Classical Molecular Dynamics: Theory and Simulation Practice

Computational Chemistry and Molecular Dynamics (MD) provide essential tools for predicting molecular behavior and material properties without costly physical experiments. This course introduces the fundamental concepts needed to simulate complex systems. By the end of this course, you will possess a strong theoretical understanding of classical molecular dynamics and the practical skills to set up, execute, and interpret basic MD simulations of small chemical and biological systems. What you'll learn: * Understand the core principles of classical mechanics and statistical mechanics as applied to molecular systems. * Master the steps for selecting, implementing, and validating common modern force fields (e.g., bonded and non-bonded interactions). * Configure and run basic molecular dynamics simulations using essential integration algorithms like the Verlet method. * Analyze simulation outputs, including trajectory data, radial distribution functions, and thermodynamic properties. * Apply concepts of boundary conditions, temperature, and pressure control (thermostats and barostats) in simulation environments. * Practice basic data analysis techniques, including using scripting tools for extracting and visualizing simulation results. The course begins by establishing the necessary background in statistical mechanics and classical mechanics. We then move into practical simulation setup, covering topics like force fields, integration algorithms, boundary conditions, and basic data analysis techniques. This course is designed for absolute beginners interested in computational chemistry, materials science, or biophysics. No prior experience with molecular simulation software is required. Begin mastering the principles of molecular simulation today.