Accueil / Master 1 / Cours / Second Semestre / To Ex M1 Second Semestre / Chimie / Chimie théorique et propriétés moléculaires

Chimie théorique et propriétés moléculaires

Informations pratiques


Discipline :

Chimie

Niveau :

Master 1

Semestre :

S2

Crédits ECTS :

3

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

Pré-requis

Visualisation Moléculaire, physique statistique

Modalité de l'examen

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

Mots-clés

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