[gmx-users] PMF decompostion

Christopher Neale chris.neale at alum.utoronto.ca
Fri Dec 2 23:40:43 CET 2016

PMF gives free energy, which can not be decomposed into VDW and Q without leaving a remainder, though I guess that doesn't affect your question. Enthalpy is simply the average potential energy plus the pressure volume component. So you can compute average potential energy VDW and Q components at each umbrella if you want (from the .edr files with gmx energy). Be aware that the statistical uncertainty on the enthalpy tends to be greater than the relevant differences on achievable simulation timescales (i.e., convergence is hard), so you'll want to evaluate error explicitly.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Salman Zarrini <salman.zarrini at gmail.com>
Sent: 02 December 2016 17:16:15
To: gmx-users at gromacs.org
Subject: [gmx-users] PMF decompostion

Dear gromacs user,

I was wondering if something has been already implemented in gromacs to
make possible the potential of mean force (PMF) decomposition into the van
der waals and electrostatic energies?

Would you please also let me know if the desolvation energy originated from
protein-water or in my case solid surface-water interaction, will be taken
into account automatically when one calculates the PMF in aqueous solution
in gromacs?


Salman Zarrini
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