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.
Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis
Giorgino Toni
2019
Abstract
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
