molecular-dynamics

There are 69 repositories under molecular-dynamics topic.

lammps
lammps / lammps
Public development project of the LAMMPS MD software package
molecular-dynamics lammps simulation kokkos
Language:C++ 2029
openmm / openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
molecular-dynamics simulation
Language:C++ 1375
deepmd-kit
deepmodeling / deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
ase c computational-chemistry cpp cuda deep-learning deepmd ipi lammps materials-science molecular-dynamics nodejs potential-energy python pytorch rocm tensorflow
Language:C++ 1357
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 1218
FoldingAtHome / coronavirus
Folding@home COVID-19 efforts
covid-19 folding-at-home foldingathome molecular-dynamics sars-cov-2
Language:Python 1095
lmmentel / awesome-python-chemistry
A curated list of Python packages related to chemistry
chemistry quantum-chemistry python-chemistry molecular-dynamics simulation computational-chemistry atomistic-simulations
1019
atomistic-machine-learning / schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
condensed-matter machine-learning molecular-dynamics neural-network quantum-chemistry
Language:Python 711
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 544
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 527
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 505
JuliaMolSim / Molly.jl
Molecular simulation in Julia
molecular-dynamics julia protein-structure physics-simulation structural-bioinformatics molecular-simulation lennard-jones
Language:Julia 363
brucefan1983 / GPUMD
Graphics Processing Units Molecular Dynamics
molecular-dynamics-simulation heat-transport cuda molecular-dynamics gpumd phonon gpu machine-learning physics-simulation simulation neural-network neuroevolution natural-evolution-strategies high-performance-computing machine-learning-potential
Language:Cuda 347
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 326
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis
Language:Python 321
plumed / plumed2
Development version of plumed 2
c-plus-plus enhanced-sampling free-energy molecular-dynamics plugin plumed plumed2 trajectory-analysis
Language:C++ 314
glotzerlab / hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
conda-forge cuda docker gpu hard-particle hoomd-blue molecular-dynamics monte-carlo-simulation particle-system python simulation singularity
Language:C++ 310
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 292
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 284
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 281
torchmd / torchmd-net
Neural network potentials
energy-functions equivariant-representations molecular-dynamics neural-networks transformer
Language:Python 272
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++ 257
jewettaij / moltemplate
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
amber coarse-grained-molecular-dynamics force-fields lammps lammps-data lammps-script-creator lammps-tool molecular-dynamics molecule-builder molecule-editor open-science opls
Language:Python 239
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
238
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 233
espresso
espressomd / espresso
The ESPResSo package
c-plus-plus scientific-computing soft-matter molecular-dynamics lattice-boltzmann physics python
Language:C++ 214
chemlab / chemlab
The chemistry library you were waiting for
chemistry python physics molecular-dynamics molecular-graphics
Language:Python 207
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
206
m3g / packmol
Packmol - Initial configurations for molecular dynamics simulations
molecular-dynamics simulation
Language:Fortran 195
msmbuilder / vde
Variational Autoencoder for Dimensionality Reduction of Time-Series
computational-biology computational-chemistry deep-learning molecular-dynamics python pytorch time-series variational-autoencoder
Language:Jupyter Notebook 183
lumol-org / lumol
Universal extensible molecular simulation engine
molecular-dynamics monte-carlo molecular-simulation computational-chemistry atomistic-simulations
Language:Rust 182
alchemistry / alchemlyb
the simple alchemistry library
science free-energy python library molecular-dynamics
Language:Python 175
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++ 175
choderalab / perses
Experiments with expanded ensembles to explore chemical space
expanded-ensembles free-energy-perturbation molecular-design molecular-dynamics openmm python relative-free-energy simulation
Language:Python 173
choderalab / yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
molecular-dynamics molecular-dynamics-simulation alchemical-free-energy-calculations drug-discovery free-energy openmm mskcc python alchemical free-energy-perturbation
Language:Python 171

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