[gmx-users] FEP vs PMF

[Billy Williams-Noonan]

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
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> > > >
> > > > *LinkedIn Profile
> > > > <http://www.linkedin.com/profile/preview?locale=en_US&
> > > > trk=prof-0-sb-preview-primary-button>
> > > > **|*   +61420 382 557
> > > >
> > > > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > > > Royal Parade, Parkville, 3052
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> >
> > --
> > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> > <http://www.linkedin.com/profile/preview?locale=en_US&
> > trk=prof-0-sb-preview-primary-button>
> > **|*   +61420 382 557
> >
> > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > Royal Parade, Parkville, 3052
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



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

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052