Molecular Simulation

Lecture 1. Introduction
Lecture 2. Properties, units & dimensions; hard-sphere MD
Lecture 3. Periodic boundaries, simulation structure, confidence limits, initialization
Lecture 4. Object oriented programming, the molecular simulation API.
Lecture 5. Study of some the Java source code.
Lecture 6. Statistical mechanics
Lecture 7. Monte Carlo integration
Lecture 8. Markov processes
Lecture 9. Monte Carlo simulation
Lecture 10. Simple biasing techniques
Lecture 11. Introduction to molecular dynamics
Lecture 12. Measurement of transport coefficients; time correlation functions
Lecture 13. Molecular dynamics at constant temperature and pressure
Lecture 14. Molecular modeling
Lecture 15. Long-range interactions and Ewald sum
Lecture 16. Dielectrics
Lecture 17. Beyond atoms: Simulating molecules
Lecture 18. Free-energy calculations
Lecture 19. Distribution methods. Accuracy and precision of FEP calculations
Lecture 20. Phase equilibria calculations
Lecture 21. Histogram reweighting method
Lecture 22. Configurational bias and methods for chain molecules
Lecture 23. Symmetry in MD integrators. RESPA.
Lecture 24. Non-equilibrium molecular dynamics, linear-response theory
Lecture 25. Efficiencies, algorithms for parallel computing platforms