OBJECTIVES: Computer simulations are an important tool for the study at a microscopic level in such different systems as isolated molecules, liquids, solutions, polymers, solid state and biological molecule. The goal of this course is to provide an overview of the concepts underlying this scientific approach together with an understanding of the methods, capabilities, and limitations of molecular simulation.
This course should allow any graduate students in chemistry to familiarize with molecular simulation : (i) ability to understand studies reported in the literature ; (ii) ability to discuss with specialists in this field to develop such applications to their problems ; (iii) understand the limitations of commercial software and, if possible, how to develop their own tools.
Moreover, this course will leave any student in chemistry with a better understanding of the molecular basis of the physical and chemical properties of matter.
COURSE CONTENT: This course consists of both theoretical lectures and practical computer exercises.
Basic concepts
- Elementary classical statistical mechanics. Ensembles and fluctuations
- Molecular interactions
- Molecular mechanics
- Equilibrium molecular dynamics simulations
- Monte Carlo methods
- Calculations of properties
Advanced methods
- Overview of various software.
- Methods of energy minimization.
- Free energy calculations.
- Computer graphics visualization.
- Elaborated interaction models.
- Ewald sum and reaction field methods for treating long-range electrostatic interactions.
The ability to use a powerful computational environment (computers, softwares, data handling) is central in this field. The lectures will link the standard molecular simulation methods together with their corresponding algorithms. Experiences in computer programming and in informatic languages are not prerequisites for this course but would be used if existed.
- Giáo viên: Jean-Christophe Soetens