Release history¶

This section features and improvements of note in each release.

The full release history can be viewed at the github yank releases page.

0.17.0 Auto Alchemical Path and Split Langevin Integrators¶

Added Langevin Splitting Integrator which allows time-substep operation order
Automatic Alchemical Path selection feature added.
Many Website additions and cleanups
Online analysis allowing simulations to be run until they reach a target free energy uncertainty
Renamed and refactored YAMLBuilder to more general ExperimentBuilder
Remove ligand rotation and displacement with Boresch restraints to improve acceptance rates
Analyze module fully tested now
Fully updated API docstrings. API auto-generated on website
Parallelize multiple experiments over MPI by splitting MPI Communicator
Anisotropic dispersion options in YAML reduced to single option
Ionic Strength ability added to setup pipeline
Centroids for restraints now selectable through DSL string instead of whole molecule
Added MDTraj, Matplotlib, and Jupyter as requirements
Analyze Jupyter Notebooks can now be exported as pre-rendered static HTML or PDF pages (LaTeX required for PDF)
Refactor some API function names and keywords

Expanded cutoff now able to be chosen automatically instead of just hard coded number
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

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

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

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 now 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

Changed YAML Syntax
New Command yank analyze extrat-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.

alchemy split to a standalone repository
YAML based input files for setting up and running simulations. Uses an AmberTools-based pipeline