timemachine
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Add HMCMove
- Add
HMCMove
- Make misc. small improvements to
moves.py
- Test
HMCMove
- Test stability etc. on vacuum ligand (using Jax potentials)
- Test stability etc. on solvated DHFR (using timemachine potentials)
- Test accurate sampling on system of independent oscillators (where 1D marginals can be computed ~exactly and compared to histograms)
Note: Standard HMC is not a practical move to apply directly to large MM systems, but it may be practical to apply to small systems (or subsystems).
(To get an acceptance rate of > 50% on the DHFR test system, for example, we need to reduce the timestep to an eye-watering 0.01 fs or so. A variety of mitigating strategies have been proposed in the literature, which may be necessary to consider if we ever need to use "global" HMC moves on these systems.)