Re: [AMBER] Doubt regarding the metadynamics simulation

From: Jason Swails <>
Date: Thu, 17 Oct 2013 12:21:20 -0400

On Thu, Oct 17, 2013 at 12:08 PM, Ravi Tripathi <>wrote:

> Dear Mr. Adrian,
> Yes, I posted my question to amber list only. Thanks alot for your kind
> reply.
> But the doubt still remains the same : If the Gaussian are added to the
> PES then how we have the measures of FES from the metadynamics simulation.
> The reconstructed surface should be the PES not FES.

Statistical mechanics provides the machinery to translate potential
energies into free energies given an ensemble of states. I believe there
are papers on metadynamics that show how free energies are computed from
metadynamics simulations. A good introduction (and source of references)
is (This was
linked to on the Wikipedia page for Metadynamics)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Oct 17 2013 - 09:30:04 PDT
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