pontibus Change Log#

vv0.5.0#

Changed:

  • In line with Interchange v0.5+, the box is no longer being scaled by 1.1 when defining the number_of_solvent_molecules. In those cases, the resulting box density will be much higher. If you were defining number_of_solvent_molecules and then you will need to scale the density by (1 / (1.1^3) instead of using the default target_density (currently default of 0.95 * unit.grams / unit.mL). In practice this means setting target_density to roughly 0.715 unit.grams / unit.mL when setting number_of_solvent_molecules.

  • The ASFE and HybridTop Protocols have been updated to work with openfe v1.9. Notably this means that the Protocols have now been split into three ProtocolUnits (PR #190).

v0.4.0#

Added:

  • AbsoluteAlchemicalFactory options to control LJ softcore parameters are now exposed in the settings and can be used with both the standard and experimental factory (PR #171).

v0.3.0#

Added:

  • Updated API documentation (PR #166)

  • ASFEProtocol now has a fully implemented validate method, you can now call these ahead of Transformation execution to check that input parameters work with the Protocol (PR #163).

Fixed:

  • Pontibus is now compatible with new GufeQuantity changes introduced with gufe v1.7 (PR #163).

v0.2.0#

Added:

  • The ability to solvate systems using OpenMM for the RFE Protocol (PR #140).

Changed:

  • The default solvation backend for RFE calculations is now OpenMM and the target density is 0.75 g/L.

v0.1#

Added:

  • Ability to neutralize systems when solvated with water (Issue #111).

  • A new experimental HybridTop Protocol (issue #73)

Fixed:

  • Fixes missing barostat in non-alchemical simulations for SFE Protocol (issue #114)

v0.0.2#

Changed:

  • Protocol now actively removes CMMotionRemover forces if present.

  • Compatibility with gufe 1.3 (added correct settings_cls definition).

  • Switched from versioningit to setuptools-scm

v0.0.1#

Added:

  • Initial release of pontibus. This includes an ASFE Protocol which supports arbitrary solvent systems that are prepared solely with the OpenFF stack.