The theory and practice behind Molecular Dynamics simulations
This guide was originally written as the introduction to my PhD thesis. I’ve gotten a lot of positive feedback from it and I think it deserves a wider readership, so I’ve reproduced it here. Errors, suggestions, questions, and comments can be submitted as GitHub issues, or you can find me on my socials.
Molecular Dynamics is a technique for computationally simulating a Newtonian approximation to complex chemical systems. It’s commonly used for studying protein folding and dynamics and modelling complex biochemical environments. In this guide, I’ll explain the basic statistical mechanics motivating MD, and also give some practical guidance on designing a computer experiment. I’ll shy away from giving explicit instructions on a particular software package.