Example Numerical Methods

Example Propagator Classes

  • Brunger-Brooks-Karplus (STS)
  • Nose-Poincare (STS)
  • RMT (STS)
  • Example Propagator Functions

  • Hybrid Monte Carlo Sampler (MTS)
  • S2HMC Sampler (MTS)
  • Verlet-I/r-RESPA (MTS)
  • Leapfrog (STS)
  • Improved Takahashi-Imada (STS)
  • Velocity Verlet+Velocity Scaling (STS)
  • Example Propagator Modifiers

  • Frictional Force (for Langevin dynamics)
  • Example Forces

  • Harmonic Dihedral

  • Example Simulation Protocols

    United Atom Butane

  • 200 steps of Hybrid Monte Carlo sampling
  • 10 ps of Langevin Impulse
  • 8 ps of Nose-Poincare
  • 0.1 ps of RMT
  • Argon

  • 0.1 ps of Leapfrog (using a propagator function)
  • 0.1 ps of Leapfrog (using a propagator class)
  • 0.1 ps of Self-consistent Leapfrog
  • 2 ps of Improved Takahashi-Imada
  • Bovine Pancreatic Tripsin Inhibitor

  • 10 ps of BBK
  • 1 ps of Leapfrog
  • Water

  • 0.5 ps of Verlet/r-RESPA
  • 1 fs of Position Verlet
  • 500 steps of S2HMC sampling
  • Decalanine

  • 1 ps of Nose Hoover
  • Alanine Dipeptide

  • 0.2 ps of Normal Mode Langevin with 40 restrained modes
  • 50 ps of Umbrella Sampling
  • String Method (unsolvated, serial)
  • String Method (solvated, parallel)
  • OpenMM, Gromacs/AMBER, Generalized Born
  • Calmodulin

  • 5 ps of Langevin Dynamics, using OpenMM
  • WW Domain

  • 5 ps of Langevin Dynamics, using OpenMM
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