OpenFreeEnergy / OpenFreeEnergy/openfe
PyMBAR (4) will create an endless loop in `get_forward_and_reverse_analysis` if there are too few samples
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Describe the bug
If you run a short simulation, there is a risk that you might end up with a situation where 10% of the simulation has too few samples for MBAR analysis. This leads to a convergence failure which loops endlessly (or at least doesn't resolve in the span of several hours).
To Reproduce
Run a ~ 500 ps AHFE simulation.
Expected behavior
Possible ways to get around this case:
- Try to automatically rebalance how the forward/reverse analysis is chunked so that we have sufficient amounts of samples in each chunk.
- If we have too few samples in each chunk (unsure what a good number would be, less than 50?) and return None.
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 at get_forward_and_reverse_analysis and reproduce the issue with a roughly 500 ps AHFE simulation. Determine how the analysis handles chunks with too few samples; done means short simulations no longer loop endlessly and the insufficient-sample case is handled explicitly.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100