awesome-molecular-dynamics
by ipudu
A curated list of awesome Molecular Dynamics libraries, tools and software.
AI summary
Molecular simulator
A curated collection of tools and software for simulating molecular interactions and analyzing resulting trajectories.
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What's in the list
26 links in 5 sections, with live GitHub stats.activeno commit in 2y
Books
- 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
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
MD Engines/Frameworks
- Amber
A suite of biomolecular simulation programs
- ASE
The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations
- CHARMM
A molecular simulation program with broad application to many-particle systems
- Gromacs
A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids
- HOOMD-Blue
A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework
- ipi
i-PI: a universal force engine
- LAMMPS
A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator
- OpenMM
A toolkit for molecular simulation using high performance GPU code
- pyiron
pyiron - an integrated development environment (IDE) for computational materials science
- Tinker
A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers
Trajectory Analysis
CppTraj
Biomolecular simulation trajectory/data analysis
- Freud
Parallel, python-based analysis with an emphasis on local particle environments
- 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
- d-SEAMS
Graph network based C++ and Lua based nucleation trajectory analysis software
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
- VMD
A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
- Plato
A python library for both interactive and figure-grade visualizations of particle systems
- PyMOL
A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger
- OVITO
OVITO is a scientific visualization and analysis software for atomistic and particle simulation data
NGLview
IPython widget to interactively view molecular structures and trajectories
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Featured in 2 awesome lists
Each link jumps to the spot where the list mentions awesome-molecular-dynamics.
