[gmx-users] PMF, Enthalpy, Entropy

Alex alexanderwien2k at gmail.com
Mon Mar 13 19:11:52 CET 2017

```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?

Any help is highly appreciated.

Best regards,
Alex
```