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Baseline method for resampling p(x[dummy] | x[anchor])

Open maxentile opened this issue 2 years ago • 0 comments

  • [x] Add a "brute-force" method for resampling the coordinates of dummy atoms, conditioned on the coordinates of anchor atoms
  • [x] Add a basic test (asserting that only the expected set of updated atom idxs are updated)
  • [ ] TBD[current PR]: think of + add a more stringent test
  • [ ] TBD[later PR]: apply performance optimizations (rather than use the whole intramolecular U_fn with some coords frozen, construct and use a cheaper U_fn using information from timemachine.fe.single_topology_v3.find_dummy_groups_and_anchors)

Illustration:

For the methane -> fluoromethane example in the test (with a single dummy atom at each endstate), the resampled atoms flap around as expected in each endstate:

image

maxentile avatar Aug 22 '22 23:08 maxentile