In this introductory chapter, you'll be introduced to the fundamental concepts of molecular dynamics, including the basic principles of classical mechanics and the role of simulations in understanding molecular behavior. You'll also learn about the history and applications of molecular dynamics, setting the stage for the rest of the course.

This chapter focuses on the foundational principles of classical mechanics, which form the basis for molecular dynamics simulations. You'll learn about Newton's laws of motion, potential energy, and kinetic energy, as well as how to apply these concepts to molecular systems.

In this chapter, you'll learn how to prepare your molecular system for simulation, including how to choose an appropriate force field, set up the simulation box, and choose integration algorithms. You'll also learn about the importance of equilibrating your system before running production simulations.

This chapter covers the practical aspects of running molecular dynamics simulations, including how to initialize velocities, integrate equations of motion, and handle boundary conditions. You'll also learn about the importance of time steps and temperature control in molecular dynamics simulations.

In this chapter, you'll learn how to analyze and interpret the data generated from molecular dynamics simulations. You'll explore various techniques for analyzing trajectories, calculating observables, and visualizing results using popular software packages.

The final chapter of the course focuses on real-world applications of molecular dynamics simulations in various fields, from chemistry and physics to biology and materials science. You'll learn about the importance of molecular dynamics in understanding complex molecular phenomena and the role it plays in advancing scientific research.