0.16.1 Auto Expanded Cutoffs and bug fixes for Transition Matrix and Reporter

• Expanded cutoff now able to be chosen automatically instead of just hard coded number
• Restraint parameters can now be specified in the YAML file which pass to restraints API
• Fixes bug causing transition matrix to be computed incorrectly, uses empirical to estimate
• Allows user to drop samples equilibration report to avoid plot scale being dominated by initial fast equilibration

0.16.0 Full API and Python 3.6

• Full feature API for setting up, running, and analyzing experiments
• Supports new generalized MCMC moves, ThermodynamicStates, and other features from improved OpenMMTools
• Checkpoint feature added to reduce file size, add portability to data analysis files.
• Simulations can now alternate between phases to allow analysis even before simulations are done
• OpenEye features compartmentalized so you don't need every OpenEye feature YANK could use to use any of them
• Major under the hood speed ups to base code and MPI behavior, includes a full code refactor.
• Mol2 files can now read in multi-molecule files
• No longer uses standalone Alchemy module, uses the one built into OpenMMTools
• Added Python 3.6 support.
• Retired Python 3.4 support

0.15.2 Health Report and Anisotropic Dispersion Control

• Added simulation Health Report through a Jupyter Notebook with CLI support
• Added ability to control Anisotropic Dispersion Correction through YAML files

0.15.0 Backend and Helpful Debugging Build

• Added support for solvent_dsl in user defined systems of YAML pages
• Removed Command Line Interface ability to do yank prepare and yank run
• Added ability to overwrite individual YAML commands from command line
• Added YAML feature to extend_simulation without modifying YAML files or command line every iteration
• NaN's generated during simulations serialize system, state, and integrator which can be passed off for debugging to others
• Backend website updating and pushes improved
• Improved GROMACS extension file handling

YANK 0.14.1: Early Access 1.0 Release

This release marks the early access phase for YANK 1.0. We intend for this to be a formal release for users to test YANK and its functionality while we refactor the underlying Python API.

In this release:

• YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0
  New features may appear in the time meantime, but scripts will be forwards compatible.
• Initial support for OpenMM XML systems and PDB files
• Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files
• clearance in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline
• Boresch Orientational Restraints fully implemented and documented.
• Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg
• Documentation updated with better algorithms and theory sections.
• Full walkthroughs of yank-examples added to online documentation
• Various other documentation improvements
• Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1)
• YANK now on MIT License
• Many bugfixes

Validation

YANK has been validated for binding against T4-Lysozyme with the binders: Benzene, Ethylbenzene, Isobutylbenzene, and Indene with the FF14SB Amber Force Field. Our binding free energies match those in the following paper within error:

David L. Mobley, Alan P. Graves, John D. Chodera, Andrea C. McReynolds, Brian K. Shoichet, and Ken A. Dill.
Predicting absolute ligand binding free energies to a simple model site.
J. Mol. Biol. 371:1118, 2007. [DOI]

We have also validated YANK hydration free energies against a reduced set in the FreeSolv Database in TIP3P water based on construction from SMILES strings. The molecular list can be found here. The paper we compared against can be found here:

David L. Mobley and J. Peter Guthrie.
FreeSolv: a database of experimental and calculated hydration free energies, with input files.
J. Comp.-Aided Mol. Design 28:7, 2014 [DOI]

YANK 0.12.0 Split Examples Release

This release splits out the examples from the main YANK repo and starts depreciating tests and functions in preparation for the removal of much of the CLI functions.

YANK 0.11.2

This version adds better long range dispersion and electrostatic corrections.

Even better documentation to YAML files, including some best practices guidelines.

YANK 0.11.0 Full YAML Documentation

YANK's YAML documentation has been fully written and published.

Due to the scope of this documentation, and the level of options it provides the users, a full release has been cut.

Documentation on how to propose and publish updates have also been added.

0.10.0

This release enables Python 3.X compatibility for YANK.

• Python 3.4 and Python 3.5 are now supported
• Online documentation has been updated to include the YAML input files
• Selftests now provide more helpful output

0.9.0

In this release:

• Changed YAML syntax.
• New command yank analyze extract-trajectory to extract data from NetCDF4 file in a common trajectory format.
• Support for solvation free energy calculations.
• Automatic detection of MPI.
• Various bug fixes.