Irfan Alibay
Irfan Alibay
A request by some users is to allow for arbitrary solvent in HFE simulations. This might be possible either by: - packmol building our own systems (see https://github.com/OpenFreeEnergy/openfe/tree/ahfe-packmol for a...
We should eventually add support for thermodynamic trailblazing - this will need some thoughts & work on decoupling units. Not currently targetted until after the end of year 1.
We have an HFE protocol, we should benchmark it and make some pretty plots. Currently WIP: - QA data from Mike needs to be analyzed - Alchemiscale-generated runs of the...
Follow-up from #569 Simulations involving charge changes probably need somewhere around 22 to 24 windows (@hannahbaumann has been using the former in testing). We should make sure that folks do...
Follow on from #601
I am generate charges using espaloma via the OpenFF toolkitwrapper interface in the following manner: https://github.com/IAlibay/partial_charge_experiments/blob/main/scripts/run-espaloma.py Calling this seems to leave behind `.model.pt` files which are somewhat unexplained. Should these...
Especially when demonstrating things to the public (particularly thinking about F@H here) - it would be great to be able to report the total number of workers being used by...
Not sure if it fully falls under the required "user stories", but we (i.e. OpenFE team) were discussing this internally after yesterday's meeting and thought it might be good to...
Related to #4624 WIth #4620 we prevent importing parmed if we have numpy 2.0 due to compatibility issues. Once parmed supports numpy 2.0, we should go ahead and remove these...
With #4620 we are adding import skips when trying to use rdkit with numpy > 2.0. Once rdkit has 2.0 support we should remove those skips. Tracking issue: https://github.com/rdkit/rdkit/issues/7477