End-To-End Molecular Dynamics (MD) Engine using PyTorch

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

A pocket volume analyzer for use in protein modeling.

PyRod - Tracing water molecules in molecular dynamics simulations

WebGL protein viewer

Public development project of the LAMMPS MD software package

Solvation Structure and Thermodynamic Mapping

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

MD pharmacophores and virtual screening

🏗️ Statistical models for biomolecular dynamics 🏗️

Differentiable, Hardware Accelerated, Molecular Dynamics

Detect and characterize binding pockets from molecular simulations.

MDAnalysis is a Python library to analyze molecular dynamics simulations.

An open library for the analysis of molecular dynamics trajectories

🚂 Python API for Emma's Markov Model Algorithms 🚂

A comprehensive macromolecular library

OpenMM plugin to define forces with neural networks

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Powerful, efficient particle trajectory analysis in scientific Python.

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation