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

The Open Free Energy toolkit

Differentiate all the things!

An interoperable Python framework for biomolecular simulation.

scalable molecular simulation

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

Sire Molecular Simulations Framework

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

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.

Tautomer ratios in solution

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

Set up relative free energy calculations using a common scaffold

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

Algorithms for various Network Layouts and Tooling for planning FE Calculations

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.

A python package for performing GROMACS simulation ensembles

A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

Endstate corrections from MM to QML potential

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

Fast estimation of ion-pairing for screening electrolytes