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For anyone curious, I’m guessing “MD simulation” means https://en.wikipedia.org/wiki/Molecular_dynamics

Folks who use this kind of distance measure might note that it also works well as a metric between angles (i.e. rotations) or between points on the projective line. For instance, see https://www.youtube.com/watch?v=oJAn--vsAzc (unfortunately not too self-contained a source)



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