AMBER Archive (2008)

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

From: David A. Case (
Date: Wed Apr 16 2008 - 16:26:13 CDT

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).


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to