domain-molecular-simulation

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

MD pharmacophores and virtual screening

A pocket volume analyzer for use in protein modeling.

Force fields produced by the Open Force Field Initiative

Differentiable, Hardware Accelerated, Molecular Dynamics

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

Molsystem provides a general class for handling molecular and periodic systems

SchNetPack - Deep Neural Networks for Atomistic Systems

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

An automated framework for generating optimized partial charges for molecules

Detect and characterize binding pockets from molecular simulations.

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Experiments with expanded ensembles to explore chemical space

OpenFF NAGL

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

PyRod - Tracing water molecules in molecular dynamics simulations

Solvation Structure and Thermodynamic Mapping

PDBFixer fixes problems in PDB files

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