ABF calculation - normalization of the PMF

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Sat Sep 19 2009 - 16:59:46 CDT

• 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 ]

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 ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:17 CST