Issues

• Update the number of lambda windows to remove redundant windows in gas phase ASFE legs

  OpenFreeEnergy/pontibus#213 · Filter by author IAlibay opened on Oct 5, 2026
  1

• Sigma=epsilon=0 for virtual sites

  OpenFreeEnergy/pontibus#210 · Filter by author IAlibay opened on Sep 1, 2026

• Use openff-packmol instead of interchange for packmol interface imports

  OpenFreeEnergy/pontibus#205 · Filter by author IAlibay opened on Aug 29, 2026
  

• Water Component isn't Named

  OpenFreeEnergy/pontibus#187 · Filter by author jaclark5 opened on Mar 6, 2026
  3

  

• Deduplicate InterchangeOpenMMSolvationSettings

  OpenFreeEnergy/pontibus#155 · Filter by author IAlibay opened on Oct 8, 2025
  1

• Clean up system creation tests

  OpenFreeEnergy/pontibus#150 · Filter by author IAlibay opened on Oct 3, 2025

• InterchangeOpenMMSolvationSettings is misleading since PackmolSolvationSettings also goes through Interchange

  OpenFreeEnergy/pontibus#149 · Filter by author IAlibay opened on Oct 3, 2025

• Review need for SLTCAP ion addition in OpenMM Solvation

  OpenFreeEnergy/pontibus#148 · Filter by author IAlibay opened on Oct 3, 2025

• Test parameter assignment of different components

  OpenFreeEnergy/pontibus#144 · Filter by author mattwthompson opened on Sep 17, 2025

• CI tests are too long

  OpenFreeEnergy/pontibus#142 · Filter by author IAlibay opened on Sep 15, 2025

• Have a library charge check for protein parsing

  OpenFreeEnergy/pontibus#129 · Filter by author IAlibay opened on Aug 12, 2025

• RFE Protocol: structural analysis is not working

  OpenFreeEnergy/pontibus#117 · Filter by author IAlibay opened on Jul 28, 2025

• Add integration tests that check equilibration (ASFEProtocol)

  OpenFreeEnergy/pontibus#116 · Filter by author IAlibay opened on Jul 24, 2025

• Add HybridTop user documentation

  OpenFreeEnergy/pontibus#106 · Filter by author IAlibay opened on Jul 20, 2025

• Add HybridTop usage notebook

  OpenFreeEnergy/pontibus#105 · Filter by author IAlibay opened on Jul 20, 2025

• Alchemiscale Deployment

  OpenFreeEnergy/pontibus#103 · Filter by author IAlibay opened on Jul 20, 2025

• Conda-forge release

  OpenFreeEnergy/pontibus#102 · Filter by author IAlibay opened on Jul 20, 2025

• Release v0.1

  OpenFreeEnergy/pontibus#101 · Filter by author IAlibay opened on Jul 20, 2025

• Update system creation tooling for virtual site support

  OpenFreeEnergy/pontibus#95 · Filter by author IAlibay opened on Jul 20, 2025

• Add virtual site support to HTF subclass

  Task

  OpenFreeEnergy/pontibus#92 · Filter by author IAlibay opened on Jul 20, 2025

• Add ExtendedSolventComponent support to HybridTopologyProtocolUnit

  Task

  OpenFreeEnergy/pontibus#88 · Filter by author IAlibay opened on Jul 20, 2025

• HybridTop Protocol Deployment and Documentation

  OpenFreeEnergy/pontibus#76 · Filter by author IAlibay opened on Jul 20, 2025

• Virtual site support: user stories

  OpenFreeEnergy/pontibus#65 · Filter by author IAlibay opened on Jun 17, 2025
  3

  

• SFEs: Experimental virtual site support

  OpenFreeEnergy/pontibus#64 · Filter by author IAlibay opened on Jun 17, 2025

• Assigning partial charges ahead of time may not work for virtual sites

  OpenFreeEnergy/pontibus#60 · Filter by author IAlibay opened on May 26, 2025