Add gentle equilibration protocol as utility function #669
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Very nice 🎉 |
| openmm.app.PDBxFile.writeFile(topology, positions, open(filename, "w"), keepIds=True) | ||
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| # Save the box vectors | ||
| if save_box_vectors: |
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Are there cases where the box vectors are not needed? When creating a DCD trajectory in mdtraj, we need the box vectors along with the positions, so at least in that use case, we always need the box vectors.
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You are right, we should always be saving the box vectors in production-ready scenarios somehow. So far, this is mostly for practical purposes, such that we don't have to keep track of other files in tests.
I'm also considering that we want to eventually return openmm objects that already have this information included, I still don't know if that's going to be easily achievable but for now I'm going to leave it as is. The default behavior is to store the box vectors.
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Looks good! Just added some minor suggestions. |
Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com>
Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com>
Description
Resolves #540
These changes add the function
gentle_equilibrationthat can be imported usingfrom openmmtools.utils import gentle_equilibration.These changes create a new utils module that should serve as a more organized API point where to locate all the utility functions.
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