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Molecular Dynamics
Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic “evolution” of the system.
- GitHub: https://github.com/topics/molecular-dynamics
- Wikipedia: https://en.wikipedia.org/wiki/Molecular_dynamics
- Related Topics: computational-chemistry, computational-biology, computational-physics,
- Aliases: molecular-dynamics-simulation,
- Last updated: 2024-07-29 13:49:37 UTC
- JSON Representation
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.
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/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