Contents

• Contents
• Introduction
  • The role of computer experiments
    • But is it theory or experiment?
  • What is molecular dynamics?
  • Historical notes
  • Today's role of molecular dynamics
  • Limitations
    • Use of classical forces
    • Realism of forces
    • Time and size limitations
• The basic machinery
  • Modeling the physical system
    • The Lennard-Jones potential
    • Potential truncation and long-range corrections
  • Periodic boundary conditions
    • The minimum image criterion
    • Geometries with surfaces
  • Time integration algorithm
    • The Verlet algorithm
    • Predictor-corrector algorithm
• Running, measuring, analyzing
  • Starting a simulation
    • Starting from scratch
    • Continuing a simulation
  • Controlling the system
  • Equilibration
  • Looking at the atoms
  • Simple statistical quantities to measure
    • Potential energy
    • Kinetic energy
    • Total energy
    • Temperature
    • The caloric curve
    • Mean square displacement
    • Pressure
  • Measuring the melting temperature
  • Real space correlations
  • Reciprocal space correlations
  • Dynamical analysis
  • Annealing and quenching: MD as an optimization tool
  • Other statistical ensembles
• Interatomic potentials
  • The Born-Oppenheimer approximation
  • The design of potentials
  • The problems with two-body potentials
  • Many-body potentials for metals
  • Many-body potentials for semiconductors
    • The Stillinger-Weber potential
    • The Tersoff potential
  • Long-range forces
  • But do we really need potentials?
  • Fitting to ab initio data by ``force matching''
• Choosing hardware and software
  • What kind of computer?
    • Selecting a computer for molecular dynamics
    • Storage space
  • What language?
    • High level languages
    • Fortran or C?
• References