Enum: ThermostatAlgorithm

Thermostat algorithm used to set the temperature in a simulation.

URI: https://CCPBioSim.ac.uk/biosim-schema/ThermostatAlgorithm

Permissible Values

Value	Meaning	Description
Langevin	None	A Langevin thermostat is a molecular dynamics algorithm that maintains a cons…
Berendsen	None	Rescales particle velocities by a factor at each step to bring the system tow…
Andersen	None	Stochastic approach that periodically reassigns particle velocities from a Ma…
Nose-Hoover	None	A deterministic method that introduces a fictitious friction variable into th…
Bussi	None	The Bussi-Donadio-Parrinello (CSVR) is a stochastic velocity rescaling thermo…

Slots

Name	Description
thermostat_algorithm	List of thermostat algorithms used in the simulation

Identifier and Mapping Information

Schema Source

• from schema: https://CCPBioSim.ac.uk/biosim-schema/

LinkML Source

name: ThermostatAlgorithm
description: Thermostat algorithm used to set the temperature in a simulation.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  Langevin:
    text: Langevin
    description: A Langevin thermostat is a molecular dynamics algorithm that maintains
      a constant temperature (canonical ensemble, NVT) by adding a viscous friction
      force and a random noise force to Newton's equations of motion. It simulates
      interaction with a heat bath, where the damping term removes energy and the
      random force inputs energy to reach equilibrium.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: ntt
          value: 3
  Berendsen:
    text: Berendsen
    description: Rescales particle velocities by a factor at each step to bring the
      system toward the target temperature.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: tcoupl
          value:
          - berendsen
          - v-rescale
        - engine: amber
          key: ntt
          value: 1
  Andersen:
    text: Andersen
    description: Stochastic approach that periodically reassigns particle velocities
      from a Maxwell-Boltzmann distribution, simulating collisions with a heat bath.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: tcoupl
          value:
          - andersen
          - andersen-massive
        - engine: amber
          key: ntt
          value: 2
  Nose-Hoover:
    text: Nose-Hoover
    description: A deterministic method that introduces a fictitious friction variable
      into the system's dynamics to achieve the desired temperature (NVT ensemble).
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: tcoupl
          value: nose-hoover
        - engine: amber
          key: ntt
          value:
          - 9
          - 10
    aliases:
    - Nose-Hoover
    - Nose_Hoover
  Bussi:
    text: Bussi
    description: The Bussi-Donadio-Parrinello (CSVR) is a stochastic velocity rescaling
      thermostat that corrects the pitfalls of the Berendsen thermostat, accurately
      sampling the canonical ensemble while maintaining correct dynamics.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: ntt
          value: 11
    aliases:
    - Bussi
    - Bussi-Donadio-Parrinello