4.1. Introduction

In this section, we will discuss the basic fundamentals of a molecular dynamics simulation. We will cover verlet integration for NVE ensemble simulations, thermostats and langevin dynamics for NVT, as well as technical topics like neighbor lists and searching, and high performance computing.

• “Simulations: The Dark Side,” Daan Frenkel, 20213 ⁴

• Braun, E., Gilmer, J., Mayes, H. B., Mobley, D. L. ., Monroe, J. I., Prasad, S., & Zuckerman, D. M. . (2018). Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living Journal of Computational Molecular Science, 1(1), 5957. ¹³