Tools

• AmberTools: open source component of the non-open source Amber package

• MMTK:
  

• 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

• LOOS: C++ library (with Python bindings) for reading and analyzing molecular dynamics trajectories
  

• MDAnalysis: MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
  

  

• MDTraj: MDTraj is a Python library for analyzing molecular dynamics trajectories, offering a wide range of functionalities for trajectory manipulation and analysis.
  

  

• PyTraj: Python interface to the cpptraj tool of AmberTools
  

• simpletraj: lightweight Python library for parsing molecular dynamics trajectories
  

Markov models

• MSMBuilder: Python library for building Markov models of high-dimensional trajectory data

• PyEMMA: Python library for performing kinetic and thermodynamic analyses of molecular dynamics simulations using Markov models

Preparation

• PDB2PQR: prepares structures for electrostatics calculations

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

  

Refinement

• MDRefine: package for refining Molecular Dynamics trajectories with experimental data