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Chimie théorique et propriétés moléculaires

Informations pratiques

Discipline :


Niveau :

Master 1

Semestre :


Crédits ECTS :


Volume Horaire :

16h Cours
8h TP

Responsable :

- Elise Dumont

Ecole Normale Supérieure de Lyon

Intervenants :

- Luca Monticelli (IBCP, INSERM)

- Claire Loison (UCBL)

La Formation



This course is an introduction to the concepts, algorithms and 
practical aspects of molecular dynamics simulations, with a focus on
all-atoms and coarse-grained models. It should help the students to
understand how modern simulations packages are built, and  to start
their own simulations.


- Force field
- The principes of MD simulations and the link with
 classical Newton's laws and statistical physics
- Details of the simulation steps : model building,boundary conditions,
 initialisation, integration of the equations of
 motion, measurement of interesting observables, statistical analysis
 of the results.
- Introduction to coarse-graining: motivation and general principles; the Martini CG model.
- Elements of structural biology and current open questions in protein and membrane biophysics.
- Applications of coarse-graining to biological systems: membranes, proteins, nucleic acids.
The practical sessions cover such topics :
- tutorial on a high-performance simulation package  NAMD ?  (ELISE ?)
- looking  into a basic code performing NVT simulations of a
 Lennard-Jones fluid


Visualisation Moléculaire, physique statistique

Modalité de l'examen

Report on a practical exercise. Oral discussion on the report.


Computational biophysics, Force field, Periodic simulations, Solvated systems, Coarse grain