**From:** Mert Gür (*gurmert_at_gmail.com*)

**Date:** Wed Dec 09 2009 - 14:19:42 CST

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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

**Next message:**David Tanner: ""-Wno-long-double" linking error"**Previous message:**gurunath katagi: "gradual increase in the temperature after minimization"**Next in thread:**Pu Tian: "Re: Free Energy Calculation of a protein"**Reply:**Pu Tian: "Re: Free Energy Calculation of a protein"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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