ABSTRACT
Molecular dynamics (MD) simulation is computer simulation method that allows one to predict the dynamical evolution of a material system that consists of interacting particles, such as atoms and molecules. In an MD system, particles interact via analytical potential functions or molecular mechanics force fields. By integrating Newton’s equations of motion for all particles simultaneously, the trajectories of atoms and molecules are determined. Since the 1980s, the development of physically sound interatomic potentials that go beyond simple pair–additive interactions and describe chemical reactions correctly has brought in impressive modeling capabilities and critical breakthroughs in materials research (Brenner et al., 1998; Erkoc, 1997; Garrison and Srivastava, 1995; Sinnott and Brenner, 2012; Srolovitz and Vitek, 2012). Interatomic potentials express the chemical bonding (e.g., bond stretching) and other interactions (e.g., van der Waals force) among particles. Besides interatomic potentials, the motions of particles are also affected by thermostat algorithm and external force field.
