awesome-awesomeness/terminal/moleculardynamics

  

  


                                                                                                        Awesome Molecular Dynamics 
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▐ 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.