YANK Roadmap

YANK 1.0 release

• general code cleanup (logging, docstrings, etc):
  • yank.py - PBG -> KAB
  • alchemy.py - JDC -> DLP
  • analyze.py - JDC -> KAB
  • thermodynamics.py / repex.py - KAB split off to repex project -> DLP review
  • restraints.py - DLP -> JDC
  • testsystems.py - KAB split off -> DLP review
• refactors
• features
• split off repex into separate PyPI-installable package (KAB)
• separate yank command-line driver from yank class (PBG+KAB)
• setup.py (KAB+DLP)
  • automatically install prerequisites from PyPI (pymbar)
• PyPI install
• alchemy improvements (JDC+DLP):
  • speed improvements
  • automated tests
  • clean up for readability and maintainability
  • AMOEBA support
  • generator function for producing sets of AlchemicalState for LJ, Coulomb, restraint, etc
  • more efficient softcore parameters a,b,c
  • take Topology object as input
  • better tests
• remove unneeded files (JDC):
  • expanded.py
  • enumerative_factories.py
  • pyopenmm.py
  • pymbar.py
• restraints.py (JDC)
  • take Topology argument
  • periodic restraint types?
  • more restraint types?
• tests
  • clean up doctests (all)
  • unit tests
  • add test systems with analytical results (JDC)
  • integration tests
• split off openmm-testsystems (KAB+PBG)

repex 1.0 release

• refactoring
• abstract IO (KAB)
• NetCDF support
• generalized MCMC moves:
  • velocity randomization + Langevin
  • ligand MC displacement/rotation
  • GHMC (Metropolized Langevin)
• temperature rescaling after successful swap
• OO design to minimize number of code paths? dummy mpi4py interface? or use a different abstraction?
• better GPU management: automated GPU selection?
• which mpi4py? How can we most easily install it?

pymbar

• correlation time analysis speed improvements
  • Benjamin Trendlekamp-Schroerer fast correlation function code
  • TICA?
  • cython?
• MBAR speed improvements
• refactoring and code cleanup

OpenMM requested changes

ForceField

• CHARMM support
• OPLS support
• GROMOS support
• More standard way to get new forcefields in
• Forcefield provenance information

Topology

• More useful Pythonic interface

AmberPrmtopFile

• Expose Topology object

pdbfixer

• PyPI-installable
• make sure good input files are unchanged
• testing

---

YANK 2.0 release

• alchemy improvements
  • automated alchemical state choice (system-dependent)
  • use Topology information
• CHARMM support
• OPLS support
• GROMOS support
• support for Schrodinger tools
• look into Maestro Schrodinger OPLS ligand parameterization
• look into CGenFF support (DLP): http://mackerell.umaryland.edu/~kenno/cgenff/
• look into ATB for GROMOS support? http://compbio.biosci.uq.edu.au/atb/

repex 2.0 release