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

The Open Free Energy toolkit

Differentiate all the things!

scalable molecular simulation

An interoperable Python framework for biomolecular simulation.

A Python library and command line interface for automated free energy calculations

Sire Molecular Simulations Framework

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

This package contains tools for setting up hybrid-topology FE calculations

Tautomer ratios in solution

Set up relative free energy calculations using a common scaffold

A repository for the final project implementing/applying Boltzmann generators for Computational Statistical Physics (PHYS 7810) at CU Boulder

Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

Algorithms for various Network Layouts and Tooling for planning FE Calculations

A python package for performing GROMACS simulation ensembles

A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

Fast estimation of ion-pairing for screening electrolytes

A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

Endstate corrections from MM to QML potential