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.

0.14.1 Early Access of 1.0 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

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