[gmx-users] bennet acceptance ratio

[Ahmet yıldırım]

Hi,

Maybe Justin can respond my questions!

I think g_bar uses two equations when it calculate free energy?

1) First equation: To calculate free energy difference between two states,
which equation does g_bar? It uses Delta_F=-kBTln(Uj/Ui), right? Where
Delta_F:Free energy difference between two states, kB:Boltzman constant,
T:Temperature, Ui:Potential energy of the real/starting system,
Uj:Potential energy of final system

2.) Second equation:Then why does g_bar  the equation 4 in Schirts' paper
"An Introduction to Best Practices in Free Energy Calculations"?

Thanks in advance

2014-11-04 4:54 GMT+01:00 Michael Shirts <mrshirts at gmail.com>:

> 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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Ahmet Yıldırım