Computational techniques for simulating chemical processes in the condensed phase will be introduced. In addition to providing a solid background in molecular simulations, a major purpose of the course is to help students to appreciate both the similarities and dissimilarities between simple liquid and biopolymers (proteins and nucleic acids) in terms of their structural and dynamical features. Lectures will be supplemented with computation exercises in which students will have the opportunity to "see molecules in action". A grand prize in the class will be presented by the end of the term for best assignment record and project presentation.

Class Schedule and Lecture ppts

Textbooks Handouts

• Understanding Molecular simulation, D. Frenkel, B. Smit, Academic Press, 2nd Ed. 2001
• Computational Biochemistry and Biophysics, O. M. Becker, A. D. MacKerell Jr., B. Roux and M. Watanabe, Dekker, 2001
• Molecular Modeling, Principles and Applications, A. R. Leach, Prentice Hall, 2001
• Computational Molecular Dynamics, Challenges, Methods and Ideas, Springer-Verlag, 1998
• Computer simulation of liquids, Allen, M. P.; Tildesley, D. J. Oxford University Press, New York, 1987
• A Guide to Monte Carlo Simulations in Statistical Physics, D. P. Landau & K. Binder, Cambridge University Press, 2000
• Proteins, A Theoretical Perspective of Dynamics, Structure and Thermodynamics, C. L. Brooks, III, M. Karplus, B. M. Pettitt, Adv. Chem. Phys. 71, John Wiley & Sons, 1988
• Dynamics of proteins and nucleic acids, J. A. McCammon, S. C. Harvey, Cambridge University Press, 1987
• Computer Modeling of Chemical Reactions in Enzymes and Solution, A. Warshel, John Wiley & Sons, 1991

• Using CHARMM for your simulation
• Using VMD for visualizing your simulation