[gmx-users] bennet acceptance ratio
Ahmet yıldırım
ahmedo047 at gmail.com
Wed Nov 5 00:50:30 CET 2014
Hi,
Interesting! Most people use g_bar but nobody says anything.
2014-11-04 9:33 GMT+01:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
> 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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Ahmet Yıldırım
>
--
Ahmet Yıldırım
More information about the gromacs.org_gmx-users
mailing list