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 -- 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-requ...@gromacs.org.
