[gmx-users] bennet acceptance ratio

[Ahmet yıldırım]

Dear Prof.Shirts,

I have a question about your paper titled "An Introduction to Best
Practices in Free Energy
Calculations".There are two equation (equation 3 and equation 4) of Bennet
Acceptance Ratio in your paper.


Which equation does "Gromacs g_bar tool" use from your paper? If it uses
equation 3, then g_bar computes potential energy difference between two
states. This potential energy difference means free energy difference
between two states?
Also I saw the same equation on alchemistry.org

Another interesting thing, the dhdl.xvg files includes dh/dl values. And
when g_bar calculates the free energy, it uses these files (dHdl.xvg).
Whereas g_bar needs the potential energy differences between states/window?

H=U+K, where H:Hamiltonian, U:Potential energy, T:Kinetic energy. You know
g_bar gives it(Delta-G) on output screen. T=3/2kT, T=constant temperature,
then H=U right. Then dH equals to dU?

Thanks in advance

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