Enum: BarostatAlgorithm

Barostat algorithm used to set the pressure in a simulation.

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

Permissible Values

Value	Meaning	Description
Berendsen	None	Rescales the system volume and (optionally) the atoms coordinates within the …
Andersen	None	Includes an additional degree of freedom, the volume of a simulation cell
Parrinello-Rahman	None	Extension of the Andersen method allowing changes in the shape of the simulat…
Nose-Hoover	None	Couples the system to a virtual “pressure bath” to control the simulation vol…
Monte Carlo	None	Maintain constant pressure by periodically attempting to scale the simulation…
Martyna-Tuckerman-Tobias-Klein	None	The MTTK barostat is an extension of the Nose-Hoover and Nose-Hoover chain th…

Slots

Name	Description
barostat_algorithm	List of barostat algorithms used in the simulation

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: BarostatAlgorithm
description: Barostat algorithm used to set the pressure in a simulation.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  Berendsen:
    text: Berendsen
    description: Rescales the system volume and (optionally) the atoms coordinates
      within the simulation box every timestep via weak coupling between the internal
      pressure and pressure.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: pcoupl
          value:
          - Berendsen
          - C-rescale
        - engine: gromacs
          key: barostat
          value: 1
  Andersen:
    text: Andersen
    description: Includes an additional degree of freedom, the volume of a simulation
      cell. Volume adjusts itself to equalize the internal and external pressure.
  Parrinello-Rahman:
    text: Parrinello-Rahman
    description: Extension of the Andersen method allowing changes in the shape of
      the simulation cell.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: pcoupl
          value: Parrinello-Rahman
    aliases:
    - Parrinello-Rahman
    - Parrinello_Rahman
  Nose-Hoover:
    text: Nose-Hoover
    description: Couples the system to a virtual "pressure bath" to control the simulation
      volume using extended Lagrangian dynamics.
    aliases:
    - Nose-Hoover
    - Nose_Hoover
  Monte Carlo:
    text: Monte Carlo
    description: Maintain constant pressure by periodically attempting to scale the
      simulation box size using random numbers.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: barostat
          value: 2
    aliases:
    - Monte Carlo
    - Monte_Carlo
  Martyna-Tuckerman-Tobias-Klein:
    text: Martyna-Tuckerman-Tobias-Klein
    description: The MTTK barostat is an extension of the Nose-Hoover and Nose-Hoover
      chain thermostat, acting as a modified Andersen barostat to control pressure
      by coupling the system to a virtual volume bath.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: pcoupl
          value: MTTK
    aliases:
    - Martyna-Tuckerman-Tobias-Klein
    - Martyna_Tuckerman_Tobias_Klein