Instructor:

Robert D. Young

I. General Information

PHY 380.02 Molecular Dynamics and Visualization. 3 sem. h.

Computer simulation of many body systems. Interaction potentials including long-range interactions. Energy minimization techniques. Constant energy and constant temperature simulations of atomic clusters and macromolecules. Free energy calculations. Statistical mechanics and treatment of simulation data. Visualization of structures and data.

Lecture, laboratory, take home assignments and semester project. Lecture meets on Mondays and Wednesdays, 11- 11:50. The laboratory is open Mondays-Fridays, 8 am-5 pm.

II. Texts and Readings

1. D.W. Heerman, Computer Simulation Methods, Springer- Verlag, New York, 1986 and 1990 (Text, DWH).

2. J.A. McCammon and Stephen C. Harvey, Dynamics of proteins and nucleic acids, Cambridge U. Press, New York, 1987 (Text, MH).

3. M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids, Oxford U. Press, New York, 1989 (Library reference, AT).

4. H. Gould and J. Tobochnik, Computer Simulation Methods, Part. 1, Ch. 6, Addison-Wesley, Reading MA, 1988 (Department reference, GT).

5. Alchemy III User's Guide, Tripos, St. Louis, 1992 (Department reference, A-III).

6. NanoVision User's Guide, American Chemical Society, 1991

(Department reference, NV).

7. QUANTA User's Guide, MSI, (Department Reference, QMSI).

8. CHARMm Command Dictionary, MSI, Waltham MA (Department Reference, CMSI).

9. CHARMm User's Guide, Polygen, Waltham MA, 1988 (Department Reference, CUG).

10. CHARMM 22 Documentation (Department Reference, C22).

11. Physics Department Computer System Manual, R. Bogue, Fall 1993. Available at Pip's or in Moulton 304.

The items indicated as "Text" are available in the local bookstores. The items marked "Library reference" are available for overnight checkout from the Reserve Desk at Milner. The items marked "Department reference" are available in Moulton 304. These items should not be removed from Room 304. They are there for the convenience of all students. Please do not abuse this resource!

You will also be given handouts for most lectures.

III. Course Requirements

Course grades will be awarded on the basis of performance on two types of assignments: (i) several take-home assignments (approximately 30% of grade), and (ii) a course project (approximately 70% of the grade). Students will present the results of the course projects at a course poster session during the last week of the semester or at the Undergraduate Research Symposium on April 29. Additional details will be provided later in a separate handout.

IV. Course Topics

1. Introduction to molecular dynamics (MD)
2. Physics Computer System
3. Model systems and interaction potentials
4. Statistical mechanics for MD, I
5. Energy minimization, I and II
6. Equations of motion-finite difference methods, I and II
7. Constraint dynamics
8. Periodic boundary conditions
9. Constant energy MD simulations
10. Organization of a MD simulation
11. Constant temperature and pressure MD simulations
12. Brownian dynamics MD simulations
13. Simulations with long--range forces
14. Introduction to biomolecules
15. Molecular visualization packages--QUANTA, BIOGRAPH, NanoVision, AlchemyIII
16. Molecular dynamics packages--CHARMM, AMBER, ...
17. Model building and coordinate manipulations of macromolecules--electronic database searches (Brookhaven Protein Data Bank,...)
18. Energy calculations for complex interaction potentials
19. Energy minimization for complex interaction potentials
20. Molecular dynamics simulation of macromolecules
21. Periodic boundary conditions and solvation of macromolecules
22. Statistical Mechanics for MD, II -- Correlation functions.
23. Free energy calculations
24. Molecular dynamics trajectories for activated processes
25. Nuclear Overhauser effects (NOE) and constraints
26. Parallel processing and molecular dynamics

Reading assignments will be handed out weekly.