Enum: MinimisationAlgorithm

Algorithm used to minimise particle interactions.

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

Permissible Values

Value	Meaning	Description
Steepest Descent	None	Moves atoms in the opposite direction of the energy gradient (forces)
Conjugate Gradient	None	Uses both current gradient information and previous search directions to find…
L-BFGS	None	L-BFGS (Limited-memory Broyden–Fletcher–Goldfarb–Shanno) approximates the inv…
XMIN	None	Minimization algorithm used to relax molecular structures to their lowest pot…
LMOD	None	LMOD (Low-Mode) minimization is a specialized conformational search and energ…
None	None	No minimisation

Slots

Name	Description
minimisation_algorithm	Name of the method used to minimise the molecular system

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: MinimisationAlgorithm
description: Algorithm used to minimise particle interactions.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  Steepest Descent:
    text: Steepest Descent
    description: Moves atoms in the opposite direction of the energy gradient (forces).
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: integrator
          value: steep
        - engine: amber
          key: ntmin
          value:
          - 1
          - 2
    aliases:
    - Steepest Descent
    - steepest_descent
  Conjugate Gradient:
    text: Conjugate Gradient
    description: Uses both current gradient information and previous search directions
      to find a more efficient path to the minimum.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: integrator
          value: cg
        - engine: amber
          key: ntmin
          value:
          - 0
          - 1
    aliases:
    - Conjugate Gradient
    - conjugate_gradient
  L-BFGS:
    text: L-BFGS
    description: L-BFGS (Limited-memory Broyden–Fletcher–Goldfarb–Shanno) approximates
      the inverse Hessian matrix (second derivatives) using a limited number of previous
      steps, making it memory-efficient.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: gromacs
          key: integrator
          value: l-bfgs
    aliases:
    - L-BFGS
  XMIN:
    text: XMIN
    description: Minimization algorithm used to relax molecular structures to their
      lowest potential energy state, particularly for finding very deep local minima.
      It is a quasi-Newton method that typically provides quadratically convergent
      minimization.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: ntmin
          value: 3
    aliases:
    - XMIN
    - xmin
  LMOD:
    text: LMOD
    description: LMOD (Low-Mode) minimization is a specialized conformational search
      and energy minimization method designed to efficiently find low-energy structures
      by navigating along the low-frequency vibrational modes of a system.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: ntmin
          value: 4
    aliases:
    - LMOD
    - lmod
  None:
    text: None
    description: No minimisation.
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: amber
          key: imin
          value: 0
    aliases:
    - None