Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a perspective of the dynamic advancement of the system. In the most common version, the directions of atoms and molecules are determined numerically solving Newtons equations of motion for an arrangement of particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanics force fields. The technique was initially developed within the field of theoretical physics but is applied today mostly in chemical physics, materials science and the modelling of biomolecules. Molecular systems typically consist of a vast number of particles, by using numerical methods it is possible to determine the properties of such complex systems. 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 completely.