[gmx-users] Calculation of binding enthalpy in vacuum

[Dr. Vitaly Chaban]

Dear John -

I think you can achieve the goal even faster if you just define two
groups, such as MOL1 and MOL2 in MDP and then see the interaction
energy between them using g_energy.

5% is a decent agreement. Usually, even basis set superposition error
is larger (if you include this correction).

Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 9:32 AM, Jong Wha Lee <jongwha12 at postech.ac.kr> wrote:
> 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
> g_energy.
>
>
>
> 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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