Molecular Dynamics

Molecular Dynamics (MD) is one of the oldest applications of computers in science and up to today one of the base pillars in many computational science areas like Biology, Chemistry and Material Sciences.

MD simulates the movement of atoms and molecules based on time integration of Newton’s equation of motion.

The forces between the atoms and molecules are modeled with an interaction potential, which is most of the time simplified by only taking into account pair-wise interactions to reduce the computational costs. Another simplification often seen is the use of a cut-off for short range potentials, which allows a reduction of the algorithmic complexity to linear order, for example, with the Linked Cell algorithm (see related algorithms).