A molecular dynamics (MD) simulation program is developed using Wolfram
Mathematica [1] as a learning guide for beginners. One can simulate particles interacting under the Lennard-Jones 12–6 potential function in a cubic cell with three-dimensional periodic boundary conditions. Microcanonical (
NEV) ensemble and canonical (
NVT) ensemble are available on the program (see Figure 2). The MD conditions, number of particles, number density, temperature, number of MD steps, and others, are set in a
Mathematica notebook file [8]. Thermodynamic properties, particle trajectories, configurations of the system, pair correlation function, velocity autocorrelation function, mean square displacement, and self-diffusion coefficient are output as a result of the MD simulation (see Figures 3–7).
View full abstract