Material from class lectures is placed here. Pdf versions contain corrections and updates that are not included in the html version.

• Lecture 1 [pdf].  Introduction
• Lecture 2 [pdf].  Properties, units & dimensions; hard-sphere MD
• Lecture 3 [pdf].  Periodic boundaries, simulation structure, confidence limits, initialization
• Lecture 4 [pdf].  Object oriented programming, the molecular simulation API.
• Lecture 5.  Study of some the Java source code.
• Lecture 6 [pdf].  Statistical mechanics
• Lecture 7 [pdf].  Monte Carlo integration
• Lecture 8 [pdf].  Markov processes
• Lecture 9 [pdf].  Monte Carlo simulation
• Lecture 10 [pdf]. Simple biasing techniques
• Lecture 11 [pdf]. Introduction to molecular dynamics
• Lecture 12 [pdf]. Measurement of transport coefficients; time correlation functions
• Lecture 13 [pdf]. Molecular dynamics at constant temperature and pressure
• Lecture 14 [pdf]. Molecular modeling
• Lecture 15 [pdf]. Long-range interactions and Ewald sum
• Lecture 16 [pdf]. Dielectrics
• Lecture 17 [pdf]. Beyond atoms:  Simulating molecules
• Lecture 18 [ppt.pdf] [opt.pdf]. Free-energy calculations
• Lecture 19. Distribution methods.  Accuracy and precision of FEP calculations
• Lecture 20 [pdf]. Phase equilibria calculations
• Lecture 21 [pdf]. Histogram reweighting method
• Lecture 22 [pdf]. 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

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