[gmx-users] FEP vs PMF

[Billy Williams-Noonan]

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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-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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