[gmx-users] FEP vs PMF

Billy Williams-Noonan billy.williams-noonan at monash.edu
Mon Nov 21 22:24:11 CET 2016


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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> > > >
> > > >
> > > > --
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-- 
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