Molecular Dynamics Simulations: Force Fields and Parameterization

This lecture covers the fundamentals of molecular dynamics simulations, focusing on force fields and parameterization. It discusses potential energy surfaces, first-principles and classical MD, empirical force fields, water models, biomolecular force fields, bonded and nonbonded terms, and standard force fields. The instructor explains the choice of interaction sites, the analytic form of interaction potentials, and the limitations of empirical force fields. Various MD packages are introduced, and the process of manual and automated parameterization is detailed, including force matching and iterative Boltzmann inversion.