From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
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
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.
>
> 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
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:19 CST