The aim of molecular dynamics is to model the detailed microscopic dynamical behavior

of many different types of systems as found in chemistry, physics or biology. The history

of molecular dynamics goes back to the mid 1950’s when first computer simulations on

simple systems were performed[1]. Excellent modern textbooks [2, 3] on this topic can be

found and collections of articles from summer schools are a very good source for in depth

information on more specialized aspects [4, 5, 6].

Molecular Dynamics is a technique to investigate equilibrium and transport properties

of many–body systems. The nuclear motion of the particles is modeled using the laws

of classical mechanics. This is a very good approximation for molecular systems as long

as the properties studied are not related to the motion of light atoms (i.e. hydrogen)

or vibrations with a frequency ν such that hν > kBT. Extensions to classical molecular

dynamics to incorporate quantum effects or full quantum dynamics (see for example

Refs. [7, 8] for a starting point) is beyond the scope of this lecture series