[gmx-users] FEP vs PMF

Wed Nov 23 15:35:20 CET 2016

Thanks Justin.

Ok, in PMF it is not DDG, but in FEP as far as I know it is DDG (binding
free energy) when one complete the thermodynamic cycle as I have done here.

Then, what is the DDG in a PMF?

What could be comparable between "PMF and experiment" or between "FEP and
experiment"?

Thanks.

regards,
Alex

On Tue, Nov 22, 2016 at 9:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/21/16 4:30 PM, Alex wrote:
>
>> what I have as PMF itself has been already harvested from gmx wham.
>>
>
> This is not a DDG, it's just DG, the difference between the plateau
> (unbound) and minimum (bound).  That's the value you compare with the FEP
> result, though I'm not clear how one obtains a reasonable and converged
> value for the FEP in bound and unbound states.  PMF is a very
> straightforward method to do this.  FEP requires lots of other restraints,
> etc that have to be accounted for.
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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