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

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

The Open Free Energy toolkit

An automated framework for generating optimized partial charges for molecules

Molsystem provides a general class for handling molecular and periodic systems

Force fields produced by the Open Force Field Initiative

pythonic interface to virtual screening software

A project (and object) for storing, manipulating, and converting molecular mechanics data.

Parameter/topology editor and molecular simulator

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.

High level API for using machine learning models in OpenMM simulations

Adding hydrogens to molecular models

Experiments with expanded ensembles to explore chemical space

Predict protein-ligand and catalytic pockets and perform molecular docking of a specific ligand to each predicted pocket.

MDAnalysis is a Python library to analyze molecular dynamics simulations.

An open library for the analysis of molecular dynamics trajectories

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

Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.

Computational Crystallography Toolbox