molecular-dynamics

There are 72 repositories under molecular-dynamics topic.

lammps
lammps / lammps
Public development project of the LAMMPS MD software package
kokkos lammps molecular-dynamics simulation
Language:C++ 2059
openmm / openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
molecular-dynamics simulation
Language:C++ 1392
deepmd-kit
deepmodeling / deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
deep-learning molecular-dynamics deepmd lammps potential-energy python tensorflow cpp cuda rocm ipi ase computational-chemistry materials-science c nodejs pytorch
Language:C++ 1375
MDAnalysis / mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
molecular-dynamics python science trajectory-analysis molecular-simulation molecular-dynamics-simulation mdanalysis computational-chemistry
Language:Python 1230
FoldingAtHome / coronavirus
Folding@home COVID-19 efforts
sars-cov-2 foldingathome folding-at-home molecular-dynamics covid-19
Language:Python 1095
lmmentel / awesome-python-chemistry
A curated list of Python packages related to chemistry
atomistic-simulations chemistry computational-chemistry molecular-dynamics python-chemistry quantum-chemistry simulation
1029
atomistic-machine-learning / schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
condensed-matter machine-learning molecular-dynamics neural-network quantum-chemistry
Language:Python 731
mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
molecular-dynamics python mdtraj rmsd dihedral-angles pdb pdb-files molecular-dynamics-trajectories
Language:Python 554
nequip
mir-group / nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch
Language:Python 534
torchmd / torchmd
End-To-End Molecular Dynamics (MD) Engine using PyTorch
molecular-dynamics coarse-grained-molecular-dynamics machine-learning neural-networks pytorch pytorch-lightning
Language:Python 511
brucefan1983 / GPUMD
Graphics Processing Units Molecular Dynamics
cuda gpu gpumd heat-transport high-performance-computing machine-learning machine-learning-potential molecular-dynamics molecular-dynamics-simulation natural-evolution-strategies neural-network neuroevolution phonon physics-simulation simulation
Language:Cuda 366
JuliaMolSim / Molly.jl
Molecular simulation in Julia
molecular-dynamics julia protein-structure physics-simulation structural-bioinformatics molecular-simulation lennard-jones
Language:Julia 366
pyiron
pyiron / pyiron
pyiron - an integrated development environment (IDE) for computational materials science.
pyiron python molecular-dynamics ab-initio development-environment simulation ide ase hdf5 vasp lammps dft
Language:Jupyter Notebook 331
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis drug-discovery
Language:Python 324
plumed / plumed2
Development version of plumed 2
molecular-dynamics plugin c-plus-plus plumed free-energy plumed2 enhanced-sampling trajectory-analysis
Language:C++ 315
glotzerlab / hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
cuda python molecular-dynamics hard-particle hoomd-blue simulation gpu singularity docker conda-forge particle-system monte-carlo-simulation
Language:C++ 314
markovmodel / PyEMMA
🚂 Python API for Emma's Markov Model Algorithms 🚂
python hidden-markov-model molecular-dynamics analysis markov-state-model tica time-series hmm bayesian-methods markov-model mbar kinetic-modeling umbrella-sampling molecular-modeling
Language:Python 304
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
molecular-dynamics force-fields openmm amber chemical-environment-perception smirnoff-force-field molecular-mechanics nsf-grant-che-1738979 open-force-field-consortium forcefield forcefield-parameterization
Language:Python 296
Allen-Tildesley / examples
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.
molecular-dynamics monte-carlo molecular-dynamics-simulation monte-carlo-simulation
Language:Fortran 285
mir-group / allegro
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
atomistic-simulations computational-chemistry deep-learning drug-discovery force-fields interatomic-potentials machine-learning materials-science molecular-dynamics pytorch
Language:Python 285
torchmd / torchmd-net
Neural network potentials
molecular-dynamics energy-functions neural-networks equivariant-representations transformer
Language:Python 280
jparkhill / TensorMol
Tensorflow + Molecules = TensorMol
tensorflow molecules neural-network chemistry molecular-dynamics molecular-simulation simulation force-field monte-carlo meta-dynamics machine-learning
Language:Python 269
freud
glotzerlab / freud
Powerful, efficient particle trajectory analysis in scientific Python.
molecular-dynamics analysis scientific-computing python monte-carlo-simulation data-analysis spatial-analysis particle-system computational-chemistry computational-physics science hacktoberfest
Language:C++ 260
JuDFTteam / best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
atomistic-machine-learning awesome-list best-of-list computational-chemistry computational-materials-science condensed-matter density-functional-theory drug-discovery electronic-structure interatomic-potentials materials-discovery materials-informatics molecular-dynamics scientific-computing surrogate-models scientific-machine-learning quantum-chemistry ai4science
250
jewettaij / moltemplate
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
molecule-builder lammps molecular-dynamics force-fields coarse-grained-molecular-dynamics molecule-editor opls amber open-science lammps-data lammps-tool lammps-script-creator
Language:Python 241
choderalab / openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
openmm molecular-dynamics alchemical-free-energy-calculations integrators free-energy-calculations molecular-simulations python mcmc markov-chain-monte-carlo replica-exchange
Language:Python 235
espresso
espressomd / espresso
The ESPResSo package
c-plus-plus scientific-computing soft-matter molecular-dynamics lattice-boltzmann physics python
Language:C++ 218
chemlab / chemlab
The chemistry library you were waiting for
chemistry python physics molecular-dynamics molecular-graphics
Language:Python 208
lammps-input-files
simongravelle / lammps-input-files
LAMMPS inputs and data files
lammps molecular-dynamics inputs scripts python octave graphene ions all-atoms atomic molecular simulation polymer soft-matter water lammps-input
208
m3g / packmol
Packmol - Initial configurations for molecular dynamics simulations
molecular-dynamics simulation
Language:Fortran 206
Colvars / colvars
Collective variables library for molecular simulation and analysis programs
simulation molecular-dynamics free-energy namd vmd lammps enhanced-sampling gromacs tinkerhp collective-variables
Language:C++ 188
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 183
msmbuilder / vde
Variational Autoencoder for Dimensionality Reduction of Time-Series
variational-autoencoder molecular-dynamics computational-chemistry computational-biology time-series deep-learning pytorch python
Language:Jupyter Notebook 183
alchemistry / alchemlyb
the simple alchemistry library
free-energy library molecular-dynamics python science
Language:Python 176
atomicarchitects / equiformer
[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs
catalyst-design computational-chemistry deep-learning drug-discovery equivariant-graph-neural-network force-fields interatomic-potentials machine-learning molecular-dynamics pytorch ai-for-science equivariant-neural-networks graph-neural-networks e3nn geometric-deep-learning materials-science
Language:Python 175
choderalab / perses
Experiments with expanded ensembles to explore chemical space
molecular-design python molecular-dynamics free-energy-perturbation simulation expanded-ensembles openmm relative-free-energy
Language:Python 173

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