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.

0.15.0 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

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