[gmx-users] Potential energy in Zwanzig relationship

[Michael Shirts]

Take a look at how the python code does EXP.  The information you want is
in the dhdl.xvg. Look at the documentation for this file, and read the
header.  Come back with specific questions about the file if the header and
documentation are not enough.

On Fri, Feb 10, 2017 at 6:47 AM, gozde ergin <gozdeeergin at gmail.com> wrote:

> Dear Michael.
>
> Thanks for the reply. I have already used this python code however I would
> like to calculate myself by using the potential energies.
> Because I need to reweigh the free energy by using exponential
> re-weighting technique.
> > On 10 Feb 2017, at 14:44, Michael Shirts <mrshirts at gmail.com> wrote:
> >
> > 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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