Re: AMBER: Potential of mean force, how to calculate rate of dissociation?

From: Thomas Steinbrecher <>
Date: Fri, 4 May 2007 08:49:03 -0700 (PDT)

Hi everyone,

I haven't much experience with US and WHAM analysis, but the way I always
thought about
it was that the PMF is a very nice thing because it gives you not only a
free energy difference between two endstates (the binding constant) but
also the maximum of the free energy curve between them and thus the
activation free energy for the process. From that you could easily
calculate the back and forth rates and even look at the conformations at
the maximum that pose the critical chokepoint for dissociation.

Someone please correct me if I'm wrong,

Kind Regards,


Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun May 06 2007 - 06:07:30 PDT
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