[gmx-users] FEP vs PMF

Tue Nov 22 21:20:18 CET 2016

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

==================================================