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We should make it clear here what Protocols this applies to, i.e. this is for HybridTop mostly (i.e. the tempfactor stuff is hybridtop only) but also applies for the most part to ABFEs, AHFEs, and SepTop.
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Good point, also is it worth adding sections specific to the other protocols to show how to extract the relevant end-state structures?
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Yeah that would be a good way to do this cleanly if it's not too much work!
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Added something for SepTop as well.
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[nit] "any OpenFE free energy protocols"
(It's already implicit in the name of the tutorial, so it's ok to also not do this)
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Try adding the -nc or --no-clobber argument to wget? That way you won't double download the file.
Also this is a big nc file but the hybrid system doesn't include water. Would it be worth pulling down one of the smaller NC files? (I think we have newer generated ones?)
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Yes good idea can you point me to some?
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Using a smaller traj now from the openfe_analysis zenodo data
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I'm thinking, in MDAnalysis, it might be easy enough to align the trajectory to the coordinates of the PDB file and write that out. That's technically "centering" for free.
Also I'd be happy with merging this as-is, but opening a separate issue to try to make an MDAnalysis-only solution work. I'm sure it's doable, just needs the right set of transformations.
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Centering is now happening using the apply alignment transformation from openfe analysis.
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Overall looks good, thanks for doing this!
Added a few comments for things that we should address.
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-06-03T13:14:02Z Two questions:
1) Could you mention what Transformations are being applied by the method? Also can you mention that there's a separate one for solvent simulations if they want it.
2) Is there anything we can link to regarding when centering is a good idea and when it's not? I can't remember what Justin Lemkhul usually links to. Essentially what I mean here is that it would be good to say "don't center / align if you need to look at how components diffuse over time, etc..." |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-06-03T13:14:03Z "We can fix this, however, using the alignment functions in openfe_analysis"
It would be good to reword this as using a helper method to add a transformation to the MDAnalysis Universe. That way folkls that know MDAnalysis things can easily understand what's going on. For those that don't it would be good to link to the Transformations documentions in MDAnalysis (just so that folks understand what that means). And then in the code block add a comment when you apply the transformation. |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-06-03T13:14:04Z Maybe add a note before this code block that says "look now it's no longer broken" |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-06-03T13:14:05Z This is great! |
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This is looking great, just a couple small things and then I think it's good to go :)
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Fixes #223