# [gmx-users] PMF, Enthalpy, Entropy

Justin Lemkul jalemkul at vt.edu
Tue Mar 14 13:24:00 CET 2017

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On 3/13/17 2:11 PM, Alex wrote:
> Hello all,
>
> I have the calculated the PMF for the adsorption of a peptide into a solid
> surface using umbrella sampling, a 60 ns of NVT-production for each window
> was considered so that the PMF is well converged.
> Now, following a nice paper by Prof. van der Spoel "*DOI: *10.1021/ct400404q"
> and in the same fashion as (Fig.4 of the paper) I also would like to
> calculate the enthalpy and entropy along the reaction coordinate of the PMF.
>
> To do so, for each window I calculated the enthalpy via "gmx energy
> case.edr ... " and selected "potential" as in the NVT ensemble, enthalpy
> and potential are identical. And then using the Gibbs free energy equationI
> calculated the "- [T*\Delat S]", so that at the end I have all of three
> quantity as a function of the reaction coordinate.
>
> I do not know why the PMF and Enthalpy (potential) are not in the same(or
> close) order of magnitude.  The trusted PMF is around "60 kcal/mol=251.0
> kj/mol" while the Enthalpy is something like "-1557.92e+03 kj/mol", I was
> wondering if the unit of enthalpy (potential) here is really meaningful?
> Does the enthalpy's unit is "kj/mol" or "j/mol", as a division to "1000"
> could give more sense to it?
>
> I know the convergence of the enthalpy is hard respect to the convergence
> of the PMF, but, here the convergence is not the matter, rather the unit of
> enthalpy is the matter.
>
> Here is the potential average of enthalpy (potential) for one of the window
> via gmx energy:
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ------------------------------------------------------------------------------------
> Potential                -1.5579e+06         14    726.909    -14.203
> (kJ/mol)
>
> Which of the "Err,Est" or "Tot-Drift" is the error bar for enthalpy
> (potential)?
>
> And finally, what does the "normalization to zero at infinite distance"
> means?
>

Because if you're just calculating the enthalpy of a system, that includes
(presumably) a ton of solvent-solvent interaction energy that doesn't affect the
binding free energy.  So the enthalpy of the window in which the binding species
are at the maximum distance is set to zero, e.g. the reference of the unbound
state.  Then all subsequent enthalpy values are offset by the same amount so you
have DeltaH and not just H.

If I've messed that up, maybe David will correct me; I read that paper but it's
been a while so I may be wrong on teh details.

-Justin

--
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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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