CS 497: Numerical Methods for Molecular Simulation

• Instructor: Stephen Bond

• Email: sdbond«at»uiuc«dot»edu

• Semester: Fall 2003

• Selected Topics: Molecular Dynamics, Force Fields, Electrostatic Computation, Minimization, Classical Monte Carlo, Constrained MD, Alternative Ensembles, Geometric Integration, Brownian Dynamics, Langevin Dynamics, Quantum Monte Carlo, Essential Dynamics.

• Course Syllabus

• Source Code for Class Demonstrations

• Select Course Notes from class.

• Course Schedule

  	Date	Lecture Topic	Assignment
  Thu	28-Aug	1. Introduction	Email instructor with suggested course topics
  Tue	2-Sep	2. Statistical Mechanics
  Thu	4-Sep	3. Statistical Mechanics
  Tue	9-Sep	4. Hamiltonian Systems and Classical Mechanics	Sign up for Presentations
  Thu	11-Sep	5. Geometric Integration Methods
  Tue	16-Sep	6. Numerical Integration
  Thu	18-Sep	7. Numerical Integration
  Tue	23-Sep	8. Numerical Integration
  Thu	25-Sep	9. Geometric Integration Methods
  Tue	30-Sep	10. Geometric Integration Methods
  Thu	2-Oct	11. Geometric Integration Methods
  Tue	7-Oct	12. Constrained Dynamics
  Thu	9-Oct	13. Virial Theorem
  Tue	14-Oct	14. Presentations: Eric Cyr: "Motion Planning & Protein Folding" Anurag Sethi: "MD at Constant Pressure"
  Thu	16-Oct	15. Presentations: Hari Govind: "Scaling MD on 3000 Processors" Instructor: Comments on the Virial Theorem
  Fri	17-Oct	Drop Deadline
  Tue	21-Oct	16. Methods for Constant Temperature
  Thu	23-Oct	17. Nosé-Hoover and Nosé-Poincaré
  Tue	28-Oct	18. Liouville Theorem
  Thu	30-Oct	19. Continuum and Classical Methods
  Tue	4-Nov	20. Presentations: Wei Wang: "Langevin Dynamics" Instructor: "Hard Sphere Systems"
  Thu	6-Nov	21. Lagrangian Mechanics and Constant Pressure
  Tue	11-Nov	22. Constant Pressure
  Thu	13-Nov	23. Presentations: Hari Govind: "Scaling QM/MM with Charm++" Daniel Go: "Multiple Timestepping"
  Tue	18-Nov	24. Presentations: Anurag Sethi: "Coarse-Grain Models for Lipid Layers" Instructor: "Ewald Summation"
  Thu	20-Nov	25. Tree Code and Multipole
  Tue	25-Nov	Thanksgiving Vacation
  Thu	27-Nov
  Tue	2-Dec	26. Presentation: Rommie Amaro: "Tale of Two Proteins"
  Thu	4-Dec	27. Presentation: Eric Cyr: "Umbrella Sampling" Wei Wang: "Estimating Diffusion Coefficients"
  Tue	9-Dec	28. Presentation: Daniel Go: "Evolutionary Algorithms" Instructor: Almost Invariant Sets
  Thu	11-Dec	29. Random Selection of Random Methods
  Mon	15-Dec	Final Exam (1:30 - 4:30 PM)