Awesome Molecular Dynamics
A curated list of awesome Molecular Dynamics libraries, tools and software.
Emoji Key
- code:
- documentation:
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Table of Contents
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.
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
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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.