Molecular Dynamics

Abstract

Molecular Dynamics, in particular classical Molecular Dynamics, encompasses a number of numeric algorithms designed to study the classical dynamics of many particles as it is described by Hamilton’s equation of motion. The particles can be subject to external forces and two-particle interactions can also be incorporated. All methods discussed here a based on the finite difference approximation of derivatives. The symplectic Euler method results in the Strömer–Verlet algorithm, the central rectangular rule in the leap-frog algorithm, and the velocity Verlet algorithm is based on an expansion of the position coordinates and of the velocities of the particles to second order in time. The numerical implementation of these algorithms focuses on the realization of boundary conditions, the initialization, and on equilibrium conditions. The caveats of these three methods are also discussed in necessary detail.