[gmx-users] Potential energy in Zwanzig relationship

[Michael Shirts]

https://github.com/MobleyLab/alchemical-analysis

Takes gromacs dhdl.xvg output and calculate free energies by many different
methods, including BAR, MBAR and Zwanzig.  See
http://www.alchemistry.org/wiki/Main_Page for more information.

On Fri, Feb 10, 2017 at 5:26 AM, gozde ergin <gozdeeergin at gmail.com> wrote:

> Dear all,
>
> I run thermodynamic integration simulation with gromacs and got the free
> energy by g_bar command.
> I also would like to estimate this free energy by using Zwanzig
> relationship of \DeltaG = -RT ln (<exp{-\Delta U_(ij)/RT}>_i
> Here U is the potential energy, right?
> However the results that I am getting with g_bar (82 kcal/mol) and with
> Zwanzig equation (406 kcal/mol) are totally different.
> Do anyone has an idea why I am getting that different results?
>
> Bests
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