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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Received on Mon Jun 04 2018 - 23:30:02 PDT
