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choderalab / perses

Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
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Fix/issue 1194 #1230

Closed mikemhenry closed 1 year ago

mikemhenry commented 1 year ago

Description

Motivation and context

Resolves #1194

How has this been tested?

Change log

Correctly set cutoff for `CustomNonbondedForce` in `HybridTopologyFactory` when using a non-default cutoff distance.
ijpulidos commented 1 year ago

Actually, I first want to run a tyk2 validation simulation with these changes before merging them

codecov[bot] commented 1 year ago

Codecov Report

Merging #1230 (b6c29f7) into 0.10.x (aca858f) will increase coverage by 0.02%. The diff coverage is 76.19%.

ijpulidos commented 1 year ago

@zhang-ivy Since you have worked with the topology factories in detail, can you please take a look into these changes? Just to make sure we didn't miss anything. Thanks!

zhang-ivy commented 1 year ago

Looks good to me! Just added a non-blocking suggestion for the test. Feel free to ignore if you disagree.

mikemhenry commented 1 year ago

Thanks!

ijpulidos commented 1 year ago

Thanks for the review! Waiting for the tyk2 benchmark results to confirm that these changes are not changing anything else along the way.

ijpulidos commented 1 year ago

Results seem correct (unaffected by these changes), we could use this for the release as well.

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