YANK is a GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations.

Features

• Modular Python framework to facilitate development and testing of new algorithms
• GPU-accelerated via the OpenMM toolkit
• Alchemical free energy calculations in both explicit and implicit solvent
• Hamiltonian exchange among alchemical intermediates with Gibbs sampling framework
• General Markov chain Monte Carlo framework for exploring enhanced sampling methods
• Built-in equilibration detection and convergence diagnostics
• Support for AMBER prmtop/inpcrd files
• Support for absolute binding free energy calculations
• Support for transfer free energies (such as hydration or partition free energies)

Install using conda

$ conda config --add channels omnia --add channels conda-forge
$ conda install yank

conda will install dependencies from binary packages automatically, including difficult-to-install packages such as OpenMM, numpy, and scipy. YANK runs on Python 3.5, and Python 3.6