Organisers

• Paul A. Madden (University of Edinburgh )
• Tristan Albaret (LPMCN Université Claude Bernard Lyon 1)

Supports

 CECAM

 Marie Curie - MolSimu

Description

The goal of this tutorial is to provide a general introduction
on classical molecular dynamics simulations through lecture
classes coupled to practical 'hands-on' sessions on molecular dynamics
softwares.

The morning sessions will be dedicated to the class lectures
which will give the basic theory
needed to understand and to run classical molecular dynamics.
This will include a
discussion on the classical potentials and the approximations associated
to their use.
More technical points as the time evolution of the atomic coordinates in
the microcanonical ensemble and the use of periodic boundary conditions
will also be presented.

The second part the lectures will focus on some simple structural
and thermodynamics
analysis needed to extract relevant physical quantities from the simulations.
Exemples will include analysis in the Fourier space
to retrieve structural and dynamical quantities such as the structure factor
and the diffusion coefficient.
The last part of the lectures will be dedicated to more advanced
topics like calculations in other ensembles, constraint dynamics,
and an introduction to DLPOLY a molecular simulation package.

During the afternoon practical sessions the students will
run some molecular dynamics simulations based on the Lennard-Jones potential.
Then they will analyse their own calculations and learn how to
tune the simulations parameters in order to obtain reliable results.
In the following practical sessions the students will modify
the routines of the Lennard-Jones code and
write their own analysis codes to
obtain and discuss physical properties.
In the last sessions the students
will be guided to implement constraints and/or thermostat in the
molecular dynamics code by writing their own algorithms.

Since the success of this tutorial partly rely on the
programmation skills of the students a brief
introduction to UNIX and FORTRAN will be given the first day.

Support for participation (travel and lodging) is available via the Marie Curie Action “MolSimu”.