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The Top 512 Molecular Dynamics Open Source Projects

Categories > Science > Molecular Dynamics
Lammps ⭐ 1,540
Public development project of the LAMMPS MD software package
most recent commit 2 days ago
Coronavirus ⭐ 1,108
[email protected] COVID-19 efforts
most recent commit 2 years ago
Openmm ⭐ 1,090
OpenMM is a toolkit for molecular simulation using high performance GPU code.
dependent packages 16total releases 4most recent commit 3 days ago
Deepmd Kit ⭐ 1,000
A deep learning package for many-body potential energy representation and molecular dynamics
total releases 33most recent commit 12 hours ago
Mdanalysis ⭐ 924
MDAnalysis is a Python library to analyze molecular dynamics simulations.
dependent packages 53total releases 38most recent commit 2 days agopypi MDAnalysis} Downloads
Awesome Python Chemistry ⭐ 733
A curated list of Python packages related to chemistry
most recent commit a month ago
Schnetpack ⭐ 538
SchNetPack - Deep Neural Networks for Atomistic Systems
dependent packages 2total releases 4most recent commit 2 days agopypi schnetpack} Downloads
Q E ⭐ 482
Mirror of the Quantum ESPRESSO repository. Please do not post Issues or pull requests here. Use gitlab.com/QEF/q-e instead.
total releases 5most recent commit a month ago
Mdtraj ⭐ 410
An open library for the analysis of molecular dynamics trajectories
dependent packages 7total releases 5most recent commit a month ago
Nequip ⭐ 289
NequIP is a code for building E(3)-equivariant interatomic potentials
total releases 2most recent commit 5 days ago
Plumed2 ⭐ 255
Development version of plumed 2
dependent packages 2total releases 12most recent commit 3 days ago
Pyemma ⭐ 254
🚂 Python API for Emma's Markov Model Algorithms 🚂
dependent packages 3total releases 46most recent commit a month agopypi pyEMMA} Downloads
Pyiron ⭐ 246
pyiron - an integrated development environment (IDE) for computational materials science.
total releases 682most recent commit 6 days ago
Molly.jl ⭐ 241
Molecular simulation in Julia
most recent commit 20 days ago
Hoomd Blue ⭐ 225
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
total releases 11most recent commit 2 days ago
Openff Toolkit ⭐ 219
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
dependent packages 10total releases 10most recent commit 4 days ago
Nanoengineer ⭐ 210
open-source nanotech CAD
most recent commit 8 years ago
Torchmd ⭐ 203
End-To-End Molecular Dynamics (MD) Engine using PyTorch
dependent packages 1total releases 2most recent commit a year agopypi torchmd} Downloads
Examples ⭐ 197
Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Clone or download" button, or follow the "...releases" link below.
most recent commit 3 months ago
Prolif ⭐ 195
Interaction Fingerprints for protein-ligand complexes and more
total releases 12most recent commit 9 days ago
Freud ⭐ 192
Powerful, efficient particle trajectory analysis in scientific Python.
dependent packages 5total releases 24most recent commit 2 days agopypi freud-analysis} Downloads
Tensormol ⭐ 190
Tensorflow + Molecules = TensorMol
most recent commit 5 years ago
Espresso ⭐ 177
The ESPResSo package
most recent commit 9 days ago
Chemlab ⭐ 173
The chemistry library you were waiting for
total releases 5most recent commit 5 years ago
Moltemplate ⭐ 165
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
total releases 108most recent commit 7 hours ago
Gpumd ⭐ 165
Graphics Processing Units Molecular Dynamics
most recent commit 3 days ago
Vde ⭐ 161
Variational Autoencoder for Dimensionality Reduction of Time-Series
most recent commit 7 months ago
Openmmtools ⭐ 150
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
dependent packages 4total releases 10most recent commit a month ago
Yank ⭐ 139
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
dependent packages 1total releases 1most recent commit 4 months ago
Colvars ⭐ 135
Collective variables module for molecular simulation and analysis programs
most recent commit 12 days ago
Molecular Design Toolkit ⭐ 131
Notebook-integrated tools for molecular simulation and visualization
most recent commit 5 years ago
Gromacswrapper ⭐ 128
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2021 supported).
dependent packages 2total releases 12most recent commit 5 months agopypi GromacsWrapper} Downloads
Msmbuilder ⭐ 124
🏗 Statistical models for biomolecular dynamics 🏗
dependent packages 1total releases 15most recent commit 2 years agopypi msmbuilder} Downloads
Mbuild ⭐ 123
A hierarchical, component based molecule builder
dependent packages 2total releases 17most recent commit 2 days ago
Pytraj ⭐ 123
Python interface of cpptraj
dependent packages 6total releases 33most recent commit 20 days agopypi pytraj} Downloads
Alchemlyb ⭐ 123
the simple alchemistry library
total releases 2most recent commit 20 days ago
Senpai ⭐ 117
Molecular dynamics simulation software
most recent commit 5 months ago
Packmol ⭐ 116
Packmol - Initial configurations for molecular dynamics simulations
most recent commit 8 days ago
Perses ⭐ 115
Experiments with expanded ensembles to explore chemical space
total releases 9most recent commit 11 days ago
Lumol ⭐ 113
Universal extensible molecular simulation engine
most recent commit 2 years ago
Nbodysimulator.jl ⭐ 110
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
most recent commit 4 days ago
Mdgrad ⭐ 108
Pytorch differentiable molecular dynamics
most recent commit 3 months ago
Drug Computing ⭐ 100
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
most recent commit 9 months ago
Loos ⭐ 99
LOOS: a lightweight object-oriented structure analysis library
most recent commit 13 days ago
Timemachine ⭐ 97
Differentiate all the things!
most recent commit 3 days ago
Torchmd Net ⭐ 92
Neural network potentials based on graph neural networks and equivariant transformers
most recent commit 4 days ago
Sgdml ⭐ 91
sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model
most recent commit a month ago
Tinker ⭐ 90
Tinker: Software Tools for Molecular Design
most recent commit 9 days ago
Lammps Input Files ⭐ 86
LAMMPS inputs and data files
most recent commit 2 months ago
Aboria ⭐ 83
Enables computations over a set of particles in N-dimensional space
most recent commit 4 years ago
Foyer ⭐ 80
A package for atom-typing as well as applying and disseminating forcefields
dependent packages 1total releases 12most recent commit 5 days ago
Allegro ⭐ 73
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
most recent commit 13 days ago
Dynaphopy ⭐ 73
Phonon anharmonicity analysis from molecular dynamics
dependent packages 2total releases 35most recent commit 7 months agopypi dynaphopy} Downloads
Iodata ⭐ 68
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
total releases 4most recent commit a year ago
Biosimspace ⭐ 60
Code and resources for the EPSRC BioSimSpace project.
most recent commit 3 days ago
Openmd ⭐ 60
Molecular Dynamics in the Open
most recent commit 17 days ago
Celllistmap.jl ⭐ 58
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbour lists, etc.
most recent commit 6 days ago
Fftool ⭐ 56
Tool to build force field input files for molecular simulation.
most recent commit a year ago
Mcmd ⭐ 53
Monte Carlo and Molecular Dynamics Simulation Package
most recent commit 2 years ago
Taichimd ⭐ 50
Interactive, GPU-accelerated Molecular Dynamics using the Taichi programming language
most recent commit 6 months ago
Pytim ⭐ 50
a python package for the interfacial analysis of molecular simulations
dependent packages 1total releases 18most recent commit 4 months agopypi pytim} Downloads
Nnpops ⭐ 50
High-performance operations for neural network potentials
most recent commit 5 days ago
Mdbenchmark ⭐ 49
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
total releases 15most recent commit 2 years ago
Pwtools ⭐ 47
pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS. It is almost, but not quite, entirely unlike ASE, with some tools extending numpy/scipy. It has a set of powerful parsers and data types for storing calculation data.
total releases 4most recent commit a month ago
Gdynet ⭐ 47
Unsupervised learning of atomic scale dynamics from molecular dynamics.
most recent commit a year ago
P4vasp ⭐ 46
p4vasp, the VASP Visualization Tool
most recent commit 3 years ago
Vermouth Martinize ⭐ 45
Describe and apply transformation on molecular structures and topologies
dependent packages 1total releases 13most recent commit 2 days agopypi vermouth} Downloads
Solarsystem ⭐ 43
A solar system simulator with Verlet, using OpenGL for displaying.
most recent commit 2 months ago
Prophet ⭐ 43
PROPhet is a code to integrate machine learning techniques with first-principles quantum chemistry approaches
most recent commit 5 years ago
Tinker9 ⭐ 38
Tinker9: Next Generation of Tinker with GPU Support
most recent commit 18 days ago
Nqcdynamics.jl ⭐ 37
Fast and flexible nonadiabatic molecular dynamics in Julia!
most recent commit 16 days ago
Symd ⭐ 36
N-Dimensional MD engine with symmetry group constraints
total releases 4most recent commit 4 days ago
Wepy ⭐ 36
Weighted Ensemble simulation framework in Python
total releases 24most recent commit 23 days ago
Pyscal ⭐ 36
Python library written in C++ for calculation of local atomic structural environment
dependent packages 2total releases 34most recent commit a month ago
Minimd ⭐ 34
MiniMD Molecular Dynamics Mini-App
most recent commit 8 months ago
Quantum Mechanics ⭐ 34
A collection of jupyter notebooks for quantum mechanics tutorials.
most recent commit 5 days ago
Libra Code ⭐ 34
most recent commit 2 months ago
Physical_validation ⭐ 33
Physical validation of molecular simulations
total releases 13most recent commit 20 days ago
Sharc ⭐ 32
The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.
most recent commit 6 months ago
Aimnet ⭐ 31
Atoms In Molecules Neural Network Potential
most recent commit 3 years ago
Openfe ⭐ 31
The Open Free Energy toolkit
most recent commit 2 days ago
Uammd ⭐ 31
A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.
most recent commit 2 days ago
Pycgtool ⭐ 30
Generate coarse-grained molecular dynamics models from atomistic trajectories.
total releases 7most recent commit 9 months ago
Lstm Predict Md ⭐ 30
Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network
most recent commit 5 months ago
Pyemma_tutorials ⭐ 29
How to analyze molecular dynamics data with PyEMMA
most recent commit 4 years ago
Awesome Molecular Dynamics ⭐ 28
😎 A curated list of awesome Molecular Dynamics libraries, tools and software.
most recent commit a year ago
Votca ⭐ 28
The source of the votca-csg and xtp packages
most recent commit 5 days ago
Hoomd Tf ⭐ 27
A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD
most recent commit a year ago
Fahbench ⭐ 27
[email protected] GPU benchmark
most recent commit 3 years ago
Contact_map ⭐ 27
Contact map analysis for biomolecules; based on MDTraj
most recent commit 3 months ago
Clandp ⭐ 27
Force field for ionic liquids.
most recent commit a year ago
Qball ⭐ 27
Qball (also known as [email protected]) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.
most recent commit 3 years ago
Molpx ⭐ 27
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
most recent commit 4 years ago
Enspara ⭐ 26
Modeling molecular ensembles with scalable data structures and parallel computing
most recent commit 5 months ago
Seams Core ⭐ 26
The d-SEAMS C++ core engine
most recent commit a month ago
Mgmol ⭐ 26
MGmol is a scalable O(N) First-Principles Molecular Dynamics code that is capable of performing large-scale electronics structure calculations and molecular dynamics simulations of atomistic systems.
most recent commit 10 months ago
Mddatasetbuilder ⭐ 25
A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.
most recent commit 10 days ago
Comd ⭐ 25
Classical molecular dynamics proxy application.
most recent commit 2 years ago
Barnaba ⭐ 25
Analyse Nucleic Acids Structure and Simulations with baRNAba
total releases 4most recent commit 2 months ago
Calphy ⭐ 25
A Python library and command line interface for automated free energy calculations
total releases 9most recent commit a month ago
1-100 of 512 projects
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