Re: [AMBER] many initial systems for a two molecules system

From: Jason Swails <>
Date: Thu, 4 Sep 2014 07:55:13 -0400

On Thu, Sep 4, 2014 at 7:37 AM, Fabian Glaser <>

> Thanks a lot Jason,
> Would it be possible that you send me an example of the RDF and PMF that I
> could use as input to amber ?
> Or a pointer to the relevant information / paper / examples ?
> I would try to implement what you suggest but I don't have experience with
> RDF or PMF.

​cpptraj computes the radial distribution function. A PMF is a potential
of mean force -- basically the free energy along a reaction coordinate.
 Since the radial distribution function is, in essence, a probability
function, the negative logarithm of the RDF _is_ the PMF.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 04 2014 - 05:00:07 PDT
Custom Search