Re: ABF calculation - normalization of the PMF

From: Jerome Henin (
Date: Sun Sep 27 2009 - 16:36:23 CDT

Hi Giovanni,
To get the dimerization free energy, you'll need an integral over the
domain of the pmf corresponding to the dimer. There is an example
although Equation (3) in there is missing a factor 2 to account for
the symmetry of the homodimer (see ref. 50 in that paper).

2009/9/19 Giovanni Bellesia <>:
> Hi all,
> I am trying to calculate the dimerization free energy of a short peptide
> using the ABF method.
> My 'reaction coordinate' is the COM-distance between the two peptides.
> I'm currently going through the JCP papers where the ABF method is
> introduced and evaluated.
> In particular, reading about the implementation of the method in JCP 121(7),
> 2904 (2004) I found at
> the end of Section IIB2 the comment about the normalization of the PMF via
> subtraction of the
> "Jacobian correction" from the free energy profile.
> Here's my question (just to be sure I understood correctly):
> Shall I subtract from the free energy profile the quantity
> k_B * T * ln |J|
> with |J| defined as in formula (16) ?
> Thanks for your help
> Best
> Giovanni

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