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Search results for molecular dynamics
molecular-dynamics
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313 search results found
Lammps
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1,944
Public development project of the LAMMPS MD software package
Openmm
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1,351
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Deepmd Kit
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1,303
A deep learning package for many-body potential energy representation and molecular dynamics
Mdanalysis
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1,154
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Coronavirus
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1,108
Folding@home COVID-19 efforts
Awesome Python Chemistry
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971
A curated list of Python packages related to chemistry
Schnetpack
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688
SchNetPack - Deep Neural Networks for Atomistic Systems
Q E
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524
Mirror of the Quantum ESPRESSO repository. Please do not post Issues or pull requests here. Use gitlab.com/QEF/q-e instead.
Mdtraj
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519
An open library for the analysis of molecular dynamics trajectories
Nequip
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478
NequIP is a code for building E(3)-equivariant interatomic potentials
Torchmd
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465
End-To-End Molecular Dynamics (MD) Engine using PyTorch
Molly.jl
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344
Molecular simulation in Julia
Pyiron
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316
pyiron - an integrated development environment (IDE) for computational materials science.
Plumed2
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308
Development version of plumed 2
Hoomd Blue
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298
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
Pyemma
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292
🚂 Python API for Emma's Markov Model Algorithms 🚂
Openff Toolkit
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286
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
Prolif
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286
Interaction Fingerprints for protein-ligand complexes and more
Gpumd
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273
Graphics Processing Units Molecular Dynamics
Examples
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265
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 "Code" button, or follow the "Releases" link below.
Freud
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248
Powerful, efficient particle trajectory analysis in scientific Python.
Torchmd Net
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238
Neural network potentials
Openmmtools
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214
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Nanoengineer
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210
open-source nanotech CAD
Espresso
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206
The ESPResSo package
Best Of Atomistic Machine Learning
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203
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
Viamd
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191
Visual Interactive Analysis of Molecular Dynamics
Tensormol
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190
Tensorflow + Molecules = TensorMol
Moltemplate
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186
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
Lammps Input Files
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181
LAMMPS inputs and data files
Packmol
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174
Packmol - Initial configurations for molecular dynamics simulations
Chemlab
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173
The chemistry library you were waiting for
Allegro
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169
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
Colvars
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167
Collective variables module for molecular simulation and analysis programs
Perses
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163
Experiments with expanded ensembles to explore chemical space
Vde
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161
Variational Autoencoder for Dimensionality Reduction of Time-Series
Alchemlyb
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161
the simple alchemistry library
Mbuild
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156
A hierarchical, component based molecule builder
Pytraj
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154
Python interface of cpptraj
Gromacswrapper
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154
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2023 supported).
Yank
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150
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Mdgrad
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150
Pytorch differentiable molecular dynamics
Timemachine
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134
Differentiate all the things!
Molecular Design Toolkit
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131
Notebook-integrated tools for molecular simulation and visualization
Drug Computing
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131
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Msmbuilder
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124
🏗️ Statistical models for biomolecular dynamics 🏗️
Senpai
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124
Molecular dynamics simulation software
Sgdml
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124
sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model
Nbodysimulator.jl
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122
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
Molecular Dynamics Simulation
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122
Sample codes for my book on molecular dynamics simulation
Fftool
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117
Tool to build force field input files for molecular simulation
Loos
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114
LOOS: a lightweight object-oriented structure analysis library
Lumol
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113
Universal extensible molecular simulation engine
Tinker
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112
Tinker: Software Tools for Molecular Design
Iodata
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108
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Foyer
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105
A package for atom-typing as well as applying and disseminating forcefields
Radonpy
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98
RadonPy is a Python library to automate physical property calculations for polymer informatics.
Aboria
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83
Enables computations over a set of particles in N-dimensional space
Awesome Molecular Docking
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81
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
Dynaphopy
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78
Phonon anharmonicity analysis from molecular dynamics
Pensa
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77
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
Celllistmap.jl
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76
Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.
Openfe
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74
The Open Free Energy toolkit
Mcmd
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74
Monte Carlo and Molecular Dynamics Simulation Package
Vermouth Martinize
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71
Describe and apply transformation on molecular structures and topologies
Openmd
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68
Molecular Dynamics in the Open
Pytim
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68
a python package for the interfacial analysis of molecular simulations
Mdbenchmark
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67
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
Lammpstutorials.github.io
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65
LAMMPS tutorials for both beginners and advanced users
Biosimspace
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64
Code and resources for the EPSRC BioSimSpace project.
Nnpops
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60
High-performance operations for neural network potentials
Quantum Mechanics
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56
A collection of interactive notebooks to explain concepts of quantum mechanics and related topics
Pyscal
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55
Python library written in C++ for calculation of local atomic structural environment
Litmatter
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55
Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.
Dockingpie
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54
A Consensus Docking Plugin for PyMOL
Pwtools
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53
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.
Physical_validation
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52
Physical validation of molecular simulations
Uf3
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51
UF3: a python library for generating ultra-fast interatomic potentials
Sharc
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50
The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.
Taichimd
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50
Interactive, GPU-accelerated Molecular Dynamics using the Taichi programming language
Mlcgmd
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49
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
Isicle
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49
In silico chemical library engine for high-accuracy chemical property prediction
Solarsystem
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49
A solar system simulator with Verlet, using OpenGL for displaying.
Biosimspace
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48
An interoperable Python framework for biomolecular simulation.
Nqcdynamics.jl
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48
Fast and flexible nonadiabatic molecular dynamics in Julia!
Gdynet
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47
Unsupervised learning of atomic scale dynamics from molecular dynamics.
P4vasp
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46
p4vasp, the VASP Visualization Tool
Tinker9
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44
Tinker9: Next Generation of Tinker with GPU Support
Calphy
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44
A Python library and command line interface for automated free energy calculations
Wepy
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44
Weighted Ensemble simulation framework in Python
Uammd
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43
A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.
Prophet
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43
PROPhet is a code to integrate machine learning techniques with first-principles quantum chemistry approaches
Clandp
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42
Force field for ionic liquids.
Mlff
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42
Build neural networks for machine learning force fields with JAX
Gdpy
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41
Generating Deep Potential with Python
Libra Code
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41
Votca
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40
The source of the votca-csg and xtp packages
Martini3 Small Molecules
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39
Martini 3 small-molecule database
Symd
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36
N-Dimensional MD engine with symmetry group constraints
Pycontact
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34
Analysis of non-covalent interactions in MD trajectories
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