Issues

• 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
  

• Add running short MD to the troubleshooting guide

  OpenFreeEnergy/openfe#2309 · Filter by author jthorton opened on Oct 26, 2026
  1

  

• [docs] Simulation health user guide

  OpenFreeEnergy/openfe#2308 · Filter by author hannahbaumann opened on Oct 26, 2026
  

• Ionized setting of membrane protocol

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

• 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
  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

  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

  blockedpriority: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] mixed networks tutorial

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

• make docs more parsable

  OpenFreeEnergy/openfe#2274 · Filter by author atravitz opened on Oct 20, 2026
  1

  

• 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

• [execution] 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