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

Public development project of the LAMMPS MD software package

WebGL protein viewer

MD pharmacophores and virtual screening

Solvation Structure and Thermodynamic Mapping

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

🏗️ 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

Powerful, efficient particle trajectory analysis in scientific Python.

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

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.