Re: [AMBER] PMF calculations in Amber 10

From: Jason Swails <>
Date: Wed, 23 Mar 2011 16:32:03 -0700

Steered MD and umbrella sampling are two *different* ways of calculating a
PMF along a reaction coordinate. Steered MD is an inherently
non-equilibrium driven MD that does not, in general, sample from the true
free energy surface. However, Jarzynski's equation relates these
non-equilibrium profiles to the true PMF (in a classical stat mech way).
Umbrella sampling DOES sample from the true free energy surface (of the
hamiltonian modified by a biassing umbrella potential). There are
advantages to each over the other, and neither method is particularly
cheaper than the other in general.

You can find tutorials for steered MD in that
uses the NCSU functionality. You can also perform steered MD and umbrella
sampling via the NMR restraint facility, but choosing a harmonic shape for
the flat-well potentials. See chapter 6 of the Amber 10 (or Amber 11)
manual for instructions on setting up NMR restraints.

Hope this helps,

On Wed, Mar 23, 2011 at 4:17 PM, Mahmoud Soliman <>wrote:

> Dear amber users,
> I wonder can I do PMF calculations for some nucleophilic attack reaction
> in
> enzyme using amber 10. I used to do that in dynamo (PMF/umbrella
> sampling)
> but I am interested to try Amber since it offers higher level methods
> (DFTB)
> for the QM part which dynamo doesn't. I looked through the tutorials and
> I
> found something called streed MD (SMD), is it the same concept? any other
> tutorials/examples I can follow??
> Thanks
> Mahmoud
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 23 2011 - 17:00:02 PDT
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