Re: AMBER: PMF calculation for binding constant or rate constant?

From: David A. Case <>
Date: Wed, 16 Apr 2008 14:26:13 -0700

On Wed, Apr 16, 2008, Catein Catherine wrote:
> I also noticed that some publication rescale the WHAM result to make the
> level off (in this case is 8 kcal/mol) to zero, while the minimum was set
> as a negative values (in this case is -8 kcal/mol). Is it necessary to be
> done? Why?

PMF's are only relative energies, so adding a constant has no physical effect,
and was probably done for convenience (setting the dissociated state
arbitrarily to zero).


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Received on Fri Apr 18 2008 - 21:19:54 PDT
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