0.20.1 - Exact treatment of PME electrostatics and optimizations

• Allow users to specify options for openmmtools.alchemy.AbsoluteAlchemicalFactory in the YAML file. In particular, this introduces exact treatment of PME electrostatics for charged ligands. (#881)
• Major optimization of the computation of the energy matrix. (#881)
• Added the YAML option max_n_contexts. (#881)
• Bumped minimum required version of openmmtools to 0.14.0.

0.20.0 - Support for processing proteins through PDBFixer

• Adds an optional pdbfixer directive to the molecules section of the YAML file through PDBFixer, a simple OpenMM-based protein structure processing tool.
• The following options are accessible through the pdbfixer directive.
  • replace_nonstandard_residues: Replace nonstandard amino acids.
  • remove_heterogens: Remove heterogens (such as ligands and waters).
  • add_missing_residues: Add missing residues from the SEQRES block.
  • add_missing_atoms: Add missing heavy atoms.
  • apply_mutations: Specify protein mutations (e.g., T315I).

0.19.4 - Schema and Parallel Setup Fixes

• Fixed bug in parallel molecule setup which caused the same molecule to be setup multiple times (#850).
• Fixed bug in Cerberus schema for LEaP where molecule parameters accumulated (#847).
• Fixed bug where options in experiment section were not coerced (#853).
• Fixed status command to print information about all combinatorial experiments (#853).
• Faster restart with combinatorial experiments (#853).

YANK 0.19.3 - Support for Amber restart files

• Added support for Amber rst7 files in phase1_path/phase2_path (#840).
• The CLI option jobid now uses 1-based numbering like Torque and LSF do for array jobs (#840).

YANK 0.19.2 - Include ions in the solute-only trajectory

Ions are now included in the solute-only trajectories (#835).

0.19.1 Trailblaze fix and restart stability from OpenMMTools

• OpenMMTools 0.13.4 now required to fix issues listed below
• Restrained atoms to absolute coordinates caused issue in Trailblaze with a Barostat
• Last restart attempt uses a slower, but more robust restart method

Regions, Cerberus, and Errors

New Features

• Added statistical inefficiency of replica state indices to the analysis (#819).
• Improve automatically generate residue names for sdf and SMILES molecules (#819).
• Improved automatic parameterization for FlatBottom restraint. An error is now raised if the restraint volume is greater than the periodic box volume (#797 ).
• Added custom region selection to Topography, including compound regions
• Custom regions can now be defined through YAML
• Restraints atom selection in restraints can now use Topography Regions
• Topography now can select from arbitrary string, either complex regions, DSL strings, and in the future SMARTS strings

Cerberus

• Changed to Cerberus for data validation (was Schema), public facing validation schemas in the future

This requirement and package change modifies the way that YAML files are validated and returns a much more complete, and detailed description of the errors in your sections. This should drastically reduce the confusion around "What went wrong with my YAML file"

Critical Bugfixes

OpenMMTools 0.13.3 now required to fix bug in SamplerState

Minor Bugfixes

• Fixed a bug where setup logs were saved in the wrong folder (#819).
• Fixed a bug that caused FlatBottom/Harmonic restraints to crash when only a single atom was selected (#819).
• Fixed a bug in extract-trajectory that was causing the trajectory to not be imaged properly (#819).
• Implemented work-around that avoid tleap problems with numerical unit names (#819).
• Added better error handling of known LEaP Errors
• Fixed issue for start_frame and end_frame were ignored for trajectory extraction
• Better MPI exception handling
• Fixed bug where one MPI thread crashing did not stop other threads, resulting in them getting stuck in a blocking action, but not dying.

Python 2 Dropped, Solute Only Trajectories, and Trailblaze Bug fixes

Dependency changes

• Python 2.X Support officially removed - YANK now runs Python 3.5 and 3.6 only

Features Added by this Release

• Added GAFF2 Torsion support based on YAML input files
• Solute-only trajectories can now be stored every iteration, regardless of checkpoint interval

Improvements in this release

• Added restraint selection flowchart to documentation
• Use infinity instead of None to specify unlimited number of iterations (#772).
• Parallelized setup of molecules and systems with MPI (#557)
• Generalized restrained atoms selection during trailblaze scheme to include non-protein receptors (see also choderalab/openmmtools#290).

Notable Bugfixes

• Fix loading of leap parameters from a local .dat files (allow us to use local versions of gaff parameters for validation)
• Trailblaze protocol crashes with MPI (#762).
• Fixed bug when computing reduced potentials of simulated energies during trailblaze scheme.
• Automatic path is saved in YAML as a mix of python and numpy floats (#763)
• Fixed the number of neutralizing counterions when receptor and ligand have opposite charges (we were adding too many in this case).
• Fixed the log file name with lists of experiments that ended up being just .log.
• Implemented workaround for fixing the net charge of cyclic multi-residue mol2 files.

Auto Alchemical Path, Split Langevin Integrators, and More

Features added by this release

• Automatic Alchemical Path Determination (#726)
• Langevin Splitting Integrator which allows custom sub-division of a timestep for more accurate simulations (#747)
• Online Free Energy Analysis with simulation stop criteria of target error in free energy difference (#712)
• Jupyter Notebooks can now be pre-rendered as static HTML or PDF files, PDF requires LaTeX (#740)
• Experiments can be parallelized by splitting MPI communicator (#726)

Improvements added by this release

• Centroids for restraints now selectable through DSL string instead of whole molecule
• Ionic Strength ability added to setup pipeline
• Website fully documented, all pages filled in
• API fully documented on website and auto-generated from docstrings
• YAML pages on website should be much easier to read

Notable Bugs Fixed

• Removed Ligand rotation/displacement attempts with Boresch restraints to improve replica exchange
• Analyze module fully tested, related bugs found and corrected

Notable Refactoring and Dependency changes

• YAMLBuilder class and yamlbuilder.py file refactored ExperimentBuilder and experiment.py respectively
• Anisotropic Dispersion correction options reduced to a single setting
• Added MDTraj, Jupyer, and Matplotlib as dependencies
• Updated OpenMMTools dependency minimum version to 0.13.0

0.16.2 Startup Speed and Reduced File Sizes

This release helps reduce the initial file sizes of your analysis files by compressing the objects to recreate the alchemical systems. This gives over 10x reduction in the initial file sizes, and saves minutes off the initial start up before simulations start.

• Automatic Expanded Cutoff Distance Selection
• Compressed stored systems drastically reduce initial file sizes
  • Requires OpenMMTools 0.11.2, minimum version updated
• Use C Yaml Dumper and Loaders to speed up YAML object processing