**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Sun Sep 27 2009 - 16:36:23 CDT

**Next message:**Thomas C. Bishop: "a timing question; 206,000atoms > 512cores not good"**Previous message:**Jerome Henin: "Re: FEP to replace a PMF calculation?"**In reply to:**Giovanni Bellesia: "ABF calculation - normalization of the PMF"**Next in thread:**Giovanni Bellesia: "Re: ABF calculation - normalization of the PMF"**Reply:**Giovanni Bellesia: "Re: ABF calculation - normalization of the PMF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

there:

http://pubs.acs.org/doi/abs/10.1021/ja050581y

although Equation (3) in there is missing a factor 2 to account for

the symmetry of the homodimer (see ref. 50 in that paper).

Jerome

2009/9/19 Giovanni Bellesia <gbellesia_at_chem.ucsb.edu>:

*> 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.
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*>
*

*> I'm currently going through the JCP papers where the ABF method is
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*> introduced and evaluated.
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*> In particular, reading about the implementation of the method in JCP 121(7),
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*> 2904 (2004) I found at
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*> the end of Section IIB2 the comment about the normalization of the PMF via
*

*> subtraction of the
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*> "Jacobian correction" from the free energy profile.
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*>
*

*> Here's my question (just to be sure I understood correctly):
*

*> Shall I subtract from the free energy profile the quantity
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*> k_B * T * ln |J|
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*> with |J| defined as in formula (16) ?
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*>
*

*> Thanks for your help
*

*>
*

*> Best
*

*>
*

*> Giovanni
*

*>
*

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