PyMM

PyMM performs QM/MM simulations using the perturbed matrix method to compute perturbed electronic properties from classical atomic trajectories and unperturbed electronic properties of ground and electronically excited states.

Key Features:

• Perturbed Matrix Method: Implements the perturbed matrix method for QM/MM treatment of electronic perturbations in molecular systems.
• Input Requirements: Requires a classical atomic trajectory of the entire system and unperturbed electronic properties of the ground and electronically excited states.
• Output Capabilities: Computes perturbed electronic properties including electronic excitation energies, transition dipole moments, and eigenvectors describing perturbed electronic states.
• Perturbed Eigenvector Behavior Analysis: Analyzes changes in electronic eigenvectors induced by environmental perturbations.
• Electronic Absorption Spectrum Calculation: Calculates electronic absorption spectra from perturbed excitation energies and transition dipole moments.
• Free Energy Difference Estimation Along Reaction Coordinates: Estimates free energy differences along reaction coordinates using perturbed electronic properties.

Scientific Applications:

• Electronic Spectroscopy: Simulation of electronic absorption spectra to study electronic transitions in molecular systems.
• Reaction Thermodynamics: Estimation of free energy differences along reaction coordinates for chemical reactions.
• Modeling Electronic Interactions: Modeling electronic interactions in chemical reactions, materials science, and biological processes at the quantum level.

Methodology:

Applies the perturbed matrix method to classical atomic trajectories and unperturbed ground- and excited-state electronic properties to compute perturbed electronic states, excitation energies, transition dipole moments, and eigenvectors, enabling analysis of perturbed eigenvector behavior, calculation of electronic absorption spectra, and estimation of free energy differences along reaction coordinates.