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

**Date:** Tue Sep 29 2009 - 10:40:01 CDT

**Next message:**Axel Kohlmeyer: "Re: g(r) GUI Plugin problem"**Previous message:**Branko: "g(r) GUI Plugin problem"**In reply to:**Jerome Henin: "Re: ABF calculation - normalization of the PMF"**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 Jerome,

thanks for your reply.

I am aware of the JACS paper and I will certainly use Equation 3 to

calculate the dimerization free energy.

However, my problem right now is with the larger values of the reaction

coordinate: the free energy profile is

flat but it does not "converge" to zero.

In more details, I have two free energy profiles calculated from two

independent simulations starting from two

different stable conformations of the peptide dimer (see Biophysical

Journal 96(3), 875-886 (2009)).

The idea is to compare the two curves and check the relative stability

of the two dimers.

As far as I understand, to make the comparison I should "normalize" the

two curves so that they both ==> 0 when

the reaction coordinate is large (and the profile is flat).

The normalization procedure in JCP 121(7), 2904 (2004) for some reason

"works" only for one of the two curves.

Alternatively I was thinking about simply calculate (for both curves)

the average value of the free energy within the flat (right) section of

the profile and then shift the curves accordingly.

Is this correct ?

Best

Giovanni

*> 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
*

*>>
*

*>>
*

*>
*

*>
*

-- ------------------------------------------ Giovanni Bellesia Department of Chemistry and Biochemistry University of California, Santa Barbara Santa Barbara, California 93106-9510, USA. Email: gbellesia_at_chem.ucsb.edu Phone: 805 893 2767 Web: http://www.chem.ucsb.edu/~gbellesia/ ------------------------------------------

**Next message:**Axel Kohlmeyer: "Re: g(r) GUI Plugin problem"**Previous message:**Branko: "g(r) GUI Plugin problem"**In reply to:**Jerome Henin: "Re: ABF calculation - normalization of the PMF"**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 - 15:53:19 CST
*