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OpenFreeEnergy / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
MIT License
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Add protein-ligand complex testing #61

Closed ijpulidos closed 2 months ago

ijpulidos commented 2 months ago

These set of changes implement a test case for a short run of a protein-ligand complex (tyk2 and two of its ligands). The aim is to test protocol creation with different components (we have been testing only small mol components so far).

At the same time, a performance improvement on the creation of the hybrid topology was implemented, avoiding generating atoms lists, but instead generating them once and re-using the created list object.

ijpulidos commented 2 months ago

We are now running the tests in ~5.5 minutes. In contrast to ~13.5 minutes before these changes. :rocket:

I marked the protein-ligand complex test as "slow" for now (that means it's getting skipped, it takes about 20 mins to run). Probably something to review once we have the self-hosted GPU CI working here (issue #21). This one should be ready to review.