Molecular Mechanics Induction Energy Calculator

[shehan807]

Description

The goal of this program is to simplify the calculation of the induction energy component using a SAPT-based, ab initio polarizable molecular dynamics force field function form. The theoretical formalism is elaborated in Shehan's U_pol Repo. In essence, each relevant atom, considered a "core" atom, is paired with a "shell" or Drude particle through which induced-dipole/induced-dipole interactions manifest. The added functions have been verified to reproduce polarization energies in OpenMM with the advantage of a Drude SCF optimization scheme implemented using JAX.

Todos

Notable points that this PR has either accomplished or will accomplish.

• match input/output schemes between nmer dictionary and Uind function in force_field.py
• verify large scale dimer/trimer energies for imidazole, pyrazole, and acetic acid

Questions

• Where would the drudeOpt function go?
• What is the best way to atom type Psi4 atoms and/or create Drude particle properties based on conventional SAPT-FF atom typing schemes?

Status

• Ready to go