method-physics

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

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

Force fields produced by the Open Force Field Initiative

Molsystem provides a general class for handling molecular and periodic systems

The Open Free Energy toolkit

Source code for molecular graphics program UCSF ChimeraX

An automated framework for generating optimized partial charges for molecules

Solvation Structure and Thermodynamic Mapping

Detect and characterize binding pockets from molecular simulations.

A pocket volume analyzer for use in protein modeling.

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

pythonic interface to virtual screening software

Experiments with expanded ensembles to explore chemical space

Adding hydrogens to molecular models

MD pharmacophores and virtual screening

High level API for using machine learning models in OpenMM simulations

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

Parameter/topology editor and molecular simulator

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

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