Re: [AMBER] umbrella sampling method or steered MD should be used?

From: <steinbrt.rci.rutgers.edu>
Date: Thu, 20 May 2010 03:41:56 -0400 (EDT)

Hi everyone

> I would like to determine the potential energy changes for drug binding
> the receptor and for the drug remove from the receptor. In practice, the
> PMF of binding should be lower than that of removing, otherwise no
> drug-receptor complex could be formed.

unless I misunderstand something here, the PMF in both directions should
be equal no matter what process you study, except for unwanted hysteresis
effects. The free energy of binding should be given by the difference in
your two curve endpoints.

Kind Regards

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu May 20 2010 - 01:00:03 PDT
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