Molecular dynamics under constraints

This lecture delves into the development of molecular dynamics simulations under holonomic constraints, focusing on the numerical integration of Cartesian equations of motion. It covers the formulation of algorithms, application to molecular simulations, and comparison with generalized coordinates. The presentation includes insights on the historical background, the impact on large molecule simulations, and the relevance for molecular dynamics calculations. The instructor discusses the significance of the SHAKE method, equilibrium statistical mechanics, and the challenges of sampling different ensembles. The lecture also explores the constraints versus stiff bonds distinction and the Lagrange equations in Cartesian and generalized coordinates.