BBK

The BBK (Brünger–Brooks–Karplus) [Brunger1984] [Pastor1988] [Loncharich1992] integrator implements a Langevin dynamics algorithm for simulating particles in the NVT ensemble. This integrator is a custom implementation in UAMMD-structured.

  • type: Langevin, BBK

  • parameters:

    • timeStep: real: Time step \([time]\)

    • temperature: real: Temperature of the system \([energy]\)

    • frictionConstant: real: Friction constant for the Langevin thermostat \([1/time]\) (optional if defined in particle data)

    • stopTransRotSteps: ullint: Number of steps between removing global translation and rotation (default: 0, disabled)

    • resetVelocities: bool: Whether to reset velocities at the start of the simulation (default: true)

Example:

"bbk":{
  "type":["Langevin","BBK"],
  "parameters":{
    "timeStep": 0.01,
    "temperature": 1.0,
    "frictionConstant": 1.0,
    "stopTransRotSteps": 1000,
    "resetVelocities": true
  }
}

Note

If frictionConstant is not provided, the integrator will use the friction constant defined in the particle data.

Warning

This integrator assumes that the particle mass is defined in the particle data.

[Brunger1984]

Brünger, Axel, Charles L. Brooks III, and Martin Karplus. “Stochastic boundary conditions for molecular dynamics simulations of ST2 water.” Chemical physics letters 105, no. 5 (1984): 495-500.

[Pastor1988]

Pastor, Richard W., Bernard R. Brooks, and Attila Szabo. “An analysis of the accuracy of Langevin and molecular dynamics algorithms.” Molecular Physics 65, no. 6 (1988): 1409-1419.

[Loncharich1992]

Loncharich, Richard J., Bernard R. Brooks, and Richard W. Pastor. “Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide.” Biopolymers: Original Research on Biomolecules 32, no. 5 (1992): 523-535.