Module 1: Intermolecular Interactions

Lecture 2: Charge – Charge Interactions

Lecture 3a: Molecular Dipoles

Lecture 3b: Charge–Dipole Interactions

Lecture 4: Dipole–Dipole Interactions

Lecture 5: Quadrupole Interactions

Lecture 6: Charge – Induced-Dipole Interactions

Lecture 6: Steric Interactions

Lecture 7: Hydrogen Bonding Interactions

Lecture 8: Rotational Averaging

Molecular Mechanical Force Fields and Parameterization

Module 2: Classical Statistical Thermodynamics

Lecture: The Theory of Classical Statistical Thermodynamics

Lecture on Population of Conformational States

Lecture 8: The Monte Carlo Algorithm

Lecture on Monte Carlo Simulations

Nonbonded Cutoffs and Periodic Boundary Conditions

Molecular Dynamics Part 1

Molecular Dynamics Part 2

Molecular Dynamics of the Canonical Ensemble

Radial Distribution Functions

Thermodynamic Properties from Molecular Simulations

Module 3: Diffusion

Diffusion

Diffusion Limited Reactions

Module 3: Free Energy Methods

Free Energy Perturbation

Lecture on Thermodynamic Integration

Lecture on Ion Solvation and the Born Model

Free Energies Along a Reaction Coordinate

The Potential of Mean Force

Umbrella Sampling

Interfaces, Hydrophobicity, and Membranes

Vapor-Liquid Interfaces

Hydrophobic Effect

Membrane Permeation

Protein–Ligand Binding

Module 4: Molecular Simulation of Biophysical Chemistry

Lecture on Protein Structure

Lecture on Protein Folding

Lecture on Protein Folding Dynamics

Lecture: The Potential of Mean Force