md.simulation_hooks.NHCThermostat

class md.simulation_hooks.NHCThermostat(*args: Any, **kwargs: Any)

Nose-Hover chain thermostat, which links the system to a chain of deterministic Nose-Hoover thermostats first introduced in [1] and described in great detail in [2]. Advantage of the NHC thermostat is, that it does not apply random perturbations to the system and is hence fully deterministic. However, this comes at an increased numerical cost compared to e.g. the stochastic thermostats described above.

Parameters:

• temperature_bath (float) – Temperature of the external heat bath in Kelvin.

• time_constant (float) – Thermostat time constant in fs

• chain_length (int) – Number of Nose-Hoover thermostats applied in the chain.

• massive (bool) – If set to true, an individual thermostat is applied to each degree of freedom in the system. Can e.g. be used for thermostatting (default=False).

• multi_step (int) – Number of steps used for integrating the NH equations of motion (default=2)

• integration_order (int) – Order of the Yoshida-Suzuki integrator used for propagating the thermostat (default=3).

References

[1]

Tobias, Martyna, Klein: Molecular dynamics simulations of a protein in the canonical ensemble. The Journal of Physical Chemistry, 97(49), 12959-12966. 1993.

[2]

Martyna, Tuckerman, Tobias, Klein: Explicit reversible integrators for extended systems dynamics. Molecular Physics, 87(5), 1117-1157. 1996.