CEM888 - SS12

Computational Chemistry

Time: 9:10 a.m. - 10:00 a.m. MWF
Room: 183 Chemistry
Office Hours: arrange by email

Link to the course web site

Lectures taught by me:

Friday3/30MD simulations in practice
Monday4/2Free energy calculations
Wednesday4/4Free energy calculations (cont'd)
Friday4/6Enhanced sampling
Monday4/9Enhanced sampling (cont'd)
Wednesday4/11Enhanced sampling (cont'd)
Friday4/13Macromolecular simulations
Monday4/16Macromolecular simulations (cont'd)
Wednesday4/18Macromolecular simulations (cont'd)
Lab sessions taught by me:

Wednesday4/4MD simulations
Wednesday4/11Umbrella sampling
Wednesday4/18Replica exchange simulations
Recommended books:

Andrew Leach: Molecular Modelling. Principles and Applications
Tamar Schlick: Molecular Modeling and Simulations. An Interdisciplinary Guide
M. P. Allen, D. J. Tildesley: Computer Simulations of Liquids
Daan Frenkel, Berend Smit: Understanding Molecular Simulation

Recommended papers:

Michael Feig: Molecular Simulation Methods: Standard Practices and Modern Challenges PDF
W. F. van Gunsteren, A. E. Mark: Validation of molecular dynamics simulations PDF
D. L. Beveridge, F. M. DiCapua: Free Energy via Molecular Simulation: Applications to Chemical and Biomolecular Systems PDF
P. Kollman: Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. PDF
A. Mitsutake, Y. Sugita, Y. Okamoto: Generalized-ensemble algorithms for molecular simulations of biopolymers PDF

In order to access class contents please connect from a campus computer or use a VPN connection.