https://github.com/lammps/lammps

Public development project of the LAMMPS MD software package

kokkos lammps molecular-dynamics simulation

Last synced: 31 Jul 2024

https://github.com/openmm/openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

molecular-dynamics simulation

Last synced: 01 Aug 2024

https://github.com/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

Last synced: 31 Jul 2024

https://github.com/FoldingAtHome/coronavirus

Folding@home COVID-19 efforts

covid-19 folding-at-home foldingathome molecular-dynamics sars-cov-2

Last synced: 01 Aug 2024

https://github.com/atomistic-machine-learning/schnetpack

SchNetPack - Deep Neural Networks for Atomistic Systems

condensed-matter machine-learning molecular-dynamics neural-network quantum-chemistry

Last synced: 02 Aug 2024

https://github.com/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

Last synced: 02 Aug 2024

https://github.com/torchmd/torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

coarse-grained-molecular-dynamics machine-learning molecular-dynamics neural-networks pytorch pytorch-lightning

Last synced: 05 Aug 2024

https://github.com/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

Last synced: 02 Aug 2024

https://github.com/torchmd/torchmd-net

Neural network potentials

energy-functions equivariant-representations molecular-dynamics neural-networks transformer

Last synced: 02 Aug 2024

https://github.com/jparkhill/TensorMol

Tensorflow + Molecules = TensorMol

chemistry force-field machine-learning meta-dynamics molecular-dynamics molecular-simulation molecules monte-carlo neural-network simulation tensorflow

Last synced: 02 Aug 2024

https://github.com/glotzerlab/freud

Powerful, efficient particle trajectory analysis in scientific Python.

analysis computational-chemistry computational-physics data-analysis hacktoberfest molecular-dynamics monte-carlo-simulation particle-system python science scientific-computing spatial-analysis

Last synced: 02 Aug 2024

https://github.com/chemlab/chemlab

The chemistry library you were waiting for

chemistry molecular-dynamics molecular-graphics physics python

Last synced: 07 Aug 2024

https://github.com/lumol-org/lumol

Universal extensible molecular simulation engine

atomistic-simulations computational-chemistry molecular-dynamics molecular-simulation monte-carlo

Last synced: 03 Aug 2024

https://github.com/atomicarchitects/equiformer

[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

ai-for-science catalyst-design computational-chemistry deep-learning drug-discovery e3nn equivariant-graph-neural-network equivariant-neural-networks force-fields geometric-deep-learning graph-neural-networks interatomic-potentials machine-learning materials-science molecular-dynamics pytorch

Last synced: 02 Aug 2024

https://github.com/Colvars/colvars

Collective variables library for molecular simulation and analysis programs

collective-variables enhanced-sampling free-energy gromacs lammps molecular-dynamics namd simulation tinkerhp vmd

Last synced: 03 Aug 2024

https://github.com/atomicarchitects/equiformer_v2

[ICLR'24] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

ai-for-science catalyst-design computational-chemistry computational-physics deep-learning drug-discovery e3nn equivariant-graph-neural-network equivariant-neural-networks force-fields geometric-deep-learning graph-neural-networks interatomic-potentials machine-learning materials-science molecular-dynamics pytorch

Last synced: 31 Jul 2024

https://github.com/torchmd/mdgrad

Pytorch differentiable molecular dynamics

chemistry differentiable-simulations force-field-optimization graph-neural-networks molecular-dynamics physics-simulation polymer quantum-dynamics quantum-isomerization statistical-mechanics

Last synced: 05 Aug 2024

https://github.com/stefanch/sGDML

sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model

gaussian-process machine-learning molecular-dynamics molecular-force-fields quantum-chemistry

Last synced: 02 Aug 2024

https://github.com/openmm/NNPOps

High-performance operations for neural network potentials

cuda gpu machine-learning molecular-dynamics molecular-modeling

Last synced: 02 Aug 2024

https://github.com/thorben-frank/mlff

Build neural networks for machine learning force fields with JAX

deep-learning force-fields machine-learning molecular-dynamics

Last synced: 02 Aug 2024

https://github.com/uf3/uf3

UF3: a python library for generating ultra-fast interatomic potentials

force-fields interatomic-potentials machine-learning materials-science molecular-dynamics

Last synced: 02 Aug 2024

https://github.com/NQCD/NQCDynamics.jl

Fast and flexible nonadiabatic molecular dynamics in Julia!

molecular-dynamics monte-carlo nonadiabatic physics-simulation quantum-classical semi-classical

Last synced: 31 Jul 2024

https://github.com/wwang2/Coarse-Graining-Auto-encoders

generative-model machine-learning molecular-dynamics statistical-mechanics

Last synced: 31 Jul 2024

https://github.com/mir-group/pair_allegro

LAMMPS pair style for Allegro deep learning interatomic potentials with parallelization support

gpu kokkos lammps machine-learning molecular-dynamics pytorch

Last synced: 02 Aug 2024

https://github.com/deepmodeling/dpti

A Python Package to Automate Thermodynamic Integration Calculations for Free Energy

atomistic-simulations free-energy molecular-dynamics thermodynamic-integration workflow

Last synced: 31 Jul 2024

https://github.com/zincware/IPSuite

Machine Learned Interatomic Potential Tools

machine-learning molecular-dynamics physics zntrack

Last synced: 02 Aug 2024

https://github.com/apax-hub/apax

A flexible and performant framework for training machine learning potentials.

computational-chemistry force-fields interatomic-potentials jax machine-learning materials-science molecular-dynamics quantum-chemistry

Last synced: 02 Aug 2024

https://github.com/Chenghao-Wu/RobertoMD.jl

Massively parallel hybrid particle-field molecular dynamics (hPF-MD) simulation method in Julia

coarse-grained julia molecular-dynamics particle-field physical-chemistry physical-modeling polymer simulation

Last synced: 31 Jul 2024

https://github.com/initqp/somd

Molecular dynamics package designed for the SIESTA DFT code.

aimd molecular-dynamics neuroevolution-potential siesta

Last synced: 02 Aug 2024

https://github.com/jdrusso/msm_we

History-augmented Markov analysis of weighted ensemble trajectories.

markov-model molecular-dynamics weighted-ensemble

Last synced: 02 Aug 2024

https://github.com/li012589/xyzFile2Animation

A small python script to create animation from multiply xyz files

animation molecular-dynamics xyz xyz-files

Last synced: 05 Aug 2024