Molecular Modelling (CH926)
Module proposal information |
| Aim: To introduce students to molecular modelling techniques as applied to biological systems with particular emphasis on the methods used and their underlying theory. The student should gain a basic understanding of the available computational methods and their theoretical foundations; what time scales and length scales are accessible; what properties can be computed and to what level of accuracy; and what methods are most appropriate for different molecular systems and properties. |
| Syllabus: Coordinate systems: how to describe 3-D molecular structure. Potential energy surfaces: quantum & empirical; conformations, vibrations and transition states. Quantum Methods: review of basic quantum mechanics; introduction to MO theory and basis sets; awareness of HF-based, DFT and semi-empirical methods; illustrative applications. Intermolecular potentials. Classical Methods: Molecular Mechanics, Molecular Dynamics & Metropolis Monte Carlo; thermodynamic and transport properties; free energies; illustrative applications. Statistical & Comparative Methods: QSAR; homology modelling. Computer Aided Design: case studies from developing materials and pharmaceuticals. Applications to examples such as: simulation of conformational changes, chemical reactions, rare events; simulations incorporating experimental (structural, NMR) data; restrained dynamics; application of computer modelling to molecular aggregates such as membranes. |
Illustrative Bibliography:
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Being taught by:
Becky Notman
2004-2005 course, taught by Peter Taylor and Mike Allen.
The software for the workshops will be VMD and NAMD, and can be obtained from Illinois TCBG web site using the following links
VMD (Visual Molecular Dynamics)
NAMD (North American Molecular Dynamics)
Tutorial and workshop files (including linux/mac instructions) can be be found from the TCGB website, and are mirrored with local links below:
VMD tutorial instructions (win/linux/mac)
NAMD tutorial instructions (win)