timemachine
timemachine copied to clipboard
Baseline method for resampling p(x[dummy] | x[anchor])
- [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 cheaperU_fn
using information fromtimemachine.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: