Fix to bootstrap of free energy surfaces, affecting timing and quantitative results

choderalab / pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

http://pymbar.readthedocs.io

MIT License

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Fix to bootstrap of free energy surfaces, affecting timing and quantitative results #535

Open mrshirts opened 2 months ago

mrshirts commented 2 months ago

Free energy surface code was calling MBAR after each call to randomizing bootstraps. It does not appear to affect the results, but slows things down by a factor of a little less than 2x (146 vs 87 seconds for one sample run).

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 52.94118% with 8 lines in your changes missing coverage. Please review.

Project coverage is 69.70%. Comparing base (85e034c) to head (4ed45db).

Additional details and impacted files

mrshirts commented 2 months ago

Couple more changes I will put in to fix uncertainties, don't do anything yet to it . . .

mrshirts commented 2 months ago

OK, I think I got the changes in I needed to.

mikemhenry commented 2 months ago

@mrshirts when you are ready for review go ahead and add whoever you want to review this PR :smile:

mrshirts commented 2 months ago

Suggestions for anyone else who should review - or if there's anyone who could take a look? We are looking at some free energy surface problems for OpenFF, so we want to get this through.