AMBER Archive (2007)

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

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri May 04 2007 - 13:05:09 CDT

Hi,

thanks for pointing this out David, I fully agree that what I said is only
true in the limit of full equilibration, which is hard enough to achieve
for a single bound ligand conformation and quite possibly impossible for
many dissociation processes. I guess one can sum it up that PMF's give you
an upper bound of the activation free energy that may be a very bad
estimate but should converge to the true one in the limit of infinite
sampling. Since the rate would depend exponentially on E(activation),
calculated rates would be even less reliable.

Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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