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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.

https://github.com/lammps/lammps

Public development project of the LAMMPS MD software package

kokkos lammps molecular-dynamics simulation

Last synced: 16 Dec 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 jax lammps materials-science molecular-dynamics nodejs paddle potential-energy python pytorch rocm tensorflow

Last synced: 17 Dec 2024

https://github.com/openmm/openmm

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

molecular-dynamics simulation

Last synced: 07 Nov 2024

https://github.com/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

Last synced: 19 Nov 2024

https://github.com/chemlab/chemlab

The chemistry library you were waiting for

chemistry molecular-dynamics molecular-graphics physics python

Last synced: 27 Nov 2024

https://github.com/becksteinlab/gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

gromacs gromacswrapper molecular-dynamics python science

Last synced: 22 Dec 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: 16 Nov 2024

https://github.com/azminewasi/Awesome-Graph-Research-ICML2024

All graph/GNN papers accepted at the International Conference on Machine Learning (ICML) 2024.

gnn graph graph-neural-network graph-neural-networks graph-theory icml icml-2024 molecular-dynamics

Last synced: 22 Nov 2024

https://github.com/autodesk/molecular-design-toolkit

Notebook-integrated tools for molecular simulation and visualization

chemistry docker jupyter molecular-dynamics notebook python quantum-chemistry simulation

Last synced: 17 Dec 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: 13 Nov 2024

https://github.com/abelcarreras/dynaphopy

Phonon anharmonicity analysis from molecular dynamics

anharmonicity lammps molecular-dynamics phonon phonopy vasp

Last synced: 22 Dec 2024

https://github.com/marrink-lab/vermouth-martinize

Describe and apply transformation on molecular structures and topologies

hacktoberfest molecular-dynamics

Last synced: 15 Dec 2024

https://github.com/openmm/NNPOps

High-performance operations for neural network potentials

cuda gpu machine-learning molecular-dynamics molecular-modeling

Last synced: 13 Nov 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: 13 Nov 2024

https://github.com/markovmodel/pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA

analysis kinetics markov-model md-simulations molecular-dynamics pyemma tutorial

Last synced: 18 Nov 2024

https://github.com/elcorto/pwtools

pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS. It is almost, but not quite, entirely unlike ASE, with some tools extending numpy/scipy. It has a set of powerful parsers and data types for storing calculation data.

ase cp2k cpmd kernel-regression kernel-ridge-regression lammps molecular-dynamics multivariate-regression parameter-sweep polynomial-regression postprocessing preprocessing python quantum-espresso quasi-harmonic-approximation radial-basis-function radial-distribution-function radial-pair-correlation-function sqlite

Last synced: 18 Dec 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: 13 Nov 2024

https://github.com/carlocamilloni/structural-bioinformatics

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

docking molecular-dynamics structural-bioinformatics structural-biology structure-prediction teaching-materials

Last synced: 18 Dec 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: 30 Oct 2024

https://github.com/llnl/qball

Qball (also known as qb@ll) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.

c-plus-plus cpp dft molecular-dynamics mpi qbox simulation tddft

Last synced: 11 Nov 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: 17 Dec 2024

https://github.com/insilichem/ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM

amber command-line molecular-dynamics openmm

Last synced: 10 Nov 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: 11 Oct 2024

https://github.com/llnl/mgmol

MGmol is a scalable O(N) First-Principles Molecular Dynamics code that is capable of performing large-scale electronics structure calculations and molecular dynamics simulations of atomistic systems.

cpp molecular-dynamics simulation

Last synced: 11 Nov 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: 12 Oct 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: 13 Nov 2024

https://github.com/mdanalysis/pmda

Parallel algorithms for MDAnalysis

analysis dask mdanalysis molecular-dynamics parallel

Last synced: 16 Dec 2024

https://github.com/ur-whitelab/hoomd-tf

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

machine-learning molecular-dynamics tensorflow

Last synced: 23 Nov 2024

https://github.com/smoren/molecular-ts

Virtual chemistry simultaion. Particle automata. Visualization of the behavior of particles in 2D and 3D space. Artifical life research.

3d artifical-life canvas cellular-automaton cheminformatics molecular-dynamics molecular-simulation particle-automata

Last synced: 28 Nov 2024

https://github.com/p-j-smith/lipyphilic

A Python toolkit for the analyis of lipid membrane simulations

lipids molecular-dynamics python3

Last synced: 16 Dec 2024

https://github.com/lilyminium/psiresp

RESP with inter- and intra-molecular constraints in Psi4.

atomic-charges molecular-dynamics psi4 python

Last synced: 15 Oct 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: 12 Oct 2024

https://github.com/becksteinlab/mdpow

Calculation of water/solvent partition coefficients with Gromacs.

free-energy gromacs gromacswrapper molecular-dynamics python science

Last synced: 20 Dec 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: 11 Oct 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: 29 Oct 2024

https://github.com/matsunagalab/mdtoolbox.jl

MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

biomolecule differentiable-programming julia molecular-dynamics

Last synced: 16 Oct 2024

https://github.com/simongravelle/nmrformd

NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.

fair gromacs lammps molecular-dynamics nmr nmr-spectroscopy open-source python simulations

Last synced: 08 Nov 2024

https://github.com/zincware/IPSuite

Machine Learned Interatomic Potential Tools

machine-learning molecular-dynamics physics zntrack

Last synced: 13 Nov 2024

https://github.com/simongravelle/peggenerator

Generate PEG topology for GROMACS and LAMMPS

gromacs lammps molecular-dynamics peg polyethylene-glycol python3

Last synced: 08 Nov 2024

https://github.com/rebelot/schrodinger_utils

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.

bioinformatics desmond maestro molecular-dynamics mutual-information plumed schrodinger structural-biology

Last synced: 28 Oct 2024

https://github.com/moldyn/clustering

Robust and stable clustering of molecular dynamics simulation trajectories.

biophysics clustering cpp cuda molecular-dynamics

Last synced: 11 Dec 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: 13 Nov 2024

https://github.com/cbouy/dashmd

Real time monitoring and visualization of Amber MD simulations

ambermd bokeh compchem computational-chemistry molecular-dynamics molecular-modeling ngl

Last synced: 11 Oct 2024

https://github.com/mdanalysis/mdanalysisdata

Access to data for workshops and extended tests of MDAnalysis.

dataset-manager mdanalysis molecular-dynamics python

Last synced: 19 Dec 2024

https://github.com/aspirincode/alphappimd

Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks

ambertools deep-generative-model dockq molecular-dynamics openmm ppi protein-protein-complexes transformers

Last synced: 01 Dec 2024

https://github.com/llnl/user-eph

LAMMPS extension to capture electron-ion interaction. This is a mirror of https://gitlab.com/artuuuro/USER-EPH.

cpp electron-phonon-coupling gpu lammps molecular-dynamics

Last synced: 11 Nov 2024

https://github.com/linux-cpp-lisp/sitator

Unsupervised landmark analysis for jump detection in molecular dynamics simulations.

materials-science molecular-dynamics site-analysis solid-state-physics

Last synced: 05 Dec 2024

https://github.com/pdebuyl/pyh5md

Read and write H5MD files

hdf5 molecular-dynamics

Last synced: 11 Oct 2024

https://github.com/initqp/somd

Molecular dynamics package designed for the SIESTA DFT code.

aimd molecular-dynamics neuroevolution-potential siesta

Last synced: 13 Nov 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: 30 Oct 2024

https://github.com/simongravelle/python-for-lammps

Python scripts for dealing with molecular dynamics script for LAMMPS

molecular-dynamics python

Last synced: 08 Nov 2024

https://github.com/ejmeitz/simplecrystals.jl

An interface for generating simple crystal structures for molecular dynamics simulations.

atomsbase bravais-lattice crystal julia molecular-dynamics simulation solid-state-physics

Last synced: 22 Nov 2024

https://github.com/becksteinlab/hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

mdanalysis molecular-dynamics python science solvation water

Last synced: 10 Nov 2024

https://github.com/chiang-yuan/csh4lmp

The computational modeling tool for custom atomistic model of calcium-silicate-hydrates (C-S-H)

computational-modeling cplusplus lammps-data molecular-dynamics

Last synced: 18 Dec 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: 08 Nov 2024

https://github.com/joaorodrigues/openmm_scripts

Collection of Python scripts to setup and run simulations with OpenMM

biophysics molecular-dynamics openmm python

Last synced: 13 Oct 2024

Molecular Dynamics Awesome Lists
awesome-python-chemistry 149 best-of-atomistic-machine-learning 289 Awesome-Graph-Research-ICML2024 295 awesome-ai4molconformation-md 248
Molecular Dynamics Categories
GNN Theories 112 Interatomic Potentials (ML-IAP) 76 Representation Learning 51 Scene Graphs 41 General Tools 37 Language Models 28 Simulations 22 Representation Engineering 19 Community resources 19 General Chemistry 19 Datasets 17 Casual Discovery and Graphs 16 Molecular Dynamics 16 Generative Models 15 Universal Potentials 14 GNN Applications 13 Mathematical tools 13 Visualization 13 Reviews 12 Density functional theory (ML-DFT) 11