Organisers

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

Supports

 CECAM

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.

Since the success of this tutorial partly rely on the programmation skills of
the students
an introduction to UNIX and FORTRAN will be given the first two days.

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, eventually, some introduction to other simulation packages.

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.