Class: Minimisation

Minimisation stage of simulation workflow.

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

         classDiagram
    class Minimisation
    click Minimisation href "../../classes/Minimisation/"
      Minimisation : energy_tolerance
        
          
    
        
        
        Minimisation --> "0..1" ForceQuantity : energy_tolerance
        click ForceQuantity href "../../classes/ForceQuantity/"
    

        
      Minimisation : minimisation_algorithm
        
          
    
        
        
        Minimisation --> "*" MinimisationAlgorithm : minimisation_algorithm
        click MinimisationAlgorithm href "../../enums/MinimisationAlgorithm/"
    

        
      Minimisation : minimisation_distance_step_size
        
          
    
        
        
        Minimisation --> "0..1" LengthQuantity : minimisation_distance_step_size
        click LengthQuantity href "../../classes/LengthQuantity/"
    

        
      Minimisation : number_of_minimisation_steps
        
      Minimisation : simulation_software
        
          
    
        
        
        Minimisation --> "*" SimulationSoftware : simulation_software
        click SimulationSoftware href "../../enums/SimulationSoftware/"
    

        
      Minimisation : simulation_tool
        
          
    
        
        
        Minimisation --> "*" SimulationTool : simulation_tool
        click SimulationTool href "../../enums/SimulationTool/"
    

        
      
    

Slots

Name	Cardinality and Range	Description	Inheritance
energy_tolerance	0..1 ForceQuantity	Tolerance energy for when minimization stops, this is when the maximum force …	direct
number_of_minimisation_steps	0..1 integer	Number of integration steps performed during minimisation of the system, give…	direct
minimisation_distance_step_size	0..1 LengthQuantity	The distance the algorithm moves in a single step, controls how large a step …	direct
minimisation_algorithm	* MinimisationAlgorithm	Name of the method used to minimise the molecular system	direct
simulation_tool	* SimulationTool	Tool used to perform simulation	direct
simulation_software	* SimulationSoftware	Name of software used to perform simulation step	direct

Usages

used by	used in	type	used
SimulationStages	minimisation	range	Minimisation

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	https://CCPBioSim.ac.uk/biosim-schema/Minimisation
native	https://CCPBioSim.ac.uk/biosim-schema/Minimisation

LinkML Source

Direct

name: Minimisation
description: Minimisation stage of simulation workflow.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- energy_tolerance
- number_of_minimisation_steps
- minimisation_distance_step_size
- minimisation_algorithm
- simulation_tool
- simulation_software

Induced

name: Minimisation
description: Minimisation stage of simulation workflow.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  energy_tolerance:
    name: energy_tolerance
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: emtol
          unit: kJ/mol/nm
        - engine: amber
          key: drms
          unit: 10−4 kcal/mol/Å
    description: Tolerance energy for when minimization stops, this is when the maximum
      force on any atom is less than this value (default is often 1000 kJ/mol/nm or
      10−4kcal), given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    range: ForceQuantity
    minimum_value: 0
  number_of_minimisation_steps:
    name: number_of_minimisation_steps
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: maxcyc
        - engine: gromacs
          key: nsteps
    description: Number of integration steps performed during minimisation of the
      system, given as an integer.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    range: integer
  minimisation_distance_step_size:
    name: minimisation_distance_step_size
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: dx0
          unit: Å
        - engine: gromacs
          key: emstep
          unit: nm
    description: The distance the algorithm moves in a single step, controls how large
      a step the optimizer takes during the initial phase of minimizing the potential
      energy of a structure, given as a float.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    range: LengthQuantity
    minimum_value: 0
  minimisation_algorithm:
    name: minimisation_algorithm
    description: Name of the method used to minimise the molecular system.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    range: MinimisationAlgorithm
    multivalued: true
  simulation_tool:
    name: simulation_tool
    description: Tool used to perform simulation.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    - Equilibration
    - Production
    range: SimulationTool
    multivalued: true
  simulation_software:
    name: simulation_software
    description: Name of software used to perform simulation step.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Minimisation
    domain_of:
    - Minimisation
    - Equilibration
    - Production
    range: SimulationSoftware
    multivalued: true