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

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
    • Release build
    • Development build
    • Upgrading your installation
    • Testing your installation
    • Testing Available Platforms
    • Configuring Non-Standard CUDA Install Locations
    • Configuring Your CUDA Devices
    • Optional Tools
  • Supported platforms and environments
    • Software
    • Hardware
  • Installing from Source
    • Installing from the GitHub Source Repository
    • Testing your Installation
    • Running on the Cloud
• Running YANK
  • Hardware
    • Running on GPUs
    • Running on the CPU
  • Parallelization
    • Serial mode
    • MPI mode
  • 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
    • options
    • molecules
    • solvents
    • systems
    • mcmc
    • samplers
    • protocols
    • experiments
    • Combinatorial Options
    • YAML Versions
    • Cookbook for YAML Options
  • Detailed Options List
• Release history
  • 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
    • Enhancements and features
    • Bugfixes
  • 0.21.2 More Post-Sams Bugfixes
  • 0.21.1 Post-SAMS Bugfixes
  • 0.21.0 SAMS and General Multistate Samplers
    • Summary of Release
    • Detailed Changes
  • 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)
• Examples
  • Installing the Examples
  • Install Location
  • List of Examples
    • Example 1: Absolute Binding of para-Xylene to T4-Lysozyme in Explicit Solvent
    • Example 2: Absolute Binding of Host cucurbit[7]uril with Guest molecule B2 in Implicit Solvent
    • Example 3: Hydration Free energy of Phenol in Explicit Solvent
    • Example 4: Binding Free Energy of a large set of ligands for T4-Lysozyme, split by ”!Combinatorial”
    • Example 5: Hydration Free Energy of the FreeSolv database (subset)
• Frequently Asked Questions (FAQ)

The Science Behind YANK

• Theory
  • The Thermodynamic Cycle of YANK
• Algorithms
  • Solvent treatment
    • Implicit solvent
    • Explicit solvent
  • Restraints and standard state correction
    • Standard state correction
    • Restraint types
    • Restraint Selection Flowchart
    • Adding new restraints
  • Alchemical protocol
    • Automatic Alchemical Protocol Selection
  • Sampling from multiple alchemical (or other thermodynamic) states
    • MultiStateSampler: Independent simulations at multiple thermodynamic states
    • ReplicaExchangeSampler: Replica exchange among thermodynamic states
    • SAMSSampler: Self-adjusted mixture sampling
  • Markov chain Monte Carlo
    • Generalized Hybrid Monte Carlo
    • Metropolis Monte Carlo displacement and rotation moves
  • Automated equilibration detection
    • Determining a timeseries to analyze in a replica-exchange simulation
    • Identifying equilibration and production regions in a replica-exchange simulations
  • Analysis with MBAR
  • Automated convergence detection
  • Simulation health report
• Analysis
  • Analysis Theory
    • Equilibration and Decorrelation
    • Replica Mixing Convergence
    • Free Energy Estimation
  • Analysis Usage
    • Automatic Analysis
    • Visual Analysis
    • Parallel Analysis
    • Programmatic Analysis
• 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.