Molecular Dynamics Simulations: Basics and Algorithms

This lecture introduces the basics of molecular dynamics simulations, comparing Monte Carlo and Molecular Dynamics methods, discussing ensemble properties via MD, different formulations of classical mechanics (Newtonian, Lagrangian, Hamiltonian), numerical integration of EOMs using Position Verlet and Leap Frog algorithms, and the importance of energy conservation and constants of motion. It also covers the choice of time step, constraints in multiple time step integrators, and constraint algorithms. The instructor emphasizes the use of intrinsic dynamics to generate relevant configurations and the conservation of energy in Hamiltonian systems.