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