[gmx-users] FEP vs PMF

[Alex]

what I have as PMF itself has been already harvested from gmx wham.
Regards

On Mon, Nov 21, 2016 at 10:24 PM, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> You could also do WHAM analysis with gmx wham. :)
>
> On 22 November 2016 at 07:48, Alex <alexanderwien2k at gmail.com> wrote:
>
> > 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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