awesome-awesomeness/html/moleculardynamics.html

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<h1 id="awesome-molecular-dynamics">Awesome Molecular Dynamics</h1>
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<blockquote>
<p>A curated list of awesome Molecular Dynamics libraries, tools and
software.</p>
</blockquote>
<h2 id="emoji-key">Emoji Key</h2>
<ul>
<li>code: :octocat:</li>
<li>documentation: :book:</li>
</ul>
<h2 id="table-of-contents">Table of Contents</h2>
<ul>
<li><a href="#books">Books</a></li>
<li><a href="#courses">Courses</a></li>
<li><a href="#md-engines">MD engines</a></li>
<li><a href="#trajectory-analysis">Trajectory Analysis</a></li>
<li><a href="#visualization-tools">Visualization Tools</a></li>
</ul>
<h2 id="books">Books</h2>
<ul>
<li><a
href="https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206">Computer
Simulation of Liquids</a> - A classic book on molecular dynamics and
Monte Carlo simulations of liquids. <a
href="https://github.com/Allen-Tildesley/examples">:octocat:</a></li>
<li><a
href="https://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514/ref=sr_1_1?ie=UTF8&amp;qid=1530897897&amp;sr=8-1&amp;keywords=understanding+molecular+simulation">Understanding
Molecular Simulation: From Algorithms to Applications</a> - Molecular
simulation bible. <a
href="http://www.acmm.nl/molsim/frenkel_smit/README.html">:octocat:</a></li>
</ul>
<h2 id="courses">Courses</h2>
<ul>
<li><a
href="http://www.pages.drexel.edu/~cfa22/msim/msim.html">Molecular
Simulations</a> - An awesome introduction class to molecular
simulations.</li>
<li><a href="https://engineering.ucsb.edu/~shell/che210d/">Principles of
modern molecular simulation methods</a> - A course focuses on molecular
simulation concepts, algorithms and tools.</li>
</ul>
<h2 id="md-enginesframeworks">MD Engines/Frameworks</h2>
<ul>
<li><a href="http://ambermd.org/">Amber</a> - A suite of biomolecular
simulation programs. <a
href="http://ambermd.org/doc12/Amber16.pdf">:book:</a></li>
<li><a href="https://wiki.fysik.dtu.dk/ase/">ASE</a> - The Atomic
Simulation Environment (ASE) is a set of tools and Python modules for
setting up, manipulating, running, visualizing and analyzing atomistic
simulations. <a href="https://gitlab.com/ase/ase">:octocat:</a></li>
<li><a href="https://www.charmm.org/">CHARMM</a> - A molecular
simulation program with broad application to many-particle systems. <a
href="https://www.charmm.org/charmm/documentation/">:book:</a></li>
<li><a href="http://www.gromacs.org/">Gromacs</a> - A molecular dynamics
package mainly designed for simulations of proteins, lipids and nucleic
acids. <a href="https://github.com/gromacs/gromacs">:octocat:</a><a
href="http://manual.gromacs.org/documentation/">:book:</a></li>
<li><a
href="http://glotzerlab.engin.umich.edu/hoomd-blue/">HOOMD-Blue</a> - A
general-purpose, python-based, GPU-accelerated molecular dynamics and
Monte Carlo simulation framework. <a
href="https://github.com/glotzerlab/hoomd-blue">:octocat:</a><a
href="https://hoomd-blue.readthedocs.io/">:book:</a></li>
<li><a href="http://ipi-code.org">ipi</a> - i-PI: a universal force
engine. <a href="https://github.com/i-pi/i-pi">:octocat:</a></li>
<li><a href="http://lammps.sandia.gov/">LAMMPS</a> - A classical
molecular dynamics code, and an acronym for Large-scale Atomic/Molecular
Massively Parallel Simulator. <a
href="https://github.com/lammps/lammps">:octocat:</a><a
href="http://lammps.sandia.gov/doc/Manual.html">:book:</a></li>
<li><a href="http://openmm.org/">OpenMM</a> - A toolkit for molecular
simulation using high performance GPU code. <a
href="https://github.com/pandegroup/openmm">:octocat:</a><a
href="http://openmm.org/documentation.html">:book:</a></li>
<li><a href="http://pyiron.org">pyiron</a> - pyiron - an integrated
development environment (IDE) for computational materials science. <a
href="https://github.com/pyiron/pyiron">:octocat:</a></li>
<li><a href="https://dasher.wustl.edu/tinker/">Tinker</a> - A complete
and general package for molecular mechanics and dynamics, with some
special features for biopolymers. <a
href="https://github.com/TinkerTools/tinker">:octocat:</a><a
href="https://dasher.wustl.edu/tinker/downloads/guide.pdf">:book:</a></li>
</ul>
<h2 id="trajectory-analysis">Trajectory Analysis</h2>
<ul>
<li><a href="https://github.com/Amber-MD/cpptraj">CppTraj</a> -
Biomolecular simulation trajectory/data analysis.</li>
<li><a href="https://freud.readthedocs.io/en/stable/">Freud</a> -
Parallel, python-based analysis with an emphasis on local particle
environments. <a
href="https://github.com/glotzerlab/freud">:octocat:</a><a
href="https://freud.readthedocs.io/">:book:</a></li>
<li><a href="https://www.mdanalysis.org/">MDAnalysis</a> - An
object-oriented Python library to analyze trajectories from molecular
dynamics (MD) simulations in many popular formats.</li>
<li><a href="http://mdtraj.org/">MDTraj</a> - A python library that
allows users to manipulate molecular dynamics (MD) trajectories.</li>
<li><a href="https://amber-md.github.io/pytraj/">PyTraj</a> - A Python
front-end of <a
href="https://github.com/Amber-MD/cpptraj">CppTraj</a>.</li>
<li><a href="https://dseams.info">d-SEAMS</a> - Graph network based C++
and Lua based nucleation trajectory analysis software.</li>
</ul>
<h2 id="visualization-tools">Visualization Tools</h2>
<ul>
<li><a href="https://avogadro.cc/">Avogadro</a> - An advanced molecule
editor and visualizer designed for cross-platform use in computational
chemistry, molecular modeling, bioinformatics, materials science, and
related areas. <a
href="https://github.com/cryos/avogadro">:octocat:</a><a
href="https://avogadro.cc/docs/">:book:</a></li>
<li><a href="http://www.ks.uiuc.edu/Research/vmd/">VMD</a> - A molecular
visualization program for displaying, animating, and analyzing large
biomolecular systems using 3-D graphics and built-in scripting. <a
href="http://www.ks.uiuc.edu/Research/vmd/current/docs.html">:book:</a></li>
<li><a href="https://plato-draw.readthedocs.io/">Plato</a> - A python
library for both interactive and figure-grade visualizations of particle
systems. <a href="https://github.com/glotzerlab/plato">:octocat:</a><a
href="https://plato-draw.readthedocs.io">:book:</a></li>
<li><a href="https://pymol.org/2/">PyMOL</a> - A user-sponsored
molecular visualization system on an open-source foundation, maintained
and distributed by Schrödinger. <a
href="http://pymol.sourceforge.net/newman/userman.pdf">:book:</a></li>
<li><a href="https://ovito.org/">OVITO</a> - OVITO is a scientific
visualization and analysis software for atomistic and particle
simulation data. <a href="http://www.ovito.org/manual/">:book:</a></li>
<li><a href="https://github.com/arose/nglview">NGLview</a> - IPython
widget to interactively view molecular structures and trajectories <a
href="http://arose.github.io/nglview/latest/">:book:</a></li>
</ul>
<h2 id="contributing">Contributing</h2>
<p>Your contributions are always welcome! Please read the <a
href="https://github.com/ipudu/awesome-molecular-dynamics/blob/master/contributing.md">contribution
guidelines</a> first.</p>
<h2 id="license">License</h2>
<p><a href="https://creativecommons.org/publicdomain/zero/1.0"><img
src="https://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg"
alt="CC0" /></a></p>
<p>This work is is licensed under the Creative Commons Zero v1.0
Universal.</p>
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Github</a></p>