UnderdampedLangevin #

UnderdampedLangevin integrator performs constant temperature simulation according to Langevin equation.

This method is developed in the following paper.

• J. D. Honeycutt and D. Thirumalai, (1992) Biopolymers
• Z. Guo and D. Thirumalai, (1995) Biopolymers.

It is the same method that is employed in CafeMol.

Example #

[simulator]
# ...
integrator.type = "UnderdampedLangevin"
integrator.gammas = [
    {index = 0, gamma = 1.0},
    {index = 1, gamma = 1.0},
    # ...
]

Input reference #

Some of the other parameters, such as delta_t, are defined in [Simulator] table.

• type: String
  • The name of Integrator. Here, it is "UnderdampedLangevin".
• gammas: Array of Tables
  • \(\gamma_i\) of the particles.
• remove: Table (Optional)
  • translation and rotation: Boolean
    • If true, it removes the total translation and rotation. Otherwise, it does nothing.
  • rescale: Boolean
    • If true, it rescales all the velocities to make kinetic energy constant.
  • By default, all the fields becomes false.