A curated list of awesome Molecular Dynamics libraries, tools and software.
- code:
- documentation: π
- Computer Simulation of Liquids - A classic book on molecular dynamics and Monte Carlo simulations of liquids.
- Understanding Molecular Simulation: From Algorithms to Applications - Molecular simulation bible.
- 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.
- Amber - A suite of biomolecular simulation programs. π
- CHARMM - A molecular simulation program with broad application to many-particle systems. π
- Gromacs - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
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- HOOMD-Blue - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework.
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- LAMMPS - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
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- OpenMM - A toolkit for molecular simulation using high performance GPU code.
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- Tinker - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
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- CppTraj - Biomolecular simulation trajectory/data analysis.
- Freud - Parallel, python-based analysis with an emphasis on local particle environments.
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- MDAnalysis - An object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.
- MDTraj - A python library that allows users to manipulate molecular dynamics (MD) trajectories.
- PyTraj - A Python front-end of CppTraj.
- Avogadro - An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
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- VMD - A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. π
- Plato - A python library for both interactive and figure-grade visualizations of particle systems.
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- PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by SchrΓΆdinger. π
- OVITO - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. π
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