Releases
0.18.0
Python 2 Dropped, Solute Only Trajectories, and Trailblaze Bug fixes
Lnaden
released this
04 Oct 13:05
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.
You can’t perform that action at this time.