Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis

Analyzing the results of molecular dynamics (MD)-based simulations usually entails extensive manipulations of file formats encoding both the topology (e.g. the chemical connectivity) and configurations (the trajectory) of the simulated system. This chapter reviews a number of software libraries developed to facilitate interactive and batch analysis of MD results with scripts written in high-level, interpreted languages. It provides a beginners' introduction to MD analysis presenting a side-by-side comparison of major scripting languages used in MD, and show how to perform common analysis tasks within the VMD, Bio3D, MDTraj, MDAnalysis and HTMD environments.