2.8 BASIC MOLECULAR DYNAMICS - Li Group 李 （2.8基本分子动力学-李组李）.pdf

2.8 BASIC MOLECULAR DYNAMICS Ju Li Department of Materials Science and Engineering, Ohio State University, Columbus, OH, USA 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: E ≡ K + U, where K is the kinetic energy, N 1 ˙ 2 K ≡ m |x (t) | , (1) i i 2 i=1 and U is the potential energy, U = U (x3N (t)). (2) x3N (t) denotes the collective of 3 D coordinates x (t), x (t), . . . , x (t). 1 2 N 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