Add simulation extraction and viewing notebook#226

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jthorton wants to merge 9 commits intomainfrom

Commits on Sep 5, 2025

add trajectory notebook
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Commits on Sep 22, 2025

add info on extracting end states, use mdtraj to image the molecules
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Commits on Oct 8, 2025

Commits on Oct 22, 2025

Merge branch 'main' into traj-view
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Commits on Dec 11, 2025

Commits on Jan 6, 2026