YANK
03 01 18 - Filed in: computational chemistry Python
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
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