I. Introduction to Computer Simulation

II. Molecular Mechanical Potentials (Forcefields)

A. Intramolecular (bonding) interactions

B. Nonbonded interactions

1. Electrostatic (Coulomb) interactions
   
2. London-van der Waals interactions
   

C. Hydrogen bonds

D. Constraints and restraints

E. Hydrophobic interactions

III. Methods for Simulating Large Systems

A. Nonbond cutoffs

1. Shifted and shifted force
   
2. Switching functions
   
3. Neighbor lists
   
4. Charge groups and switching atoms
   

B. Boundaries

1. Periodic boundary conditions
   
2. Stochastic forces at spherical boundary
   

C. Long-range forces

1. Ewald sums
   
2. Reaction field method
   

IV. Statistical Mechanics as Pertains to Simulations

A. Definitions: phase space, ensembles, probability densities, partition functions

B. Ensembles

1. Microcanonical ensemble
   
2. Canonical ensemble
   
3. Other ensembles
   

C. Ensemble averages and ergodicity

D. Fundamentals of molecular dynamics and Monte Carlo

V. Monte Carlo

A. Markov chain

B. Metropolis method

VI. Molecular Dynamics

A. Finite difference methods

1. Verlet algorithm
   
2. Velocity Verlet algorithm
   
3. Time step
   

B. Constraint dynamics

1. Fundamental concepts of constraint dynamics
   
2. RATTLE algorithm
   

C. Temperature: Maxwell-Boltzmann distribution of velocities

D. Initialization and equilibration

E. Temperature control

1. Velocity scaling
   
2. Andersen method
   
3. Nosé-Hoover dynamics
   

F. Ensembles

VII. Minimization Methods

A. Steepest descents

B. Conjugate gradient

C. Newton-Raphson

D. Comparison of methods

E. Simulated annealing

F. Vibrational frequencies

VIII. Free Energy (Relative)

A. Perturbation method

B. Thermodynamic integration

C. Finite difference thermodynamic integration

IX. Quantum Chemistry

A. Hartree-Fock molecular orbital theory

B. Correlation

C. Semiempirical methods

D. Density functional theory

E. Valence bond theory

X. Mixed Quantum Mechanical and Molecular Mechanical Potentials (QM/MM)

A. Fundamental concepts of QM/MM methods

B. Empirical valence bond method

XI. Quantum Dynamics

A. TDSCF

B. MC-TDSCF

C. Semiclassical methods

1. Gaussian wavepackets
   
2. Path integral methods
   

XII. Mixed Quantum/Classical Molecular Dynamics

A. Adiabatic methods

B. Mixed state/TDSCF methods

C. Surface hopping methods

D. Path integral methods