that RDF? Is it the Center of Mass of those atoms, or what?
>
> Best,
>
> Diego SP
>
>
>
> Quoting Gustaf Olsson <gustaf.olsson.lnu.se>:
>
>> Something like this should do it…
>>
>> parm ../[YOUR-PRMTOP]
>> trajin ../[YOUR-TRAJECTORY/(IES)]
>> radial [OUTPUT] 0.1 20 :XXX.YYY :ZZZ intrdf [OUTPUT] volume nointramol
>>
>> Where XXX is the residue, YYY is the atom and ZZZ is “WAT”/“HOH" or
>> whatever water residues are called in your simulation.
>>
>> The “intrdf” includes the integrated RDF function values in a
>> separate column in the [OUTPUT] file though can be skipped if not of
>> interest to you.
>>
>> Just check the documentation for details.
>>
>> // Gustaf
>>
>>> On 4 Jun 2018, at 17:08, diego.soler.uam.es wrote:
>>>
>>>
>>> Hi,
>>>
>>> After having run a simulation, I would like, given a certain atom A,
>>> to calculate the radial distribution function of waters with respect
>>> to atom A. That is, I would like to use the info from the simulation
>>> to construct a function P(r) giving me the average number of water
>>> molecules at a distance r of atom A.
>>>
>>> In principle this should be doable by hacking the appropriate data out
>>> of the output file (the one with the coordinates), but I have no idea
>>> of how to achieve this.
>>>
>>> I don't know if it is possible to do this easily in AMBER.
>>>
>>> Thank you for your time!
>>>
>>>
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>>
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>
>
>
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Received on Tue Jun 05 2018 - 06:30:03 PDT
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