Classical Molecular Dynamics

Classical Molecular Dynamics (MD) is a computational simulation technique that models the physical movements of atoms and molecules over time using Newton's laws of motion. It approximates atomic interactions through empirical force fields to predict structural, dynamic, and thermodynamic properties of molecular systems, such as proteins, materials, or liquids. This method is widely used in chemistry, physics, biology, and materials science to study processes like protein folding, drug binding, and phase transitions.

Also known as: Molecular Dynamics, MD, Classical MD, Atomistic Simulation, Force Field Simulation

Why learn Classical Molecular Dynamics?

Developers should learn Classical Molecular Dynamics when working in scientific computing, computational chemistry, or bioinformatics to simulate complex molecular systems that are impractical to study experimentally. It is essential for applications like drug discovery, where it helps predict how molecules interact with biological targets, or in materials science for designing new materials with specific properties. Knowledge of MD is also valuable for optimizing high-performance computing workflows and integrating simulations with data analysis pipelines.

Learning Resources

• docs: Molecular Dynamics: Theory and Practice
• course: Introduction to Molecular Dynamics Simulation
• tutorial: GROMACS Tutorial
• book: Understanding Molecular Simulation by Frenkel and Smit
• video: Molecular Dynamics Basics - YouTube Series