Molecular Dynamics - Potentials in MD Simulations

Potentials in MD Simulations

A molecular dynamics simulation requires the definition of a potential function, or a description of the terms by which the particles in the simulation will interact. In chemistry and biology this is usually referred to as a force field. Potentials may be defined at many levels of physical accuracy; those most commonly used in chemistry are based on molecular mechanics and embody a classical treatment of particle-particle interactions that can reproduce structural and conformational changes but usually cannot reproduce chemical reactions.

The reduction from a fully quantum description to a classical potential entails two main approximations. The first one is the Born–Oppenheimer approximation, which states that the dynamics of electrons is so fast that they can be considered to react instantaneously to the motion of their nuclei. As a consequence, they may be treated separately. The second one treats the nuclei, which are much heavier than electrons, as point particles that follow classical Newtonian dynamics. In classical molecular dynamics the effect of the electrons is approximated as a single potential energy surface, usually representing the ground state.

When finer levels of detail are required, potentials based on quantum mechanics are used; some techniques attempt to create hybrid classical/quantum potentials where the bulk of the system is treated classically but a small region is treated as a quantum system, usually undergoing a chemical transformation.