Issues

• 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] clean up installation guide

  documentationpriority:high
  OpenFreeEnergy/openfe#2285 · Filter by author atravitz opened on Oct 20, 2026
  

• [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

  blockedpriority:low
  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

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

• [docs] document structure prep edge cases

  blockeddocumentation
  OpenFreeEnergy/openfe#2279 · 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] improve conda-lock installation instructions

  documentationpriority:medium
  OpenFreeEnergy/openfe#2277 · Filter by author atravitz opened on Oct 20, 2026
  

• [docs] add link to from FAQ to restart guide

  documentationpriority:medium
  OpenFreeEnergy/openfe#2276 · Filter by author atravitz opened on Oct 20, 2026
  

• docs: mixed networks tutorial

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

• add AGENTS.md

  OpenFreeEnergy/openfe#2274 · Filter by author atravitz opened on Oct 20, 2026
  

• docs: add domain of applicability page

  documentation
  OpenFreeEnergy/openfe#2273 · Filter by author atravitz opened on Oct 20, 2026
  1

  

• Generating results.json from separate simulations

  OpenFreeEnergy/openfe#2269 · Filter by author mathilfiker opened on Oct 16, 2026
  2

• Should the get_aromatic_rings function check if the default RDKit aromaticity is used?

  OpenFreeEnergy/openfe#2261 · Filter by author hannahbaumann opened on Oct 12, 2026

• add exit codes to openfe run_task

  OpenFreeEnergy/openfe#2254 · Filter by author atravitz opened on Oct 7, 2026
  

• openfe status command reports more "in progress" tasks than I have tasks being executed

  execution
  OpenFreeEnergy/openfe#2252 · Filter by author IAlibay opened on Oct 6, 2026

• add small example alchemical network (mcl1?) to openfe fetch

  OpenFreeEnergy/openfe#2250 · Filter by author atravitz opened on Oct 6, 2026

• Remove support for legacy SepTop & AHFE settings

  OpenFreeEnergy/openfe#2247 · Filter by author IAlibay opened on Oct 6, 2026

• Task-based execution generates over 1500 task files for a network with only ~ 80 ligands.

  execution
  OpenFreeEnergy/openfe#2246 · Filter by author IAlibay opened on Oct 5, 2026
  1

• feat / enh: progress bar for setup-task-campaign

  execution
  OpenFreeEnergy/openfe#2245 · Filter by author IAlibay opened on Oct 5, 2026 · v1.14

• feat: add exists_okay option to setup_task_campaign

  execution
  OpenFreeEnergy/openfe#2244 · Filter by author atravitz opened on Oct 5, 2026
  1

• Enable structural analysis for vacuum legs in AHFE transformations

  OpenFreeEnergy/openfe#2239 · Filter by author IAlibay opened on Oct 5, 2026