Molecular Dynamics Simulation

By G. Ciccotti, M. Ferrario, C. Schuette. Mechanics of Particle‐ and Fiber‐Reinforced Polymer Nanocomposites, 2014

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Theory I: Solving Newtons Laws for collection of particles ........................................................ 1 Figure 1: Diagram defining particle-particle interaction variables. ................................................ 2 Simple Molecular Dynamics Simulation ................................................................................. 3 Experimental Parameters (particle) ........................................................................................ 3 Experimental Parameters (space-domain) ................................................................................ 3 Experimental Parameters (initial conditions) ............................................................................ 4 Experimental Parameters (time-domain) ................................................................................. 4 Display Parameters ............................................................................................................. 4 Theory II: Numeric integration of Newton's laws Part I ............................................................. 4 Figure 2: Euler vs. Semi-implicit Euler Integration. .................................................................. 5 Theory II: Numeric integration of Newton's laws Part II ............................................................ 6 Figure 3: Velocity Verlet vs. Semi-implicit Euler Integration. ..................................................... 7 Figure 3: Velocity Verlet vs. Semi-implicit Euler Integration (caption). ........................................ 8 Simulation Parameters ......................................................................................................... 8 Initial Conditions (Positions) ................................................................................................ 8 Initial Conditions (Velocities) ............................................................................................... 9 Initial Conditions (Accelerations) .......................................................................................... 9 Save variables .................................................................................................................... 9 Figure 3: Setup Plotting ....................................................................................................... 9 Main Loop ...................................................................................................................... 10 m-files ............................................................................................................................ 11

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