Issues

• gather gives different DG header than gather-septop and gather-abfe for the --report dg

  OpenFreeEnergy/openfe#2346 · Filter by author hannahbaumann opened on Nov 9, 2026

• Move lambda settings validation to model_validate (SepTop and ABFE)

  OpenFreeEnergy/openfe#2342 · Filter by author jthorton opened on Nov 6, 2026
  1

• Make structural analysis settings configurable in RelativeHybridTopologyProtocol

  OpenFreeEnergy/openfe#2338 · Filter by author hannahbaumann opened on Nov 3, 2026

• Update docs after moving the Boresch analysis to ABFE and SepTop Analysis Unit

  OpenFreeEnergy/openfe#2337 · Filter by author hannahbaumann opened on Nov 3, 2026

• Planning section updates

  Task

  OpenFreeEnergy/openfe#2336 · Filter by author hannahbaumann opened on Nov 3, 2026
  

• Working with results: Add missing content

  Task

  OpenFreeEnergy/openfe#2335 · Filter by author hannahbaumann opened on Nov 3, 2026
  

• openfe and ExampleNotebooks release should be pinned together

  OpenFreeEnergy/openfe#2333 · Filter by author atravitz opened on Nov 3, 2026
  

• Restructure the tutorials

  OpenFreeEnergy/openfe#2331 · Filter by author hannahbaumann opened on Nov 2, 2026
  

• Restructure the docs

  OpenFreeEnergy/openfe#2329 · Filter by author hannahbaumann opened on Nov 2, 2026
  

• cli viz should support json as input

  OpenFreeEnergy/openfe#2323 · Filter by author atravitz opened on Oct 30, 2026
  

• Should we use konnektor.draw_ligand_network instead of openfe.utils.atommapping_network_plotting.plot_atommapping_network?

  OpenFreeEnergy/openfe#2315 · Filter by author hannahbaumann opened on Oct 28, 2026
  

• Common settings changes cookbook

  OpenFreeEnergy/openfe#2314 · Filter by author jthorton opened on Oct 28, 2026
  

• Ionized setting of membrane protocol

  OpenFreeEnergy/openfe#2306 · Filter by author Kamecs opened on Oct 26, 2026
  1

  

• Add validation for double to triple bond mappings in RBFE

  OpenFreeEnergy/openfe#2300 · Filter by author jthorton opened on Oct 23, 2026

• Trying to set up RBFE with a membrane protein solvated and prepped by packmol (AMBERtools)

  OpenFreeEnergy/openfe#2294 · Filter by author debarati-iambic2026 opened on Oct 21, 2026
  1

  

• add n_retries as a command line argument of openfe quickrun

  OpenFreeEnergy/openfe#2291 · Filter by author candidechamp opened on Oct 21, 2026 · v1.14
  3

  

• SepTop (and maybe ABFE) structural analysis stalls for certain molecule types

  OpenFreeEnergy/openfe#2290 · Filter by author IAlibay opened on Oct 21, 2026

• SepTop solvent analysis unit speed

  OpenFreeEnergy/openfe#2289 · Filter by author jthorton opened on Oct 21, 2026
  2

• [docs] review showcase notebook

  priority:high
  OpenFreeEnergy/openfe#2284 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] add docs on importing custom force fields

  priority:medium
  OpenFreeEnergy/openfe#2283 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] add more analysis tutorials and link to them

  blockedpriority:high
  OpenFreeEnergy/openfe#2282 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] add guide for improving performance

  blocked
  OpenFreeEnergy/openfe#2281 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] mapping CLI to API in the docs

  blockedpriority:high
  OpenFreeEnergy/openfe#2280 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] tutorial on how to explore and validate settings changes

  documentationpriority:high
  OpenFreeEnergy/openfe#2278 · Filter by author atravitz opened on Oct 20, 2026
  3

  

• [docs] mixed networks tutorial

  documentation
  OpenFreeEnergy/openfe#2275 · Filter by author atravitz opened on Oct 20, 2026