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

Published February 26, 2019 | Version 0.24.0

Software Open

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).

Files

Name	Size	Download all
choderalab/yank-0.24.0.zip md5:dd605ee933701ea575b452f89a18d7c2	8.6 MB	Preview Download