On Thu, Sep 4, 2014 at 7:37 AM, Fabian Glaser <fglaser.technion.ac.il>
wrote:
> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 04 2014 - 05:00:07 PDT
