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openforcefield / openff-benchmark

Comparison benchmarks between public force fields and Open Force Field Initiative force fields
MIT License
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Don't check for connectivity rearrangements after MM optimizations #98

Open j-wags opened 2 years ago

j-wags commented 2 years ago

I think that the root cause of the failing connectivity checks that @ldamore reported in bicyclopentanes are due to erroneous bond detection.

Failed connectivity check:

Screen Shot 2021-08-04 at 8 38 22 AM

Passed connectivity check:

Screen Shot 2021-08-04 at 8 38 36 AM

Since MM optimizations can't meaningfully make/break bonds, the best solution to this problem is probably to skip the connectivity check after MM optimizations altogether.