Class: MolecularDynamics

Molecular dynamics simulation — a method for computing the time evolution

of a system of interacting particles by integrating the equations of motion.

Used to study diffusion, reaction kinetics, and thermal properties.

 classDiagram
    class MolecularDynamics
    click MolecularDynamics href "../../classes/MolecularDynamics/"
      SimulationMethod <|-- MolecularDynamics
        click SimulationMethod href "../../classes/SimulationMethod/"

      MolecularDynamics : description

      MolecularDynamics : ensemble_type

      MolecularDynamics : force_field

      MolecularDynamics : number_of_atoms

      MolecularDynamics : rdf_type





        MolecularDynamics --> "0..1 _recommended_" DefinedTerm : rdf_type
        click DefinedTerm href "../../classes/DefinedTerm/"



      MolecularDynamics : simulation_time

      MolecularDynamics : simulation_timestep

      MolecularDynamics : title

      MolecularDynamics : type





        MolecularDynamics --> "0..1" DefinedTerm : type
        click DefinedTerm href "../../classes/DefinedTerm/"

Inheritance

Plan [ ClassifierMixin]
- SimulationMethod
  - MolecularDynamics

Slots

Name	Cardinality and Range	Description	Inheritance
force_field	* String	Force field or interatomic potential used (e.g. ReaxFF, CHARMM, Tersoff, EAM). Include parametrisation source or reference.	direct
simulation_timestep	* Float	Integration timestep used in molecular dynamics.	direct
simulation_time	* Float	Total simulated physical time of the MD trajectory.	direct
ensemble_type	* String	Statistical ensemble used in MD (e.g. NVE, NVT, NPT). Determines which thermodynamic quantities are conserved.	direct
number_of_atoms	* Integer	Number of atoms in the simulation cell or supercell.	direct
title	0..1 String	This slot is described in more detail within the class in which it is used.	Plan
description	0..1 String	This slot is described in more detail within the class in which it is used.	Plan
type	0..1 DefinedTerm	This slot is described in more detail within the class in which it is used.	ClassifierMixin
rdf_type	0..1 recommended DefinedTerm	The slot to specify the ontology class that is instantiated by an entity.	ClassifierMixin

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nfdi4cat/coremeta4cat

Mappings

Mapping Type	Mapped Value
self	NCIT:C18097
native	coremeta4cat:MolecularDynamics

LinkML Source

Direct

name: MolecularDynamics
description: 'Molecular dynamics simulation — a method for computing the time evolution

  of a system of interacting particles by integrating the equations of motion.

  Used to study diffusion, reaction kinetics, and thermal properties.'
from_schema: https://w3id.org/nfdi4cat/coremeta4cat
is_a: SimulationMethod
slots:
- force_field
- simulation_timestep
- simulation_time
- ensemble_type
- number_of_atoms
class_uri: NCIT:C18097

Induced

name: MolecularDynamics
description: 'Molecular dynamics simulation — a method for computing the time evolution

  of a system of interacting particles by integrating the equations of motion.

  Used to study diffusion, reaction kinetics, and thermal properties.'
from_schema: https://w3id.org/nfdi4cat/coremeta4cat
is_a: SimulationMethod
attributes:
  force_field:
    name: force_field
    description: 'Force field or interatomic potential used (e.g. ReaxFF, CHARMM,
      Tersoff,

      EAM). Include parametrisation source or reference.'
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: coremeta4cat:force_field
    alias: force_field
    owner: MolecularDynamics
    domain_of:
    - MolecularDynamics
    range: string
    multivalued: true
  simulation_timestep:
    name: simulation_timestep
    description: Integration timestep used in molecular dynamics.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: APOLLO_SV:00000012
    alias: simulation_timestep
    owner: MolecularDynamics
    domain_of:
    - MolecularDynamics
    range: float
    multivalued: true
    unit:
      ucum_code: fs
  simulation_time:
    name: simulation_time
    description: Total simulated physical time of the MD trajectory.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: coremeta4cat:simulation_time
    alias: simulation_time
    owner: MolecularDynamics
    domain_of:
    - MolecularDynamics
    range: float
    multivalued: true
    unit:
      ucum_code: ps
  ensemble_type:
    name: ensemble_type
    description: 'Statistical ensemble used in MD (e.g. NVE, NVT, NPT). Determines
      which

      thermodynamic quantities are conserved.'
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: coremeta4cat:ensemble_type
    alias: ensemble_type
    owner: MolecularDynamics
    domain_of:
    - MolecularDynamics
    range: string
    multivalued: true
  number_of_atoms:
    name: number_of_atoms
    description: Number of atoms in the simulation cell or supercell.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: coremeta4cat:number_of_atoms
    alias: number_of_atoms
    owner: MolecularDynamics
    domain_of:
    - MolecularDynamics
    range: integer
    multivalued: true
  title:
    name: title
    description: This slot is described in more detail within the class in which it
      is used.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: MolecularDynamics
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - DefinedTerm
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
  description:
    name: description
    description: This slot is described in more detail within the class in which it
      is used.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: MolecularDynamics
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
  type:
    name: type
    description: This slot is described in more detail within the class in which it
      is used.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: dcterms:type
    alias: type
    owner: MolecularDynamics
    domain_of:
    - Agent
    - ClassifierMixin
    - Dataset
    - LicenseDocument
    range: DefinedTerm
    inlined: true
  rdf_type:
    name: rdf_type
    description: The slot to specify the ontology class that is instantiated by an
      entity.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: rdf:type
    alias: rdf_type
    owner: MolecularDynamics
    domain_of:
    - ClassifierMixin
    range: DefinedTerm
    recommended: true
    inlined: true
class_uri: NCIT:C18097