[gmx-users] Potential energy in Zwanzig relationship

[gozde ergin]

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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