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

Dr. Vitaly Chaban vvchaban at gmail.com
Mon Sep 23 15:23:31 CEST 2013

On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee <jongwha12 at postech.ac.kr> wrote:
> 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
> file.

This might be because of electrostatics treatment method. Use simple
cut-off scheme and specify a really large cut-off radius, which
exceeds the sum of the sizes of your binding particles.

I made tons of such comparisons, QM vs. MM. It works pretty well.

> 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.

The binding energy is an energy gain, dE, in the following reaction
A + B -> AB, dE

A, B, and AB are optimized geometries: in vacuum, in solvent or
anywhere. So, if a molecule changes its conformation during binding,
this energy gain/loss should be a part of the binding energy, I see no
methodological problem here.

Dr. Vitaly V. Chaban

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