**From:** Giovanni Bellesia (*gbellesia_at_chem.ucsb.edu*)

**Date:** Sat Sep 19 2009 - 16:59:46 CDT

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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

**Next message:**Jagan Mohan: "Regarding Lipid Order Parameter Calculation"**Previous message:**Sebastian Stolzenberg: "FEP to replace a PMF calculation?"**Next in thread:**Jerome Henin: "Re: ABF calculation - normalization of the PMF"**Reply:**Jerome Henin: "Re: ABF calculation - normalization of the PMF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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