AMBER Archive (2008)

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

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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).

...dac

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• Next message: Tom Darden: "Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms"
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