**Main Text:**

*Molecular Modelling: Principles and Applications*, by Andrew Leach

**Other Useful Texts:**

See the Book List for a list of other helpful texts. We will be referring most frequently to Frenkel & Smit when the primary text doesn't contain a topic of interest.

**Course Outline:**

- Introduction
- Force fields and molecular representations of matter
- Intramolecular (bonding) interactions
- Non-bonded interactions
- Electrostatic (Coulomb, Dipolar) interactions
- London (van der Waals) interactions

- Hydrogen bonds
- Constraints and Restraints
- United atom and other coarse-grained approaches
- Non-pairwise interactions
- Just how accurate are force fields?

- Methods for Simulating Large systems
- Non-bonded Cutoffs
- Shifted potential and shifted force
- Switching functions
- Neighbor lists

- Boundaries
- Periodic Boundary conditions
- Stochastic forces at spherical boundary

- Long-range interactions
- The Ewald Sum
- The Reaction field method
- Real-space methods

- Non-bonded Cutoffs
- Energy Minimization and related analysis techniques
- Steepest descent
- Conjugate gradient
- Newton-Raphson
- Comparison of methods
- Advanced techniques: Simulated Annealing, Branch-and-bound, simplex
- What's the big deal about the minimum anyway?

- Introduction to Equilibrium Statistical Mechanics
- Phase space, ergodicity, and Liouville's theorem
- Ensemble theory, thermodynamic averages
- Microcanonical Ensemble
- Canonical Ensemble
- Other ensembles

- Statistical mechanics of fluids

- Monte Carlo
- MC integration and Markov chains
- The Metropolis method
- Biased MC

- Molecular Dynamics
- Classical mechanics: equations of motion
- Finite Difference methods
- Verlet algorithm
- Velocity verlet
- The Time step: practical issues
- Multiple time-step algorithms

- Constraint Dynamics
- Fundamental concepts
- SHAKE and RATTLE

- Temperature: Maxwell-Boltzmann distribution of velocities
- Temperature control
- Velocity scaling
- Andersen's method
- Nose-Hoover dynamics

- Calculating properties from MD trajectories
- Hybrid MC

- Free Energy
- Perturbation methods
- Thermodynamic integration

- Brownian dynamics and the Langevin Equation