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
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Set up relative free energy calculations using a common scaffold
Algorithms for various Network Layouts and Tooling for planning FE Calculations
A python package for performing GROMACS simulation ensembles
Structural analysis tools for OpenFE free energy calculations, built on MDAnalysis.
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 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
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