Awesome Molecular Dynamics

A curated list of awesome Molecular Dynamics libraries, tools and software.

Emoji Key

• code:
• documentation: 📖

Table of Contents

• Books
• Courses
• MD engines
• Trajectory Analysis
• Visualization Tools

Books

• Computer Simulation of Liquids - A classic book on molecular dynamics and Monte Carlo simulations of liquids.
• Understanding Molecular Simulation: From Algorithms to Applications - Molecular simulation bible.

Courses

• Molecular Simulations - An awesome introduction class to molecular simulations.
• Principles of modern molecular simulation methods - A course focuses on molecular simulation concepts, algorithms and tools.

MD Engines/Frameworks

• Amber - A suite of biomolecular simulation programs. 📖
• ASE - The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
• CHARMM - A molecular simulation program with broad application to many-particle systems. 📖
• Gromacs - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. 📖
• HOOMD-Blue - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. 📖
• ipi - i-PI: a universal force engine.
• LAMMPS - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 📖
• OpenMM - A toolkit for molecular simulation using high performance GPU code. 📖
• pyiron - pyiron - an integrated development environment (IDE) for computational materials science.
• Tinker - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. 📖

Trajectory Analysis

• CppTraj - Biomolecular simulation trajectory/data analysis.
• Freud - Parallel, python-based analysis with an emphasis on local particle environments. 📖
• MDAnalysis - An object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
• MDTraj - A python library that allows users to manipulate molecular dynamics (MD) trajectories.
• PyTraj - A Python front-end of CppTraj.
• d-SEAMS - Graph network based C++ and Lua based nucleation trajectory analysis software.

Visualization Tools

• Avogadro - An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. 📖
• VMD - A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. 📖
• Plato - A python library for both interactive and figure-grade visualizations of particle systems. 📖
• PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. 📖
• OVITO - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. 📖
• NGLview - IPython widget to interactively view molecular structures and trajectories 📖

Contributing

Your contributions are always welcome! Please read the contribution guidelines first.

License

This work is is licensed under the Creative Commons Zero v1.0 Universal.