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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Received on Tue Jun 05 2018 - 06:00:02 PDT
