A concise introduction to molecular dynamics simulation: theory and programming

TL;DR

This paper offers a clear, self-contained overview of molecular dynamics simulation fundamentals and provides a Python code implementation for simulating particles with Lennard-Jones interactions.

Contribution

It introduces core MD concepts and presents a Python-based simulation code with different design approaches, aiding beginners and practitioners.

Findings

Provides a comprehensive MD introduction for new users.

Includes a functional Python code for Lennard-Jones particle simulation.

Demonstrates two programming design strategies for MD code.

Abstract

We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting via the Lennard-Jones pairwise potential, was also written in Python programming language in both top-down and function-based designs.