Hello Dr. Tyler,
Thank you for the information you have provided. It clears my mind
regarding the difference between solvation energy and excess chemical
potential.
Cheers, and stay strong!
Alexis Azucena
Instructor
School of Technology | University of the Philippines Visayas
+639175841130
agazucena.up.edu.ph
On Tue, Mar 1, 2022 at 3:36 AM tluchko <tluchko.protonmail.com> wrote:
> Hi Alexis,
>
> The excess chemical potential is equal to the Gibbs/Helmholtz solvation
> *free* energy in 3D-RISM, not the solvation energy. I.e., it includes both
> the solvation energy and entropy. The solvation free energy is the most
> commonly used output from implicit solvent models.
>
> The solvation energy (rism_solvationEnergy) is described in section 7.1.3
> of the Amber 21 manual. It is composed of the solute-solvent interaction
> potential energy (rism_solventPotentialEnergy) and the solvent
> reorganization energy (not reported). The solute-solvent potential energy
> is always reported, but you need to use the `--entropicDecomp` flag to get
> the solvation energy and entropy.
>
> You can find more on the equivalence of the chemical potential, Helmholtz
> free energy and Gibbs free energy in
>
> Chong S-H, Ham S (2015) Thermodynamic-Ensemble Independence of Solvation
> Free Energy. Journal of Chemical Theory and Computation, 11(2):378–380.
> https://doi.org/10.1021/ct500876x
>
> and on solvation energy and entropy in
>
> Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T (2016)
> Small molecule hydration energy and entropy from 3D-RISM. Journal of
> Physics: Condensed Matter, 28(34):344002.
> https://doi.org/10.1088/0953-8984/28/34/344002
>
> Hope this helps,
>
> Tyler
>
> Sent with ProtonMail Secure Email.
>
> ------- Original Message -------
>
> On Saturday, February 26th, 2022 at 6:52 PM, Alexis Azucena <
> agazucena.up.edu.ph> wrote:
>
> > G
> >
> > Greetings!
> >
> > I have a question for AMBER users who have some knowledge regarding
> 3DRISM.
> >
> > My goal is to find the solvation Gibbs energy, and I have already
> conducted
> >
> > a 3DRISM analysis using `rism3d.snglpnt`. An output will generate data of
> >
> > `rism_excesssChemicalPotential` and `rism_solvationEnergy`. As I read the
> >
> > Amber 2021 Reference Manual, it stated that the excess chemical potential
> >
> > is equal to Gibbs solvation energy (please see section 7.1.2 page 112).
> My
> >
> > question is, what is the RISM solvation energy that I've got in my
> >
> > analysis? Is it different from the Gibbs solvation energy?
> >
> > I hope someone can answer my inquiry. Thank you, and stay safe!
> >
> > Alexis
> >
> > _______________________________________________
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> >
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> >
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Received on Mon Feb 28 2022 - 18:00:02 PST
