What is "molecular dynamics"

n. (context physics English) The study of the physical movement of collections of atoms and molecules as they interact

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, and is thus a type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamical evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are calculated using interatomic potentials or molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules.

Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters, but not eliminated entirely.

For systems which obey the ergodic hypothesis, the evolution of a single molecular dynamics simulation may be used to determine macroscopic thermodynamic properties of the system: the time averages of an ergodic system correspond to microcanonical ensemble averages. MD has also been termed "statistical mechanics by numbers" and " Laplace's vision of Newtonian mechanics" of predicting the future by animating nature's forces and allowing insight into molecular motion on an atomic scale.