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Libraries

  • MMTK:
    Code Last Commit Link
  • 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.
    Code Last Commit Publication
  • QUIP:
    Link

Analysis

  • MDAnalysis: MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
    Code Last Commit Publication Link
  • MDTraj: MDTraj is a Python library for analyzing molecular dynamics trajectories, offering a wide range of functionalities for trajectory manipulation and analysis.
    Code Last Commit Publication

Preparation

  • Packmol: Packmol creates initial configurations for molecular dynamics simulations by packing molecules to meet specified conditions, aiding in the setup of simulation boxes.
    Publication Link