YANK

A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations

Note

YANK is now in Early Access for its 1.0 release! YAML syntax should be fully operational while we prepare the underlying Python API. The program has not yet been extensively validated. Use at your own risk!

Features

• Modular Python framework to facilitate development and testing of new algorithms
• GPU-accelerated via the OpenMM toolkit (see benchmarks)
• Alchemical free energy calculations in both explicit (PME, reaction field) and implicit (GBSA) solvent
• Multi-state sampling schemes, including replica exchange with Gibbs sampling and self-adjusted mixture sampling (SAMS)
• Extensible Markov chain Monte Carlo framework for exploring enhanced sampling methods
• Built-in [automated equilibration detection](http://dx.doi.org/10.1021/acs.jctc.5b00784) and convergence diagnostics
• Support for reading Amber, gromacs, and CHARMM input files
• Support for absolute binding free energy calculations and transfer free energies (such as hydration, partition, or relative solvation free energies)

Get going

• Get YANK up and running now
• Read the YAML syntax tutorial

Get involved

• Download the code or fork the repo on GitHub
• See YANK in action
• Report a bug or request a feature on the GitHub issue tracker

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Getting YANK Up and Running

• Quickstart (for the impatient)
• Installation
  • Installing via conda
  • Supported platforms and environments
  • Installing from Source
• YAML syntax tutorial
  • A first example: Hydration free energy
  • Add an absolute binding free energy experiment
  • Combinatorial experiments: implicit and explicit solvents
  • Changing sampling method
  • Starting from different input files
• Running YANK
  • Hardware
  • Parallelization
  • Getting help
  • Running in serial mode
  • Running in MPI mode
  • Selecting a platform
  • Breaking up Simulations
  • Specifying Simulation Stop Conditions
• YAML Files for Simulation
  • All Pages
  • Detailed Options List
• Examples
  • Installing the Examples
  • Install Location
  • List of Examples
• Frequently Asked Questions (FAQ)
• Release history
  • 0.23.7 Bugfix release
  • 0.23.6 Bugfix release
  • 0.23.5 Bugfix release
  • 0.23.4 Bugfix release
  • 0.23.3 Adds support for single mutations using Modeller
  • 0.23.2 More Multi-Experiment Cleanup
  • 0.23.1 Multi-Experiment and Online Bug
  • 0.23.0 Multi-Analysis
  • 0.22.3 Balance Checkpoint with IO
  • 0.22.2 Topography Property Copy
  • 0.22.1 Online Analysis Default
  • 0.22.0 RMSD the Casbah
  • 0.21.2 More Post-Sams Bugfixes
  • 0.21.1 Post-SAMS Bugfixes
  • 0.21.0 SAMS and General Multistate Samplers
  • 0.20.1 Alchemical factory options and fast computation of the energy matrix
  • 0.20.0 Support for processing proteins through PDBFixer
  • 0.19.4 Schema and Parallel Setup Fixes
  • 0.19.3 Support for Amber restart files
  • 0.19.2 Include ions in solute-only trajectory
  • 0.19.1 Trailblaze fix and restart stability from OpenMMTools
  • 0.19.0 Regions, Cerberus, and Errors
  • 0.18.0 Python 2 Dropped, Solute Only Trajectories, and Trailblaze Bugfixes
  • 0.17.0 Auto Alchemical Path and Split Langevin Integrators
  • 0.16.2 Startup Speed and Reduced File Sizes
  • 0.16.1 Auto Expanded Cutoffs and bug fixes for Transition Matrix and Reporter
  • 0.16.0 Full API and Python 3.6
  • 0.15.2 Health Report and Anisotropic Dispersion Control
  • 0.15.0 Backend and Helpful Debugging Build
  • 0.14.1 Early Access of 1.0 Release
  • 0.12.0 (development)
  • 0.11.2 (development)
  • 0.11.0 (development)
  • 0.10.0 (development)
  • 0.9.0 (development)
  • 0.8.0 (development)
  • 0.7.0 (development)
  • v0.6.1 (development)
  • v0.6.0 (development)
  • v0.5.0 (development)

The Science Behind YANK

• Theory
  • The Thermodynamic Cycle of YANK
• Algorithms
  • Solvent treatment
  • Restraints and standard state correction
  • Alchemical protocol
  • Sampling from multiple alchemical (or other thermodynamic) states
  • Markov chain Monte Carlo
  • Automated equilibration detection
  • Analysis with MBAR
  • Automated convergence detection
  • Simulation health report
• Analysis
  • Analysis Theory
  • Analysis Usage
• Validation and Accuracy Benchmarks

Citations and Thanks

• References
• Authors and contributors

API Reference

• API Reference

Developing

• NetCDF store file format specification
• Building the documentation

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License

YANK is licensed under the MIT License. See the LICENSE file distributed with YANK for more details.