OpenFreeEnergy / OpenFreeEnergy/openfe
Add equilibration step to RBFE protocol or "equilibration pre-processing"
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
From @hannahbaumann
We should try to do an extra equilibration for our RFE protocols.
We could run a standard equilibration on the system after creating the HTF (could just add it as a step ~ https://github.com/OpenFreeEnergy/openfe/blob/915d11022c31ce5e6835aa220965eb6c5698f794/openfe/protocols/openmm_rfe/equil_rfe_methods.py#L964 and then update the positions in the HTF object).
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with openfe/protocols/openmm_rfe/equil_rfe_methods.py around line 964, then trace how the HTF is created and how positions are updated. Determine how to add a standard equilibration after HTF creation and ensure the resulting positions are stored in the HTF object. Done means RBFE protocols perform this additional equilibration consistently.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100