Chapter 1: MD Theory and Simulation Practices
This chapter introduces the theory behind molecular dynamics (MD) and some common simulation practices. Starting from Newton's laws, we outline the physics behind the dynamics of point particles and rigid bodies, discuss iterative updating and the relevance of temperature, and end by listing computational practices.
In this chapter, we will cover the follow topics:
- Introducing MD theory
- Understanding the dynamics of point particles
- Performing iterative updates using the Velocity Verlet algorithm
- Understanding rotational motion
- Examining temperature and velocity distribution of particles
- Implementing MD simulation practices including cutoff, periodic boundaries, and neighbor lists
By the end of this chapter, you will have grasped an understanding of the theoretical fundamentals implemented in MD software.
