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# Awesome Molecular Dynamics 
[![Awesome](https://awesome.re/badge.svg)](https://awesome.re) [![GitHub stars](https://img.shields.io/github/stars/ipudu/awesome-molecular-dynamics.svg?style=social&label=Stars)](https://github.com/ipudu/awesome-molecular-dynamics/stargazers) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/ipudu)


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


## Emoji Key

* code: :octocat:
* documentation: :book:

## Table of Contents

+ [Books](#books)
+ [Courses](#courses)
+ [MD engines](#md-engines)
+ [Trajectory Analysis](#trajectory-analysis)
+ [Visualization Tools](#visualization-tools)

## Books

* [Computer Simulation of Liquids](https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206) - A classic book on molecular dynamics and Monte Carlo simulations of liquids. [:octocat:][csol-code]
* [Understanding Molecular Simulation: From Algorithms to Applications](https://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514/ref=sr_1_1?ie=UTF8&qid=1530897897&sr=8-1&keywords=understanding+molecular+simulation) - Molecular simulation bible. [:octocat:][ums-code]

[csol-code]: https://github.com/Allen-Tildesley/examples
[ums-code]: http://www.acmm.nl/molsim/frenkel_smit/README.html

## Courses

* [Molecular Simulations](http://www.pages.drexel.edu/~cfa22/msim/msim.html) - An awesome introduction class to molecular simulations.
* [Principles of modern molecular simulation methods](https://engineering.ucsb.edu/~shell/che210d/) - A course focuses on molecular simulation concepts, algorithms and tools.

## MD Engines/Frameworks

* [Amber](http://ambermd.org/) - A suite of biomolecular simulation programs. [:book:][amber-doc]
* [ASE](https://wiki.fysik.dtu.dk/ase/) - The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. [:octocat:][ase-code]
* [CHARMM](https://www.charmm.org/) - A molecular simulation program with broad application to many-particle systems. [:book:][charmm-doc]
* [Gromacs](http://www.gromacs.org/) - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. [:octocat:][gromacs-code][:book:][gromacs-doc]
* [HOOMD-Blue](http://glotzerlab.engin.umich.edu/hoomd-blue/) - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. [:octocat:][hoomd-code][:book:][hoomd-doc]
* [ipi](http://ipi-code.org) - i-PI: a universal force engine. [:octocat:][ipi-code]
* [LAMMPS](http://lammps.sandia.gov/) - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. [:octocat:][lammps-code][:book:][lammps-doc]
* [OpenMM](http://openmm.org/) - A toolkit for molecular simulation using high performance GPU code. [:octocat:][openmm-code][:book:][openmm-doc]
* [pyiron](http://pyiron.org) - pyiron - an integrated development environment (IDE) for computational materials science. [:octocat:][pyiron-code]
* [Tinker](https://dasher.wustl.edu/tinker/) - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. [:octocat:][tinker-code][:book:][tinker-doc]

[amber-doc]: http://ambermd.org/doc12/Amber16.pdf
[ase-code]: https://gitlab.com/ase/ase
[charmm-doc]: https://www.charmm.org/charmm/documentation/
[gromacs-code]: https://github.com/gromacs/gromacs
[gromacs-doc]: http://manual.gromacs.org/documentation/
[hoomd-code]: https://github.com/glotzerlab/hoomd-blue
[hoomd-doc]: https://hoomd-blue.readthedocs.io/
[ipi-code]: https://github.com/i-pi/i-pi
[lammps-code]: https://github.com/lammps/lammps
[lammps-doc]: http://lammps.sandia.gov/doc/Manual.html
[openmm-code]:https://github.com/pandegroup/openmm
[openmm-doc]:http://openmm.org/documentation.html
[pyiron-code]: https://github.com/pyiron/pyiron
[tinker-code]: https://github.com/TinkerTools/tinker
[tinker-doc]:https://dasher.wustl.edu/tinker/downloads/guide.pdf

## Trajectory Analysis

* [CppTraj](https://github.com/Amber-MD/cpptraj) - Biomolecular simulation trajectory/data analysis.
* [Freud](https://freud.readthedocs.io/en/stable/) - Parallel, python-based analysis with an emphasis on local particle environments. [:octocat:][freud-code][:book:][freud-doc]
* [MDAnalysis](https://www.mdanalysis.org/) - An object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
* [MDTraj](http://mdtraj.org/) - A python library that allows users to manipulate molecular dynamics (MD) trajectories.
* [PyTraj](https://amber-md.github.io/pytraj/) - A Python front-end of [CppTraj](https://github.com/Amber-MD/cpptraj).
* [d-SEAMS](https://dseams.info) - Graph network based C++ and Lua based nucleation trajectory analysis software.

[freud-code]: https://github.com/glotzerlab/freud
[freud-doc]: https://freud.readthedocs.io/

## Visualization Tools

* [Avogadro](https://avogadro.cc/) - An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. [:octocat:][avogadro-code][:book:][avogadro-doc]
* [VMD](http://www.ks.uiuc.edu/Research/vmd/) - A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. [:book:][vmd-doc]
* [Plato](https://plato-draw.readthedocs.io/) - A python library for both interactive and figure-grade visualizations of particle systems. [:octocat:][plato-code][:book:][plato-doc]
* [PyMOL](https://pymol.org/2/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. [:book:][pymol-doc]
* [OVITO](https://ovito.org/) - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. [:book:][ovito-doc]
* [NGLview](https://github.com/arose/nglview) - IPython widget to interactively view molecular structures and trajectories [:book:][nglview-doc]

[avogadro-code]: https://github.com/cryos/avogadro
[avogadro-doc]: https://avogadro.cc/docs/
[vmd-doc]: http://www.ks.uiuc.edu/Research/vmd/current/docs.html
[plato-code]: https://github.com/glotzerlab/plato
[plato-doc]: https://plato-draw.readthedocs.io
[pymol-doc]: http://pymol.sourceforge.net/newman/userman.pdf
[ovito-doc]: http://www.ovito.org/manual/
[nglview-doc]: http://arose.github.io/nglview/latest/

## Contributing

Your contributions are always welcome! Please read the [contribution guidelines](https://github.com/ipudu/awesome-molecular-dynamics/blob/master/contributing.md) first.

## License

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

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