Enum: SimulationTool

Tools/utility used within simulation engines to perform simulations.

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

Permissible Values

Value	Meaning	Description
sander	None	A tool with AmberTools that is a basic energy minimizer and molecular dynamic…
pmemd	None	Part of Amber and is a version of the sander simulation tool that is optimize…
gem.pmemd	None	gem
mdrun	None	The main molecular dynamics engine of GROMACS, used to perform energy minimiz…

Slots

Name	Description
simulation_tool	Tool used to perform simulation

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: SimulationTool
description: Tools/utility used within simulation engines to perform simulations.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  sander:
    text: sander
    description: A tool with AmberTools that is a basic energy minimizer and molecular
      dynamics program.
  pmemd:
    text: pmemd
    description: Part of Amber and is a version of the sander simulation tool that
      is optimized for speed and for parallel scaling.
  gem.pmemd:
    text: gem.pmemd
    description: gem.pmemd is a part of AmberTools that is a CPI-only variant of the
      pmemd program that is designed for calculations using "advanced" force fields,
      such as AMOEBA and GEM.
    aliases:
    - gem.pmemd
    - gem_pmemd
  mdrun:
    text: mdrun
    description: The main molecular dynamics engine of GROMACS, used to perform energy
      minimization, molecular dynamics simulations, and analysis. It executes the
      simulation based on input files prepared by other GROMACS tools, supporting
      a wide range of simulation types and parallelization options.