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choderalab/yank: 0.24.0 - Experimental support for online status files

Andrea Rizzi; John Chodera; Levi Naden; Kyle Beauchamp; Steven Albanese; Patrick Grinaway; Bas Rustenburg; ajsilveira; Shyam Saladi; Kevin Boehm

  • Added an experimental feature that allows --status to be provided with yank script invocations to emit a status.pkl file in the experiment directory at the conclusion of each experiment switch interval (#1135). This feature is experimental, and its invocation may be changed in a future release.
  • This release requires OpenMMTools >= 0.17.0, which includes a much faster way of implementing exact treatment of PME during alchemical calculations (#1136).
  • Some NetCDF robustness improvements.
  • SAMS improvements:
    • SAMS now properly restores t0 and stage, which should correctly persist the stage across phase switches and resumes.
    • Added SAMS logZ_history plot to notebook reports.
    • SAMS self._stage is now an integer to more easily store this in storage (0 is initial, 1 is asymptotic phase).
    • Suppress some verbose outputs.
    • If an asymptotically optimal stage is present in a SAMS simulation, the initial stage is discarded to equilibration and automatic equilibration detection is applied to the asymptotically optimal weight adjustment region only.
    • Jupyter notebook reports now show SAMS weight convergence if present.
  • The yank.multistate package was deprecated. In the future, this package will be available in OpenMMTools (#1146).
Known issues
  • The use of more than one process per experiment via MPI has known issues that are being debugged (#1130).
  • Simulations restored from a checkpoint file have their velocities reset to zero (#1115).
  • Forward and backward convergence analysis free energy traces in the Jupter notebook are incorrect (#971).
  • Peptide ligands are not currently supported (#376).
  • Setup will fail if .mol2 atom substructure ID matches filename (#703).

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