Ecosyste.ms: Awesome

https://github.com/lammps/lammps

Public development project of the LAMMPS MD software package

kokkos lammps molecular-dynamics simulation

Last synced: 30 Sep 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: 30 Sep 2024

https://github.com/mdanalysis/mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

computational-chemistry mdanalysis molecular-dynamics molecular-dynamics-simulation molecular-simulation python science trajectory-analysis

Last synced: 01 Oct 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/foldingathome/coronavirus

Folding@home COVID-19 efforts

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

Last synced: 30 Sep 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/whitead/symd

N-Dimensional MD engine with symmetry group constraints written in C

c crystallography molecular-dynamics python symmetry

Last synced: 30 Sep 2024

https://github.com/markovmodel/molpx

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

free-energy ipython-notebook jupyter-notebook molecular-dynamics tica visualization widget

Last synced: 27 Sep 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/tongzhugroup/mddatasetbuilder

A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.

chemistry dataset md molecular-dynamics neural-network python

Last synced: 29 Sep 2024

https://github.com/d-seams/seams-core

The d-SEAMS C++ core engine

analysis-framework d-seams lua molecular-dynamics molecular-dynamics-simulation nix trajectories trajectory-analysis

Last synced: 30 Sep 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/arm61/pylj

Teaching Utility for Classical Atomistic Simulation.

chemistry computational-chemistry computational-physics education jupyter-notebook molecular-dynamics monte-carlo physics

Last synced: 27 Sep 2024

https://github.com/labioquim/visualdynamics

Web Platform made with Python and NextJS for automating GROMACS simulations

grace gromacs md molecular-dynamics molecular-dynamics-automation molecular-dynamics-simulation

Last synced: 29 Sep 2024

https://github.com/pdebuyl-lab/tidynamics

A tiny package to compute the dynamics of stochastic and molecular simulations

correlation molecular-dynamics numpy stochastic-process

Last synced: 28 Sep 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/kevinshen56714/emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

lammps lammps-data lammps-python-interface molecular-dynamics molecular-dynamics-simulation monte-carlo smiles-strings

Last synced: 02 Oct 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/seatonullberg/velvet

[WIP] Classical atomistic simulation engine with a focus on user-friendliness and extensibility

atomistic-simulation-engine chemistry computational-chemistry materials-science molecular-dynamics physics simulation

Last synced: 02 Oct 2024

https://github.com/janjoswig/commonnnclustering

A Python package for common-nearest-neighbours clustering

clustering common-nearest-neighbours density-based-clustering markov-model molecular-dynamics scikit-learn

Last synced: 26 Sep 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

https://github.com/seatonullberg/cmstk

Computational Materials Science Tool Kit

density-functional-theory dft materials-science molecular-dynamics simulation vasp

Last synced: 02 Oct 2024

https://github.com/jaimergp/phd-biotechnology-thesis

My PhD dissertation

biotechnology computational-chemistry docking molecular-design molecular-dynamics phd-thesis python

Last synced: 02 Oct 2024

https://github.com/seatonullberg/lammps-trajectory-explorer

Bokeh dashboard to visualize LAMMPS trajectory files

bokeh lammps molecular-dynamics visualization

Last synced: 02 Oct 2024

https://github.com/kolaru/normalmodes.jl

Small utilities to deal with normal modes in molecular physics

molecular-dynamics molecule normal-modes

Last synced: 26 Sep 2024

https://github.com/toruniina/trajan

trajectory analysis

molecular-dynamics science trajectory-analysis

Last synced: 02 Oct 2024

https://github.com/kevinshen56714/polymer-molecular-dynamics

Modern, fast, python framework for building LAMMPS input and data files for predicting polymer properties

computing computing-framework data-science high-performance-computing informatics lammps lammps-data lammps-input machine-learning machine-learning-pipelines materials-informatics molecular-dynamics molecular-dynamics-simulation polymer pypi pypi-package python python-library python3 simulations

Last synced: 02 Oct 2024

https://github.com/snapex2409/komd

Small MD framework

kokkos md molecular-dynamics simulation

Last synced: 29 Sep 2024

https://github.com/vtlim/plot_potential

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

computational-chemistry cosine coulomb-interactions energy-functions forcefield harmonic lennard-jones matplotlib molecular-dynamics molecular-modeling molecular-simulation morse potential presentation-materials vdw

Last synced: 01 Oct 2024

https://github.com/toruniina/rustymill

MD toolbox written in rust

molecular-dynamics pdb rust science

Last synced: 02 Oct 2024