GitHub topics: molecular-dynamics
TinkerTools/tinker
Tinker: Software Tools for Molecular Design
Language: Fortran - Size: 118 MB - Last synced at: about 4 hours ago - Pushed at: about 4 hours ago - Stars: 140 - Forks: 69
cmelab/flowerMD
Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics.
Language: Python - Size: 35.6 MB - Last synced at: about 9 hours ago - Pushed at: about 10 hours ago - Stars: 17 - Forks: 9
mdtraj/mdtraj
An open library for the analysis of molecular dynamics trajectories
Language: Python - Size: 35 MB - Last synced at: about 12 hours ago - Pushed at: about 13 hours ago - Stars: 635 - Forks: 288
MDAnalysis/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Language: Python - Size: 511 MB - Last synced at: about 2 hours ago - Pushed at: 4 days ago - Stars: 1,423 - Forks: 711
NQCD/NQCDynamics.jl
Fast and flexible nonadiabatic molecular dynamics in Julia!
Language: Julia - Size: 59.5 MB - Last synced at: about 3 hours ago - Pushed at: about 3 hours ago - Stars: 63 - Forks: 7
Fraunhofer-SCAI/VMDatomistic
A minimal package for providing pretrained machine learning force fields (e.g. multi-fidelity M3GNet) for material simulations.
Language: Python - Size: 2.02 MB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 0 - Forks: 0
chemosim-lab/ProLIF
Interaction Fingerprints for protein-ligand complexes and more
Language: Python - Size: 11.3 MB - Last synced at: about 5 hours ago - Pushed at: about 6 hours ago - Stars: 410 - Forks: 80
rodyherrera/Trybo
Nanotribology Simulation Framework. Create modern workflows to automate the study of friction wear with Lammps and OVITO 🚀
Language: Python - Size: 62.3 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
sb-ncbr/gromacs-metadump
A tool to describe Gromacs molecular dynamics simulations with powerful metadata
Language: TypeScript - Size: 575 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0
Martini-Force-Field-Initiative/M3_Ionizable_Lipids
Martini 3 Building Blocks for Lipid Nanoparticle Design
Language: Jupyter Notebook - Size: 167 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 15 - Forks: 3
lammpstutorials/lammpstutorials.github.io
LAMMPS tutorials for both beginners and advanced users
Language: Shell - Size: 733 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 114 - Forks: 20
metatensor/metatrain
Training and evaluating machine learning models for atomistic systems.
Language: Python - Size: 92.6 MB - Last synced at: about 6 hours ago - Pushed at: about 16 hours ago - Stars: 32 - Forks: 8
hozeren/multigro
MultiGRO: Automated methods for GROMACS simulations.
Language: Python - Size: 245 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 2
ci-lab-cz/streamd
Fully automated high-throughput MD pipeline
Language: Python - Size: 6.23 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 60 - Forks: 16
markovmodel/PyEMMA 📦
🚂 Python API for Emma's Markov Model Algorithms 🚂
Language: Python - Size: 10.3 MB - Last synced at: about 17 hours ago - Pushed at: over 1 year ago - Stars: 324 - Forks: 122
OpenFreeEnergy/openfe
The Open Free Energy toolkit
Language: Python - Size: 65.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 162 - Forks: 25
espressomd/espresso
The ESPResSo package
Language: C++ - Size: 152 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 241 - Forks: 188
ccp5UK/dl-poly
mirrored from https://gitlab.com/ccp5/dl-poly/
Language: Fortran - Size: 39 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 1
inductiva/inductiva
Large scale simulations made simple.
Language: Python - Size: 754 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 35 - Forks: 5
MrRezaeiUofT/IDFF
Implicit Dynamical Flow Fusion (IDFF) for Generative Modeling
Language: Jupyter Notebook - Size: 172 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0
svats73/mdml
mdml: Deep Learning for Molecular Simulations
Language: Python - Size: 5.92 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 2
Ladme/gorder
Calculate lipid order parameters from Gromacs simulations
Language: Rust - Size: 333 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0
glotzerlab/hoomd-examples
HOOMD-blue example scripts.
Language: Jupyter Notebook - Size: 63.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 35 - Forks: 14
glotzerlab/freud
Powerful, efficient particle trajectory analysis in scientific Python.
Language: C++ - Size: 82.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 292 - Forks: 51
RaulPPelaez/UAMMD
A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.
Language: Cuda - Size: 15.9 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 56 - Forks: 14
glotzerlab/hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
Language: C++ - Size: 72 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 373 - Forks: 141
ISISNeutronMuon/MDANSE
MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
Language: Python - Size: 863 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 26 - Forks: 6
huichenggong/GrandFEP
Alchemical Free Energy Calculations with Grand Canonical Ensemble
Language: Python - Size: 12 MB - Last synced at: about 8 hours ago - Pushed at: about 9 hours ago - Stars: 1 - Forks: 0
JuliaMolSim/Molly.jl
Molecular simulation in Julia
Language: Julia - Size: 83.9 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 427 - Forks: 58
macrocosm-os/mainframe
Generalized Scientific Compute on BIttensor
Language: Python - Size: 45.8 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 20 - Forks: 21
NMRDfromMD/dataset-LJ-fluid
This repository contains a dataset for the NMRDfromMD Python package.
Language: Jupyter Notebook - Size: 57 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
brucefan1983/GPUMD
Graphics Processing Units Molecular Dynamics
Language: Cuda - Size: 305 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 560 - Forks: 135
pujanajmera/pycpet
Computing Protein Electric Field Topology in python, built for high-throughput accelerated calculations
Language: Python - Size: 28.2 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 0
molmod/psiflow
scalable molecular simulation
Language: Python - Size: 25.7 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 136 - Forks: 13
apax-hub/apax
A flexible and performant framework for training machine learning potentials.
Language: Python - Size: 5.22 MB - Last synced at: about 13 hours ago - Pushed at: about 15 hours ago - Stars: 19 - Forks: 3
lab-cosmo/pet-mad
PET-MAD, a universal interatomic potential for advanced materials modeling
Language: Python - Size: 146 KB - Last synced at: 5 days ago - Pushed at: 14 days ago - Stars: 62 - Forks: 3
lammps/lammps
Public development project of the LAMMPS MD software package
Language: C++ - Size: 762 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2,465 - Forks: 1,811
gph82/mdciao
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data
Language: Python - Size: 76.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 33 - Forks: 5
JuDFTteam/best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
Size: 5.63 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 490 - Forks: 44
rinikerlab/Physical_Chemistry_Practicum-Molecular_Dynamics_Simulations
This repository is the used for teaching the Physical Chemistry Practicum about Molecular Dynamics (MD) simulations for pharmacy and biology students at ETHZ
Language: Jupyter Notebook - Size: 11.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 11 - Forks: 0
hheelweg/PyeDNA
create DNA/dye structures, perform AMBER MD and analyze trajectory data classically and quantum-mechanically (pyscf)
Language: Python - Size: 23.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0
AspirinCode/awesome-AI4MolConformation-MD
List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
Size: 4.45 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 184 - Forks: 17
NMRDfromMD/nmrdfrommd.github.io
This repository contains the documentation for the NMRDfromMD Python package.
Size: 31.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 0
SciML/NBodySimulator.jl
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
Language: Julia - Size: 600 KB - Last synced at: 5 days ago - Pushed at: 7 months ago - Stars: 136 - Forks: 19
Colvars/colvars
Collective variables library for molecular simulation and analysis programs
Language: C++ - Size: 42.6 MB - Last synced at: 3 days ago - Pushed at: 6 days ago - Stars: 222 - Forks: 58
yesint/molar
Repository for molar crate and its dependencies
Language: Rust - Size: 84.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 31 - Forks: 2
zincware/ZnH5MD
ZnH5MD - High Performance Interface for H5MD Trajectories
Language: Python - Size: 775 KB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 0
zincware/MDSuite
A post-processing engine for particle simulations
Language: Python - Size: 52.2 MB - Last synced at: about 8 hours ago - Pushed at: about 9 hours ago - Stars: 41 - Forks: 8
zincware/IPSuite
Machine Learned Interatomic Potential Tools
Language: Python - Size: 4.12 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 23 - Forks: 11
deepmodeling/deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
Language: Python - Size: 63.5 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1,635 - Forks: 544
ACEsuit/mace-foundations
MACE foundation models (MP, OMAT, Matpes)
Language: Shell - Size: 37.1 KB - Last synced at: 5 days ago - Pushed at: about 2 months ago - Stars: 103 - Forks: 10
jxxcr/mdkits
kits for md or dft
Language: Python - Size: 170 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 2 - Forks: 0
mosdef-hub/foyer
A package for atom-typing as well as applying and disseminating forcefields
Language: Python - Size: 31.6 MB - Last synced at: about 7 hours ago - Pushed at: about 7 hours ago - Stars: 128 - Forks: 78
m3g/packmol
Packmol - Initial configurations for molecular dynamics simulations
Language: Fortran - Size: 11.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 265 - Forks: 51
mqcomplab/MDANCE
MDANCE is a flexible n-ary clustering package for all applications.
Language: Python - Size: 62.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 55 - Forks: 5
GMPavanLab/dynsight
A framework for the analysis of the dynamics of particle trajectories
Language: Python - Size: 47 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 6
plumed/plumed2
Development version of plumed 2
Language: C++ - Size: 184 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 423 - Forks: 300
lab-cosmo/torch-pme
Particle-mesh based calculations of long-range interactions in PyTorch
Language: Python - Size: 8.07 MB - Last synced at: 5 days ago - Pushed at: 8 days ago - Stars: 47 - Forks: 5
lab-cosmo/atomistic-cookbook
A collection of simulation recipes for the atomic-scale modeling of materials and molecules
Language: Python - Size: 86.5 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 22 - Forks: 2
Syrocco/Voronoi
Voronoi based molecular dynamics of cell
Language: C - Size: 325 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0
ricalessandri/Martini3-small-molecules
Martini 3 small-molecule database
Language: Shell - Size: 27.9 MB - Last synced at: 4 days ago - Pushed at: 9 months ago - Stars: 60 - Forks: 12
simongravelle/simongravelle
README file for Github profile
Language: Jupyter Notebook - Size: 49.7 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 4 - Forks: 0
CCPBioSim/BioSim-analysis-workshop
Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations
Language: Jupyter Notebook - Size: 144 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 3 - Forks: 3
tjira/acorn
Fast and simple way to electronic structure methods.
Language: Zig - Size: 46.2 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0
torchmd/torchmd-net
Training neural network potentials
Language: Python - Size: 179 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 399 - Forks: 85
marrink-lab/vermouth-martinize
Describe and apply transformation on molecular structures and topologies
Language: Python - Size: 6.98 MB - Last synced at: 7 days ago - Pushed at: 12 days ago - Stars: 112 - Forks: 49
NMRDfromMD/dataset-peg-water-mixture
This repository contains a dataset for the NMRDfromMD Python package.
Language: Python - Size: 7.81 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0
simongravelle/nmrformd
NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.
Language: Python - Size: 309 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 23 - Forks: 4
Sergi-Ortiz/CompChem-TFG
Scripts used in the Chemistry final BSc project (Treball de Fi de Grau)
Language: C - Size: 220 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0
pnnl/isicle
In silico chemical library engine for high-accuracy chemical property prediction
Language: Python - Size: 19.9 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 60 - Forks: 20
openmm/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Language: C++ - Size: 119 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1,591 - Forks: 547
BradyAJohnston/MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Language: Python - Size: 885 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1,013 - Forks: 98
jparkhill/TensorMol
Tensorflow + Molecules = TensorMol
Language: Python - Size: 102 MB - Last synced at: 9 days ago - Pushed at: about 4 years ago - Stars: 273 - Forks: 73
Yuanming-Song/gmx2charmm
GROMACS to CHARMM Force Field File Converter
Language: Shell - Size: 383 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
mosdef-hub/mbuild
A hierarchical, component based molecule builder
Language: Python - Size: 74.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 192 - Forks: 82
mir-group/pair_nequip_allegro
LAMMPS pair styles for NequIP and Allegro deep learning interatomic potentials
Language: C++ - Size: 390 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 41 - Forks: 8
pyscal/pyscal
Python library written in C++ for calculation of local atomic structural environment
Language: C++ - Size: 13.1 MB - Last synced at: 10 days ago - Pushed at: 8 months ago - Stars: 61 - Forks: 16
mir-group/allegro
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
Language: Python - Size: 309 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 389 - Forks: 54
DestinEcarma/t-ccd-prototype
A Trajectory-Based Continuous Collision Detection for 2D Particle Systems
Language: Jupyter Notebook - Size: 395 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0
ADicksonLab/wepy
Weighted Ensemble simulation framework in Python
Language: Python - Size: 49.2 MB - Last synced at: 8 days ago - Pushed at: 10 days ago - Stars: 54 - Forks: 20
choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Language: Python - Size: 33 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 271 - Forks: 85
mir-group/nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
Language: Python - Size: 3.8 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 718 - Forks: 154
pyiron/pyiron
pyiron - an integrated development environment (IDE) for computational materials science.
Language: Jupyter Notebook - Size: 45.3 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 397 - Forks: 51
alchemistry/alchemlyb
the simple alchemistry library
Language: Python - Size: 2.26 MB - Last synced at: 10 days ago - Pushed at: 5 months ago - Stars: 213 - Forks: 52
uf3/uf3
UF3: a python library for generating ultra-fast interatomic potentials
Language: Python - Size: 18.6 MB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 65 - Forks: 26
azminewasi/Awesome-Graph-Research-ICML2024
All graph/GNN papers accepted at the International Conference on Machine Learning (ICML) 2024.
Size: 188 KB - Last synced at: 11 days ago - Pushed at: 6 months ago - Stars: 204 - Forks: 14
openforcefield/openff-toolkit
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
Language: Python - Size: 218 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 339 - Forks: 97
MolarVerse/PQAnalysis
PQAnalysis is a API/CLI python package for the analysis of MD simulations
Language: Python - Size: 13.9 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 6 - Forks: 1
deepmodeling/dpti
A Python Package to Automate Thermodynamic Integration Calculations for Free Energy
Language: Python - Size: 766 KB - Last synced at: about 7 hours ago - Pushed at: about 9 hours ago - Stars: 27 - Forks: 20
bjmorgan/kinisi
A Python package for estimating diffusion properties from molecular dynamics simulations.
Language: Python - Size: 154 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 66 - Forks: 12
multi-ego/multi-eGO
Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations
Language: Python - Size: 384 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 14 - Forks: 10
thorben-frank/mlff
Build neural networks for machine learning force fields with JAX
Language: Python - Size: 14.1 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 115 - Forks: 26
PHOTOX/ABIN
Multipurpose ab initio MD program.
Language: Fortran - Size: 12.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 9 - Forks: 5
atomistic-machine-learning/schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
Language: Python - Size: 42.1 MB - Last synced at: 9 days ago - Pushed at: 14 days ago - Stars: 841 - Forks: 228
lmmentel/awesome-python-chemistry
A curated list of Python packages related to chemistry
Size: 224 KB - Last synced at: 12 days ago - Pushed at: 7 months ago - Stars: 1,220 - Forks: 220
theochem/iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Language: Python - Size: 5.07 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 137 - Forks: 48
wolearyc/ramannoodle
Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and machine learning..
Language: Python - Size: 11 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 3
alexrmelnick/Molecular-Dynamics-Simulation
EC527 High Performance Programming with Multicore and GPUs Final Project: Molecular Dynamics Simulator with Cell Lists and Range-Limited Forces
Language: Jupyter Notebook - Size: 959 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0
omidshy/aMD
A collection of Python codes to calculate physical properties from molecular dynamics simulations.
Language: Python - Size: 7.42 MB - Last synced at: 15 days ago - Pushed at: 16 days ago - Stars: 15 - Forks: 2
quantaosun/Ambertools-OpenMM-MD
Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.
Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 34 - Forks: 6
