ProDy: ProDy is a Python package for analyzing protein dynamics and sequence co-evolution, offering tools for comparative modeling and analysis of protein structural dynamics.
QUIP:
Analysis
MDAnalysis:
MDTraj: MDTraj is a Python library for analyzing molecular dynamics trajectories, offering a wide range of functionalities for trajectory manipulation and analysis.
Preparation
Packmol: Packmol creates initial configurations for molecular dynamics simulations by packing molecules to meet specified conditions, aiding in the setup of simulation boxes.
