[gmx-users] Re: Re: Calculation of binding enthalpy in vacuum

Jong Wha Lee jongwha12 at postech.ac.kr
Mon Sep 23 14:40:43 CEST 2013

Dear Vitaly,


Thank you for your suggestion.


I have also tried calculating interaction energies by specifying energygrps
in .mdp file, but calculated energies deviate greatly from QM calculated
energies and experimental results. I suspect that the structure of each
component in complex differs from the structures when they were alone,
because this will lead to a deviation in equilibrium binding enthalpy from
the interaction energies that is calculated with energygrps line in .mdp


My guest of interest have two charges at a short distance, which is very
unfavorable and the charges will try to be furthest apart. However, my host
molecule can stability the charges via oppositely charged groups, and so now
the guest molecule forms a bent structure. In this case, shouldn't the
change in energy due to the different conformation of the guest be taken
into account, to discuss equilibrium binding enthalpy? I feel maybe this
wouldn't be well represented with interaction energies.

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