The aim of this course is to give students an overview of molecular simulation methods , and the types of properties that can be obtained, depending on the level of description used. The major concepts of molecular simulations will be given during the lectures and various applications will be presented. For the applications, a particular focus will be made on simulations of biomolecular systems. A practical session on Molecular Dynamics will be organized.
Below is a list of the major concepts that will be discussed during the lectures:
- Concepts for molecular simulations: potential energy surface, statistical ensembles, Boltzmann probabilities, time and ensemble averages
- Principles of molecular simulation methods: energy minimization, classical and ab initio (DFT) Molecular Dynamics, Monte Carlo
- Molecular description levels: Molecular Mechanics , Quantum Mechanics, QM/MM
Practical aspects of Molecular simulations
At the end of the course, the students should be able to design a simple simulation protocol, to understand the “Materials ad Methods” section of a theoretical paper and to discuss its relevance.
- M. Allen and D.J. Tildesley, “Computer simulation of liquids”, Oxford Science Publications, 1997.
- D. Frenkel and B. Smit, “Understanding molecular simulations”, 2nd edition, Academic Press, 2006.
- A. Leach, “Molecular Modelling: Principles and Applications”, 2nd edition, Pearson, 2001.
- C.J. Cramer, “Essentials of Computational Chemistry: Theories and Models”, 2nd edition, Wiley, 2004.