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Add HMCMove

Open maxentile opened this issue 2 years ago • 0 comments

  • 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.)

maxentile avatar Aug 03 '22 14:08 maxentile