awesome-molecular-dynamics
Molecular simulator
A curated collection of tools and software for simulating molecular interactions and analyzing resulting trajectories.
A curated list of awesome Molecular Dynamics libraries, tools and software.
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awesome-listmolecular-dynamics
Awesome Molecular Dynamics / 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 | ||
Awesome Molecular Dynamics / 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 | ||
Awesome Molecular Dynamics / 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 | ||
Awesome Molecular Dynamics / Trajectory Analysis | |||
| CppTraj | 139 | 11 months ago | 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 | ||
Awesome Molecular Dynamics / 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 | 827 | 11 months ago | IPython widget to interactively view molecular structures and trajectories |
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