proteneer / timemachine

Differentiate all the things!
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Diagnostics for computing the effective excluded volume #1232

Closed proteneer closed 9 months ago

proteneer commented 9 months ago

This PR adds basic utilities for computing effective excluded volumes for a molecule and investigates how our current all-at-once-4D decoupling scheme lead to poor intermediate states (both in terms of monotonicity and in terms of sharpness. This may motivate us to move to a better, atom-by-atom, decoupling scheme to better mitigate these issues.

Some caveats:

1) Single conformation 2) Crude heuristic for estimating radii derived from a generalization of r_min 3) May not be fully indicative of replica-state problems we're seeing in practice

Screenshot from 2024-01-10 17-46-08

excluded_vol_pr

proteneer commented 9 months ago

(closing and moving this to internal dev)