This page will contain PDF files for the class notes. They are posted after we complete a one- to-two week section of material:
- Part 1 – Introduction to force fields: bonds, bends, torsions, out-of-plane bends, cross-terms, electrostatics and van der Waals interactions.
- Part 2 – More on force fields: Hydrogen Bond potentials, Constraints, Restraints, and water models.
- Part 3 – Conformational searching, Levinthal’s Paradox, refinement (minimization methods), finding transition states, nudged elastic band methods
- Part 4 – Methods for Simulating Large Systems: non-bonded cutoffs and corrections, neighbor lists, periodic boundaries, minimum vs. explicit images, spherical boundary conditions
- Part 5 – Long range interactions, Conditional Convergence, The Ewald Sum
- Part 6 – Classical mechanics, integrators, balance and constitutive equations, diffusion, mean squared displacement, velocity autocorrelation functions, Einstein and Green-Kubo formulas for transport properties.
- Part 7 – Ensembles, time averages, constant temperature and constant pressure methods, constraints, rigid body motion.
- Part 8 – Simplification methods: Implicit solvent and Langevin dynamics, United atom (UA) models, Statistical Potentials and Coarse Graining, Gay-Berne models for liquid crystals, measuring orientational ordering.
- Part 9 – QM/MM, electronegativity equalization and fluctuating charge approaches, CPMD.