Re: [AMBER] free energy calculation of folding

From: Jason Swails <>
Date: Thu, 28 Jan 2016 11:55:17 -0500

On Thu, Jan 28, 2016 at 7:14 AM, Asmita Gupta <> wrote:

> Dear users,
> I performed an SMD simulation on a simple RNA duplex structure and
> calculated the associated PMF values using Jarzynski equality. From SMD
> trajectory, i have extracted structures at different stages of distortion.
> I removed the external restraints from these structures and performed
> relaxed conventional MD on them to see how many native contacts can be
> regained from each stage. Can you please suggest how i can monitor the
> free energy profiles of these relaxed simulations ?

​What do you mean "free energy profiles"? You can't map results from these
simulations back to what you got doing the Jarzynski averaging (at least
there's no way I'm aware of to do this, and I doubt it would be
straightforward if it did exist).

Also, your steered MD simulations are inherently non-equilibrium, which
means that you will need to discard part of the relaxation simulations
until you get back to the true free energy surface (i.e., back to
equilibrium). Then you can analyze those simulations like any other
unbiased MD simulation. You could histogram along a degree of freedom to
construct an unbiased PMF, but you would need sufficient sampling along the
entire reaction coordinate to converge a meaningful result (which, if you
could do, would have meant SMD was unnecessary to begin with).

But maybe I'm not understanding what you are trying to do...


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 28 2016 - 09:00:04 PST
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