A working definition of molecular dynamics (MD) simulation is technique by which one generates the atomic trajectories of a system of N particles by numerical integration of Newton's equation of motion, for a specific interatomic potential, with certain initial condition (IC) and boundary condition (BC). Consider, for example (see Fig. 1 ), a system with N atoms in a volume . We can define its internal energy: and U is the potential energy, x 3N (t) denotes the collective of 3 D coordinates x 1

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... (t), x 2 (t), . . . , x N (t). Note that E should be a conserved quantity, i.e., a constant of time, if the system is truly isolated. One can often treat a MD simulation like an experiment. Below is a common flowchart of an ordinary MD run: [system setup] [equilibration] [simulation run] [output] sample selection → sample preparation → property average → data analysis (pot., N , IC, BC) (achieve T, P) (run L steps) (property calc.) in which we fine-tune the system until it reaches the desired condition (here, temperature T and pressure P), and then perform property averages, for instance calculating the radial distribution function g(r) [1] or thermal conductivity [2]. One may also perform a non-equilibrium MD calculation, during which the system is subjected to perturbational or large external driving forces, 565 S. Yip (ed.), Handbook of Materials Modeling, 565-588.