[gmx-users] bennet acceptance ratio

Michael Shirts mrshirts at gmail.com
Tue Nov 4 04:54:51 CET 2014

I didn't write the g_bar script, so I can't answer all of the questions
about it.

Equation 3 in that paper is a general equation true for any weight function
alpha.  It is not Bennett's acceptance ratio. Equation 4 is the one that's
actually Bennett's equations, which chooses an alpha that gives a minimum
variance answer.

So you'll have to ask others about the exact usage of g_mbar. The tutorials
on the Alchemistry.org web page show how to use the tool I wrote for
analyzing free energy calculations with gromacs.  Gromacs has plenty of
functionality for printing out the energy differences between states.

On Wed, Oct 29, 2014 at 8:03 AM, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:

> 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
> --
> Ahmet Yıldırım
> --
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