Molecular dynamics simulation
MD (molecular dynamics) simulation is a computational technique that describes the movement of atoms based on their interactions.The interactions among atoms can be described by empirical potentials (force field) or quantum chemical models, or a mix of the two. The most commonly seen MD in polymer or bio- physics uses force fields, and follows classical mechanics: solving Newton's equations of motion numerically to get the atom trajectory. By tracking where the atoms have been, structural and dynamical information can be extracted.
This type of classical MD has force field describing both intra- and inter-molecular interactions. Usually the force field refers to a set of empirical equations to describe the most essential part of the interaction. For example, the bonding between two atoms are often described in harmonic potential:
Depending on the complexity of the potentials, MD simulation could achieve different levels of realism. The force fields that use harmonic equation for bonding is capable of agreeing to some extent the structural and dynamical information, but incapable of describing any chemical reactions. Ab initio based MD simulation could provide very accurate electron distribution and bond breaking/forming, but the trade of is that the large amount of computational time required.
It is important to know what properties one's interested in finding out using MD simulation, and choose the force field accordingly. There is always a compromise between accuracy and time/length scales of MD simulation.Read more about MD: MD simulation on wikipedia
