Enum: BoxType

Types of box used to simulate the system.

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

Permissible Values

Value	Meaning	Description
Cubic	None	3D rectangular prism where all sides are equal in length
Tetragonal	None	Simulation boundaries form a rectangular prism, where two sides are equal (a …
Orthorhombic	None	3D unit cell defined by three mutually perpendicular axes of unequal length (…
Truncated Octahedron	None	A 14-sided 3D shape (8 hexagonal and 6 square faces) used as a simulation cel…
Triclinic	None	Non-orthogonal simulation cell defined by three arbitrary, non-coplanar vecto…

Slots

Name	Description
box_type	The type of box used to simuluate the system

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: BoxType
description: Types of box used to simulate the system.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  Cubic:
    text: Cubic
    description: 3D rectangular prism where all sides are equal in length
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_type
          value: cubic
    aliases:
    - Cubic
    - cubic
  Tetragonal:
    text: Tetragonal
    description: Simulation boundaries form a rectangular prism, where two sides are
      equal (a = b ≠ c) and all angles are exactly 90°.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_type
          value: tetragonal
    aliases:
    - Tetragonal
    - tetragonal
  Orthorhombic:
    text: Orthorhombic
    description: 3D unit cell defined by three mutually perpendicular axes of unequal
      length (a ≠ b ≠ c), where all angles are exactly 90°
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_type
          value: orthorhombic
    aliases:
    - Orthorhombic
    - orthorhombic
  Truncated Octahedron:
    text: Truncated Octahedron
    description: A 14-sided 3D shape (8 hexagonal and 6 square faces) used as a simulation
      cell in molecular dynamics. Because its geometry closely approximates a sphere,
      it is ideal for solvating roughly spherical or globular proteins
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_type
          value: truncated octahedron
    aliases:
    - Truncated Octahedron
    - truncated_octahedron
  Triclinic:
    text: Triclinic
    description: Non-orthogonal simulation cell defined by three arbitrary, non-coplanar
      vectors. Unlike standard cubic or orthorhombic boxes (which have 90° angles),
      triclinic boxes can have arbitrary angles and varying edge lengths to model
      sheared systems, complex crystal lattices, and anisotropic stress tensors
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: box_type
          value: triclinic
    aliases:
    - Triclinic
    - triclinic