Class: Interactions¶

Settings used to define particle interactions.

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

         classDiagram
    class Interactions
    click Interactions href "../../classes/Interactions/"
      Interactions : bond_length_constraints_algorithm
        
          
    
        
        
        Interactions --> "0..1" BondLengthConstraintsAlgorithm : bond_length_constraints_algorithm
        click BondLengthConstraintsAlgorithm href "../../enums/BondLengthConstraintsAlgorithm/"
    

        
      Interactions : electrostatic_cutoff_distance
        
          
    
        
        
        Interactions --> "0..1" LengthQuantity : electrostatic_cutoff_distance
        click LengthQuantity href "../../classes/LengthQuantity/"
    

        
      Interactions : long_range_interaction_method
        
          
    
        
        
        Interactions --> "0..1" LongRangeInteractionMethod : long_range_interaction_method
        click LongRangeInteractionMethod href "../../enums/LongRangeInteractionMethod/"
    

        
      Interactions : restraints
        
      Interactions : vdw_cutoff_distance
        
          
    
        
        
        Interactions --> "0..1" LengthQuantity : vdw_cutoff_distance
        click LengthQuantity href "../../classes/LengthQuantity/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
restraints	0..1 boolean	Are any positional restraints applied to molecule dynamics? (Restraints usual…	direct
electrostatic_cutoff_distance	0..1 LengthQuantity	Distance in Angstrom at which a electrostatic interaction is turned off and a…	direct
vdw_cutoff_distance	0..1 LengthQuantity	Distance in Angstrom at which a Van der Waals interaction is turned off and a…	direct
bond_length_constraints_algorithm	0..1 BondLengthConstraintsAlgorithm	Constraints applied to bonds between two particles in the simulated system	direct
long_range_interaction_method	0..1 LongRangeInteractionMethod	Method used to describe long-range interactions between particles	direct

Usages¶

used by	used in	type	used
SimulationSettings	interactions	range	Interactions

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/Interactions
native	https://CCPBioSim.ac.uk/biosim-schema/Interactions

LinkML Source¶

Direct¶

name: Interactions
description: Settings used to define particle interactions.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- restraints
- electrostatic_cutoff_distance
- vdw_cutoff_distance
- bond_length_constraints_algorithm
- long_range_interaction_method

Induced¶

name: Interactions
description: Settings used to define particle interactions.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  restraints:
    name: restraints
    description: Are any positional restraints applied to molecule dynamics? (Restraints
      usually use harmonic potentials to keep a value near a target).
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Interactions
    domain_of:
    - Interactions
    range: boolean
  electrostatic_cutoff_distance:
    name: electrostatic_cutoff_distance
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: rcoulomb
          unit: nm
        - engine: amber
          key: cut
          unit: Å
    description: Distance in Angstrom at which a electrostatic interaction is turned
      off and a long-range non-bonded method is turned on, given as a float.
    examples:
    - value: 10 Å
    - value: 1.2 nm
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Interactions
    domain_of:
    - Interactions
    range: LengthQuantity
  vdw_cutoff_distance:
    name: vdw_cutoff_distance
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: rvdw
          unit: nm
    description: Distance in Angstrom at which a Van der Waals interaction is turned
      off and a long-range non-bonded method is turned on.
    examples:
    - value: 10 Å
    - value: 1.2 nm
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Interactions
    domain_of:
    - Interactions
    range: LengthQuantity
  bond_length_constraints_algorithm:
    name: bond_length_constraints_algorithm
    description: Constraints applied to bonds between two particles in the simulated
      system.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Interactions
    domain_of:
    - Interactions
    range: BondLengthConstraintsAlgorithm
  long_range_interaction_method:
    name: long_range_interaction_method
    description: Method used to describe long-range interactions between particles.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Interactions
    domain_of:
    - Interactions
    range: LongRangeInteractionMethod