Irfan Alibay issues

Results 265 issues of


                                            Irfan Alibay

Clean up `ligands.yaml` files

These are out of sync, we should clean them up before a release.

JSON roundtrip doesn't work with `from_openmm` generated system

**Description** `Interchange.parse_raw()` yields a `KeyError: 'name'` when passing a JSON generated from an Interchange object that was created from an OpenMM System & Topology (via `Interchange.from_openmm`). Note: the openmm System...

Some AWS CI updates

Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the...

Document supported version of key software

Follow-up from https://github.com/OpenFreeEnergy/openfe/pull/673 We should at least document which versions of OpenMM we support (we only ever test on 8.0+ so we should probably say that somewhere!).

Add nvidia-smi step to GPU runners

Ethan rightly recommends we have that to make sure we have a GPU.

[meta] Membrane support in OpenFE Protocols

## Motivation Membrane-protein systems account for ~ 60% of possible target space. Being able to calculate binding free energies for membrane-containing systems would be a significant advantage. ## Current status...

Cron CI is failing due to timeout

Cron CI jobs are just taking too long and end up failing.

2D RMSD plots are unreadable at high replica counts

See ![image](https://github.com/user-attachments/assets/290650d1-d9ea-4fba-8d0f-b91a27c0d390)

Add support for GPU runners

The OMSF GPU runner actions are now ready for alpha testing, we should do a trial on this repo with some GPU-enabled tests (integration tests w/ CUDA as the engine...