lammps / lammps

Public development project of the LAMMPS MD software package

BradyAJohnston / MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

deepmodeling / deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

openmm / openmm

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

MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

brucefan1983 / GPUMD

Graphics Processing Units Molecular Dynamics

JuDFTteam / best-of-atomistic-machine-learning

🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

plumed / plumed2

Development version of plumed 2

K-Dense-AI / drug-discovery-agent-skills

Agent Skills for small-molecule and protein therapeutics: cheminformatics, molecular ML, docking and dynamics, protein design platforms, and target-discovery knowledge graphs.

mdtraj / mdtraj

An open library for the analysis of molecular dynamics trajectories

chemosim-lab / ProLIF

Interaction Fingerprints for protein-ligand complexes and more

mir-group / nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

atomistic-machine-learning / schnetpack

SchNetPack - Deep Neural Networks for Atomistic Systems

3dem / relion

Image-processing software for cryo-electron microscopy

SamDozer / crc-ca7-rnaseq-docking-md

Colorectal cancer RNA-seq to CA7 zinc-site docking and molecular dynamics