Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

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 Apr 2026

https://github.com/openmm/openmm

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

molecular-dynamics simulation

Last synced: 17 Dec 2025

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: 13 May 2025

https://github.com/chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit

Last synced: 20 Nov 2025

https://github.com/pyiron/pyiron

pyiron - an integrated development environment (IDE) for computational materials science.

ab-initio ase development-environment dft hdf5 ide lammps molecular-dynamics pyiron python simulation vasp

Last synced: 11 Mar 2026

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: 21 Jul 2025

https://github.com/m3g/packmol

Packmol - Initial configurations for molecular dynamics simulations

molecular-dynamics simulation

Last synced: 27 Jan 2026

https://github.com/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

Last synced: 21 Oct 2025

https://github.com/chemlab/chemlab

The chemistry library you were waiting for

chemistry molecular-dynamics molecular-graphics physics python

Last synced: 20 Jul 2025

https://github.com/mosdef-hub/mbuild

A hierarchical, component based molecule builder

mbuild molecular-dynamics molecular-simulation molecule-builder mosdef python

Last synced: 21 Oct 2025

https://github.com/choderalab/yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

alchemical alchemical-free-energy-calculations drug-discovery free-energy free-energy-perturbation molecular-dynamics molecular-dynamics-simulation mskcc openmm python

Last synced: 21 Oct 2025

https://github.com/paduagroup/fftool

Tool to build force field input files for molecular simulation

force-field lammps molecular-dynamics packmol

Last synced: 20 Nov 2025

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: 08 Apr 2025

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: 10 May 2025

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: 09 Apr 2025

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: 04 May 2025

https://github.com/sciml/nbodysimulator.jl

A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics

algorithmic-differentiation automatic-differentiation differentiable-programming geometric-algorithms molecular-dynamics molecular-dynamics-simulation scientific-machine-learning sciml symbolic-integration

Last synced: 21 Oct 2025

https://github.com/mosdef-hub/foyer

A package for atom-typing as well as applying and disseminating forcefields

atom-typing disseminating-forcefields force-field foyer molecular-dynamics molecular-simulation python

Last synced: 21 Oct 2025

https://github.com/ipudu/awesome-molecular-dynamics

:sunglasses: A curated list of awesome Molecular Dynamics libraries, tools and software.

awesome-list molecular-dynamics

Last synced: 17 Jan 2026

https://github.com/abelcarreras/dynaphopy

Phonon anharmonicity analysis from molecular dynamics

anharmonicity lammps molecular-dynamics phonon phonopy vasp

Last synced: 06 Apr 2025

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

Describe and apply transformation on molecular structures and topologies

hacktoberfest molecular-dynamics

Last synced: 16 May 2025

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: 04 May 2025

https://github.com/openmm/nnpops

High-performance operations for neural network potentials

cuda gpu machine-learning molecular-dynamics molecular-modeling

Last synced: 20 Jun 2025

https://github.com/openmm/NNPOps

High-performance operations for neural network potentials

cuda gpu machine-learning molecular-dynamics molecular-modeling

Last synced: 04 May 2025

https://github.com/lab-cosmo/upet

A universal interatomic potential for advanced materials modeling

machine-learned-interatomic-potentials machine-learning molecular-dynamics universal-potential

Last synced: 19 Jan 2026

https://github.com/ci-lab-cz/streamd

Fully automated high-throughput MD pipeline

gromacs gromacs-tools molecular-dynamics molecular-dynamics-simulation

Last synced: 14 Jan 2026

https://github.com/kyonofx/mlcgmd

[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks

coarse-grained-molecular-dynamics coarse-graining graph-neural-networks molecular-dynamics

Last synced: 16 Jun 2026

https://github.com/pyscal/pyscal

Python library written in C++ for calculation of local atomic structural environment

bond-order-parameters lammps molecular-dynamics nucleation order-parameters solid-state-physics steinhardt steinhardt-bond-order-parameters

Last synced: 12 Dec 2025

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: 13 May 2025

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: 19 Aug 2025

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: 04 May 2025

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: 21 Oct 2025

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: 14 Oct 2025

https://github.com/lab-cosmo/pet-mad

A universal interatomic potential for advanced materials modeling

machine-learned-interatomic-potentials machine-learning molecular-dynamics universal-potential

Last synced: 21 Aug 2025

https://github.com/jag1g13/pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

coarse-grained-molecular-dynamics computational-chemistry gromacs molecular-dynamics python science

Last synced: 21 Oct 2025

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: 27 Mar 2025

https://github.com/minkaixu/egno

ICML2024: Equivariant Graph Neural Operator for Modeling 3D Dynamics

dynamic-simulations geometric-deep-learning graph-neural-networks molecular-dynamics neural-operator

Last synced: 11 Jul 2025

https://github.com/metatensor/metatrain

Train, fine-tune, and manipulate machine learning models for atomistic systems

atomistic-simulations machine-learning molecular-dynamics torch

Last synced: 12 Jan 2026

https://github.com/choderalab/openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

jupyter-notebook molecular-dynamics openmm python python-tutorial

Last synced: 04 Feb 2026

https://github.com/lab-cosmo/torch-pme

Particle-mesh based calculations of long-range interactions in PyTorch

electrostatics fast-fourier-transform machine-learning material-science molecular-dynamics particle-mesh-ewald pytorch

Last synced: 07 May 2025

https://github.com/whitead/symd

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

c crystallography molecular-dynamics python symmetry

Last synced: 14 Apr 2025

https://github.com/qcxms/qcxms

Quantum mechanic mass spectrometry calculation program

computational-chemistry computational-mass-spectrometry mass-spectrometry molecular-dynamics

Last synced: 19 Feb 2026

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: 01 Aug 2025

https://github.com/sissaschool/sportran

A code to estimate transport coefficients from the cepstral analysis of a (multi)variate current stationary time series -- [FKA "thermocepstrum"]

cepstral-analysis data-analysis green-kubo heat-flux molecular-dynamics spectral-analysis sportran thermal-conductivity thermocepstrum time-series-analysis transport

Last synced: 14 Jan 2026

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: 29 Apr 2025

https://github.com/zincware/mdsuite

A post-processing engine for particle simulations

hdf5 molecular-dynamics particle-simulation python tensorflow

Last synced: 22 Jul 2025

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

LAMMPS pair styles for NequIP and Allegro deep learning interatomic potentials

gpu kokkos lammps machine-learning molecular-dynamics pytorch

Last synced: 21 Jul 2025

https://github.com/insilichem/ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM

amber command-line molecular-dynamics openmm

Last synced: 01 Mar 2026

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: 28 Oct 2025

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: 23 Oct 2025

https://github.com/gph82/mdciao

mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

amino-acids computational-chemistry g-protein gpcr gpcr-numbering kinases molecular-dynamics pdb-database protein-structure python structural-biology

Last synced: 18 Jan 2026

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: 10 Apr 2025

https://github.com/openkim/kliff

KIM-based Learning-Integrated Fitting Framework for interatomic potentials.

force-fields interatomic-potentials kim machine-learning materials-modelling molecular-dynamics

Last synced: 22 Feb 2026

https://github.com/ecp-copa/examinimd

Molecular dynamics proxy application based on Kokkos

kokkos lammps molecular-dynamics proxy-application

Last synced: 19 Feb 2026

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: 23 Feb 2026

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: 12 Jul 2025

Molecular Dynamics Awesome Lists
awesome-python-chemistry 152 best-of-atomistic-machine-learning 330 awesome-ai4molconformation-md 773 Awesome-Graph-Research-ICML2024 295
Molecular Dynamics Categories
AI4MD 318 GNN Theories 112 Deep Learning-molecular conformations 108 Molecular dynamics 106 Molecular conformational ensembles by methods 102 Reviews 89 Simulations 85 Interatomic Potentials (ML-IAP) 81 Representation Learning 53 Scene Graphs 41 General Chemistry 37 General Tools 37 Universal Potentials 32 Representation Engineering 31 Datasets 29 Language Models 28 Community resources 26 Machine Learning 24 Molecular Dynamics 21 Density functional theory (ML-DFT) 17