Re: [AMBER] Radial distribution function of waters

From: Gustaf Olsson <>
Date: Tue, 5 Jun 2018 06:12:25 +0000

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, 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
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