domain-molecular-simulation

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

SchNetPack - Deep Neural Networks for Atomistic Systems

A pocket volume analyzer for use in protein modeling.

Differentiable, Hardware Accelerated, Molecular Dynamics

Detect and characterize binding pockets from molecular simulations.

An automated framework for generating optimized partial charges for molecules

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

MD pharmacophores and virtual screening

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

Molsystem provides a general class for handling molecular and periodic systems

Force fields produced by the Open Force Field Initiative

The Open Free Energy toolkit

Dynamic pharmacophore modeling of molecular interactions

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

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

PyRod - Tracing water molecules in molecular dynamics simulations

MoleculeKit: Your favorite molecule manipulation kit

Standalone charge assignment from Espaloma framework.

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196