OpenFreeEnergy / OpenFreeEnergy/openfe
SepTop optimization: Pre-equilibration in separate units
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- Dominant language
- Python
- Stars
- 332
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
We are currently running the pre equilibration in SepTop of both end states in the same unit. In order to not overwrite outputs, settings have to be modified, e.g.
unfrozen_outsettings = settings['equil_output_settings'].unfrozen_copy()
if endstate == 'A' or endstate == 'B':
if unfrozen_outsettings.production_trajectory_filename:
unfrozen_outsettings.production_trajectory_filename = (
unfrozen_outsettings.production_trajectory_filename + f'_state{endstate}.xtc')
The non-alchemical equilibration for both end states could instead be run in separate units, then the settings would not need to be modified. This would require a rearrangement of the SetupUnit as it currently creates the systems for the end states and the SepTop combined system.
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 by examining SetupUnit, which currently creates the end-state systems and the combined SepTop system, and review the equilibration output settings shown in the issue. Rearrange setup so non-alchemical pre-equilibration for the two end states runs in separate units; done means outputs no longer require state-specific settings modifications.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100