[gmx-users] FEP vs PMF

Alex alexanderwien2k at gmail.com
Mon Nov 21 21:48:52 CET 2016

```Yes, indeed the thermodynamic cycle is closed.
If I am not wrong an integration like below should be done over PMF in
order to get adsorption energy which is equivalent to \Delta\Delta G in FEP.

\Delta F_{ads} = -K_{B}*T Log[ Integrate(exp(-PMF/K_{B}*T)/L)]

in which L is the interval where PMF starts to its plateau.

Regards,

Alex

On Mon, Nov 21, 2016 at 9:24 PM, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> Assuming you have closed the thermodynamic cycle correctly (which no doubt
> you have), then I would think you have just measured the same quantity with
> absolute FEP as you did using PMF with umbrella sampling.  You have the
> same dG of binding, but with different methods. :-)
>
> Cheers,
>
> Billy
>
> On 22 November 2016 at 07:19, Alex <alexanderwien2k at gmail.com> wrote:
>
> > Hi Billy,
> >
> > Thanks for your response,  whatever you want to call it, it is the
> > difference between the free energies of the system in bonded(or complex)
> > and unbounded(or ligand) states, so it is [\Delta G_{bounded} - \Delta
> > G_{unbounded}].
> >
> > Regards,
> > Alex
> >
> > On Mon, Nov 21, 2016 at 9:06 PM, Billy Williams-Noonan <
> > billy.williams-noonan at monash.edu> wrote:
> >
> > > If you're calculating an absolute free energy of dissociation, why
> would
> > it
> > > be a "\Delta\Delta G"?
> > >
> > > Kind Regards,
> > >
> > > Billy
> > >
> > > On 22 November 2016 at 04:12, Alex <alexanderwien2k at gmail.com> wrote:
> > >
> > > > Dear gromacs user,
> > > >
> > > > For a reaction (dissociation of a amino acid from a solid surface in
> > > > aqueous solution), I have calculated the "\Delta\Delta G" by free
> > energy
> > > > perturbation method in alchemical analysis, and also for the same
> > > reaction
> > > > I have calculated the PMF by umbrella sampling.
> > > >
> > > > I was wondering how I can compare these two results together?
> > > >
> > > > Thanks,
> > > >
> > > > Regards,
> > > > Alex
> > > > --
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```