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[38;5;12m                                                                                                        [39m[38;2;255;187;0m[1m[4mAwesome Molecular Dynamics [0m
[38;5;14m[1m![0m[38;5;12mAwesome[39m[38;5;14m[1m [0m[38;5;14m[1m(https://awesome.re/badge.svg)[0m[38;5;12m [39m[38;5;12m(https://awesome.re)[39m[38;5;12m [39m[38;5;14m[1m![0m[38;5;12mGitHub[39m[38;5;12m [39m[38;5;12mstars[39m[38;5;14m[1m [0m[38;5;14m[1m(https://img.shields.io/github/stars/ipudu/awesome-molecular-dynamics.svg?style=social&label=Stars)[0m[38;5;12m [39m
[38;5;12m(https://github.com/ipudu/awesome-molecular-dynamics/stargazers)[39m[38;5;12m [39m[38;5;14m[1m![0m[38;5;12mSay[39m[38;5;12m [39m[38;5;12mThanks![39m[38;5;14m[1m [0m[38;5;14m[1m(https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)[0m[38;5;12m [39m[38;5;12m(https://saythanks.io/to/ipudu)[39m


[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mA curated list of awesome Molecular Dynamics libraries, tools and software.[39m


[38;2;255;187;0m[4mEmoji Key[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;12mcode: :octocat:[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;12mdocumentation: :book:[39m

[38;2;255;187;0m[4mTable of Contents[0m

[38;5;12m+ [39m[38;5;14m[1mBooks[0m[38;5;12m (#books)[39m
[38;5;12m+ [39m[38;5;14m[1mCourses[0m[38;5;12m (#courses)[39m
[38;5;12m+ [39m[38;5;14m[1mMD engines[0m[38;5;12m (#md-engines)[39m
[38;5;12m+ [39m[38;5;14m[1mTrajectory Analysis[0m[38;5;12m (#trajectory-analysis)[39m
[38;5;12m+ [39m[38;5;14m[1mVisualization Tools[0m[38;5;12m (#visualization-tools)[39m

[38;2;255;187;0m[4mBooks[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mComputer Simulation of Liquids[0m[38;5;12m (https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206) - A classic book on molecular dynamics and Monte Carlo simulations of liquids. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mcsol-code[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mUnderstanding[0m[38;5;14m[1m [0m[38;5;14m[1mMolecular[0m[38;5;14m[1m [0m[38;5;14m[1mSimulation:[0m[38;5;14m[1m [0m[38;5;14m[1mFrom[0m[38;5;14m[1m [0m[38;5;14m[1mAlgorithms[0m[38;5;14m[1m [0m[38;5;14m[1mto[0m[38;5;14m[1m [0m[38;5;14m[1mApplications[0m[38;5;12m [39m
[38;5;12m(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)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mMolecular[39m[38;5;12m [39m[38;5;12msimulation[39m[38;5;12m [39m[38;5;12mbible.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mums-code[0m[38;5;12m [39m

[38;5;14m[1mcsol-code[0m[38;5;12m : https://github.com/Allen-Tildesley/examples[39m
[38;5;14m[1mums-code[0m[38;5;12m : http://www.acmm.nl/molsim/frenkel_smit/README.html[39m

[38;2;255;187;0m[4mCourses[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolecular Simulations[0m[38;5;12m (http://www.pages.drexel.edu/~cfa22/msim/msim.html) - An awesome introduction class to molecular simulations.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPrinciples of modern molecular simulation methods[0m[38;5;12m (https://engineering.ucsb.edu/~shell/che210d/) - A course focuses on molecular simulation concepts, algorithms and tools.[39m

[38;2;255;187;0m[4mMD Engines/Frameworks[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAmber[0m[38;5;12m (http://ambermd.org/) - A suite of biomolecular simulation programs. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mamber-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mASE[0m[38;5;12m (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. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mase-code[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCHARMM[0m[38;5;12m (https://www.charmm.org/) - A molecular simulation program with broad application to many-particle systems. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mcharmm-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mGromacs[0m[38;5;12m (http://www.gromacs.org/) - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mgromacs-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mgromacs-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mHOOMD-Blue[0m[38;5;12m (http://glotzerlab.engin.umich.edu/hoomd-blue/) - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mhoomd-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mhoomd-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mipi[0m[38;5;12m (http://ipi-code.org) - i-PI: a universal force engine. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mipi-code[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mLAMMPS[0m[38;5;12m (http://lammps.sandia.gov/) - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mlammps-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mlammps-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOpenMM[0m[38;5;12m (http://openmm.org/) - A toolkit for molecular simulation using high performance GPU code. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mopenmm-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mopenmm-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mpyiron[0m[38;5;12m (http://pyiron.org) - pyiron - an integrated development environment (IDE) for computational materials science. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mpyiron-code[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mTinker[0m[38;5;12m (https://dasher.wustl.edu/tinker/) - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mtinker-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mtinker-doc[0m[38;5;12m [39m

[38;5;14m[1mamber-doc[0m[38;5;12m : http://ambermd.org/doc12/Amber16.pdf[39m
[38;5;14m[1mase-code[0m[38;5;12m : https://gitlab.com/ase/ase[39m
[38;5;14m[1mcharmm-doc[0m[38;5;12m : https://www.charmm.org/charmm/documentation/[39m
[38;5;14m[1mgromacs-code[0m[38;5;12m : https://github.com/gromacs/gromacs[39m
[38;5;14m[1mgromacs-doc[0m[38;5;12m : http://manual.gromacs.org/documentation/[39m
[38;5;14m[1mhoomd-code[0m[38;5;12m : https://github.com/glotzerlab/hoomd-blue[39m
[38;5;14m[1mhoomd-doc[0m[38;5;12m : https://hoomd-blue.readthedocs.io/[39m
[38;5;14m[1mipi-code[0m[38;5;12m : https://github.com/i-pi/i-pi[39m
[38;5;14m[1mlammps-code[0m[38;5;12m : https://github.com/lammps/lammps[39m
[38;5;14m[1mlammps-doc[0m[38;5;12m : http://lammps.sandia.gov/doc/Manual.html[39m
[38;5;14m[1mopenmm-code[0m[38;5;12m :https://github.com/pandegroup/openmm[39m
[38;5;14m[1mopenmm-doc[0m[38;5;12m :http://openmm.org/documentation.html[39m
[38;5;14m[1mpyiron-code[0m[38;5;12m : https://github.com/pyiron/pyiron[39m
[38;5;14m[1mtinker-code[0m[38;5;12m : https://github.com/TinkerTools/tinker[39m
[38;5;14m[1mtinker-doc[0m[38;5;12m :https://dasher.wustl.edu/tinker/downloads/guide.pdf[39m

[38;2;255;187;0m[4mTrajectory Analysis[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCppTraj[0m[38;5;12m (https://github.com/Amber-MD/cpptraj) - Biomolecular simulation trajectory/data analysis.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mFreud[0m[38;5;12m (https://freud.readthedocs.io/en/stable/) - Parallel, python-based analysis with an emphasis on local particle environments. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mfreud-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mfreud-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMDAnalysis[0m[38;5;12m (https://www.mdanalysis.org/) - An object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMDTraj[0m[38;5;12m (http://mdtraj.org/) - A python library that allows users to manipulate molecular dynamics (MD) trajectories.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPyTraj[0m[38;5;12m (https://amber-md.github.io/pytraj/) - A Python front-end of [39m[38;5;14m[1mCppTraj[0m[38;5;12m (https://github.com/Amber-MD/cpptraj).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1md-SEAMS[0m[38;5;12m (https://dseams.info) - Graph network based C++ and Lua based nucleation trajectory analysis software.[39m

[38;5;14m[1mfreud-code[0m[38;5;12m : https://github.com/glotzerlab/freud[39m
[38;5;14m[1mfreud-doc[0m[38;5;12m : https://freud.readthedocs.io/[39m

[38;2;255;187;0m[4mVisualization Tools[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAvogadro[0m[38;5;12m [39m[38;5;12m(https://avogadro.cc/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mAn[39m[38;5;12m [39m[38;5;12madvanced[39m[38;5;12m [39m[38;5;12mmolecule[39m[38;5;12m [39m[38;5;12meditor[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mvisualizer[39m[38;5;12m [39m[38;5;12mdesigned[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mcross-platform[39m[38;5;12m [39m[38;5;12muse[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mcomputational[39m[38;5;12m [39m[38;5;12mchemistry,[39m[38;5;12m [39m[38;5;12mmolecular[39m[38;5;12m [39m[38;5;12mmodeling,[39m[38;5;12m [39m[38;5;12mbioinformatics,[39m[38;5;12m [39m[38;5;12mmaterials[39m[38;5;12m [39m[38;5;12mscience,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mrelated[39m[38;5;12m [39m[38;5;12mareas.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mavogadro-code[0m
[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mavogadro-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVMD[0m[38;5;12m (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. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mvmd-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPlato[0m[38;5;12m (https://plato-draw.readthedocs.io/) - A python library for both interactive and figure-grade visualizations of particle systems. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mplato-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mplato-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPyMOL[0m[38;5;12m (https://pymol.org/2/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mpymol-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOVITO[0m[38;5;12m (https://ovito.org/) - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1movito-doc[0m[38;5;12m [39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mNGLview[0m[38;5;12m (https://github.com/arose/nglview) - IPython widget to interactively view molecular structures and trajectories [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mnglview-doc[0m[38;5;12m [39m

[38;5;14m[1mavogadro-code[0m[38;5;12m : https://github.com/cryos/avogadro[39m
[38;5;14m[1mavogadro-doc[0m[38;5;12m : https://avogadro.cc/docs/[39m
[38;5;14m[1mvmd-doc[0m[38;5;12m : http://www.ks.uiuc.edu/Research/vmd/current/docs.html[39m
[38;5;14m[1mplato-code[0m[38;5;12m : https://github.com/glotzerlab/plato[39m
[38;5;14m[1mplato-doc[0m[38;5;12m : https://plato-draw.readthedocs.io[39m
[38;5;14m[1mpymol-doc[0m[38;5;12m : http://pymol.sourceforge.net/newman/userman.pdf[39m
[38;5;14m[1movito-doc[0m[38;5;12m : http://www.ovito.org/manual/[39m
[38;5;14m[1mnglview-doc[0m[38;5;12m : http://arose.github.io/nglview/latest/[39m

[38;2;255;187;0m[4mContributing[0m

[38;5;12mYour contributions are always welcome! Please read the [39m[38;5;14m[1mcontribution guidelines[0m[38;5;12m (https://github.com/ipudu/awesome-molecular-dynamics/blob/master/contributing.md) first.[39m

[38;2;255;187;0m[4mLicense[0m

[38;5;14m[1m![0m[38;5;12mCC0[39m[38;5;14m[1m (https://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg)[0m[38;5;12m (https://creativecommons.org/publicdomain/zero/1.0)[39m

[38;5;12mThis work is is licensed under the Creative Commons Zero v1.0 Universal.[39m
