Molecular Dynamics Simulation: Fundamentals and Implementation

Computer simulations play a vital role in modeling atomic behavior and analyzing material properties at the microscopic scale. This course introduces the fundamental mechanics of molecular dynamics (MD) and guides you through constructing a working simulation engine from the ground up. You will explore core physical definitions, numerical integration methods, force fields, and essential computational efficiency techniques. What you'll learn: Understand key terminology, interatomic forces, and thermodynamic concepts in computational physics. Implement force calculations using the Lennard-Jones potential energy model. Integrate equations of motion using the Velocity Verlet algorithm. Apply periodic boundary conditions and the minimum image convention. Optimize computational performance using neighbor lists and interaction cutoffs. Analyze simulation trajectories to measure system temperature, pressure, and energy conservation. The material begins with foundational physics concepts and mathematical definitions, gradually progressing into step-by-step algorithm design and efficient code execution. Clear written explanations and structured code snippets lead you through constructing a practical simulation project. This course is tailored for beginners in computational science and scientific programming who want to understand simulation algorithms from scratch. Begin your study today and gain practical insight into molecular dynamics software design.