Free Energy Calculation of a protein

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Dec 09 2009 - 14:19:42 CST

Dear all,
To start with I am familliar with SMD,WHAM, ABF,FE . So my problem is not
regarding the evaluation of a PMF or free energy change.
I am interested in evaluating the free energy of a protein at specified
temperature and pressure.

Let assume that I have a very long simulation so that I have enough sampling
in the phase space.(I know this is a hard job)

For an T,V,N simulation I should be able to evaluate the Helmholtz Free
Energy as

F=-kT ln[ <exp(b E_i)> ]

What I do here is to simply evaluate exp(b E_i) for every snapshot(i) and
then take the average of them.

Now when I perform an T,P,N ensemble I got stucked. Because I have to
evaluate the Gibbs Free energy with the same methodology as

G=-kT ln[ <exp( b [E_i+P V_i] )> ]

But what is the volume of the protein at the ith snapshot in Namd? I know
that the volume of the water box fluctuate, but how about the volume of the
protein?
Or is the fluctuation in the proteins volume so small that we can ignore it.
Best,
Mert

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