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PyMBAR (4) will create an endless loop in get_forward_and_reverse_analysis if there are too few samples #1173

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IAlibay opened this issue Mar 3, 2025 · 0 comments

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@IAlibay
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IAlibay commented Mar 3, 2025

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.
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