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awesome-molecular-dynamics
:sunglasses: A curated list of awesome Molecular Dynamics libraries, tools and software.
https://github.com/ipudu/awesome-molecular-dynamics
Last synced: 3 days ago
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Books
- Computer Simulation of Liquids - A classic book on molecular dynamics and Monte Carlo simulations of liquids. [:octocat:][csol-code]
- Understanding Molecular Simulation: From Algorithms to Applications - Molecular simulation bible. [:octocat:][ums-code]
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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.
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MD Engines/Frameworks
- Amber - A suite of biomolecular simulation programs. [:book:][amber-doc]
- 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 - A molecular simulation program with broad application to many-particle systems. [:book:][charmm-doc]
- Gromacs - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. [:octocat:][gromacs-code][:book:][gromacs-doc]
- HOOMD-Blue - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. [:octocat:][hoomd-code][:book:][hoomd-doc]
- ipi - i-PI: a universal force engine. [:octocat:][ipi-code]
- LAMMPS - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. [:octocat:][lammps-code][:book:][lammps-doc]
- OpenMM - A toolkit for molecular simulation using high performance GPU code. [:octocat:][openmm-code][:book:][openmm-doc]
- Tinker - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. [:octocat:][tinker-code][:book:][tinker-doc]
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Trajectory Analysis
- Freud - Parallel, python-based analysis with an emphasis on local particle environments. [:octocat:][freud-code][:book:][freud-doc]
- MDAnalysis - An object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
- d-SEAMS - Graph network based C++ and Lua based nucleation trajectory analysis software.
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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. [:octocat:][avogadro-code][:book:][avogadro-doc]
- 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 - A python library for both interactive and figure-grade visualizations of particle systems. [:octocat:][plato-code][:book:][plato-doc]
- OVITO - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. [:book:][ovito-doc]
- OVITO - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. [:book:][ovito-doc]
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