[gmx-users] Calculation of binding enthalpy in vacuum

Jong Wha Lee jongwha12 at postech.ac.kr
Mon Sep 23 09:32:55 CEST 2013

Dear Gromacs users,


I’m trying to calculate the binding enthalpy of a host molecule with a
guest molecule in vacuum. I cannot perform QM calculations because some
systems I’m studying are too large.


I know that free energy calculations are possible with Gromacs, but they
require some cautions.


Instead of calculating free energies, I have subtracted the total energy of
the guest (△EG) and the host (△EH) from the total energy of the complex
(△EC). In other words,


△E = △EC - △EH - △EG, where all energies are total energy obtained from


In this case, would the calculated △E be the binding enthalpy in vacuum
(gas phase)?


I’ve tried QM calculations, and the △E obtained with Gromacs matches QM
calculations in ~ 5% range. But I’m still unsure on how proper this method
is. Could you advise me on this?


Thank you in advance, 


John Lee

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