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thermostat

Apply a thermostat in a molecular dynamics simulation. This command can appear in the global context.

Options

coupling_time

Characteristic time for temperature coupling.

  • The type is quantity
  • The default is 0.0 ps
  • The value must be nonnegative
rng_seed

Seed used to initialize a pseudo-random number generator. By default, rng_seed is set to -1, which uses a pseudo random seed.

  • The type is int
  • The default is -1
temperature

Specify the target temperature for thermostating.

  • The type is quantity
  • The default is 300.0 kelvin
  • The value must be nonnegative
type

Specify type of the thermostat.

  • The type is string
  • The default is andersen
  • The value must be one of:
    • velocity rescaling - Temperature coupling using the simple velocity rescaling. If coupling_time is set to zero, this thermostat will rescale velocities every time step; otherwise, it will rescale the velocities in every coupling_time.
    • berendsen - Temperature coupling using Berendsen thermostat. For this thermostat to work, coupling_time has to be non-zero, and should correspond to the characteristic relaxation time of the system.
    • andersen - Temperature coupling using Andersen thermostat. If coupling_time is set to zero, this thermostat will reset velocities of all atoms at every time step; otherwise, it will reset velocities of randomly selected atoms such that they will be reset over the coupling_time on avarage. For the justification of the algorithm, refer to the original paper: Andersen (1980) JCP 72(4), 2384–2393
    • langevin - Temperature coupling using the velocity update at every time step based on Langevin dynamics. If coupling_time (inverse of friction) is set to 0, velocities are resampled every time step. Otherwise, coupling_time controls the level of thermal damping. Implemented method from Bussi and Parrinello (2007) Phys. Rev. E, 75, 056707.