Course Overview

Computer simulation is 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 be
familiar 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.

Learning Achievement

Competence

Course prerequisites

No prerequisites.

Grading Philosophy

> First session:

- Personal projects (presentation of a scientific article and
programming) (30% weight of overall mark),

- Final written exam (70% weight of overall mark).

> Second session (in case of failure):

- Written exam (70% weight of overall mark),

- Recall of the first session intermediate evaluation (30% weight of
overall mark).

Course schedule

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 applications.
- Methods of energy minimization.
- Free energy calculations.
- Computer graphics visualization.
- Elaborated interaction models (electrostatics and polarizability).
- Ewald sum and reaction field methods for treating long-range
electrostatic interactions.

The ability to use a powerful computational environment (computers,
softwares, datahandling) is central in this field. The lectures will
link the standard molecular simulation methods together with their
corresponding algorithms. Experience in computer programing and in
informatic languages are not prerequisites for this course but would
be useful.

Course type

> Lectures, tutorials and practicals. > 154 hours: - 51 contact hours (28 lectures, 23 tutorials). - 100 hours self-study. - 3 hours written assessment exam.

Online Course Requirement

Instructor

Other information

Duration: 12 weeks

Language of instruction: English
Mode of delivery: Face-to-face teaching: lectures, tutorials, practical work.

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