Enum: SimulationMethod

Options for simulation methods.

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

Permissible Values

Value	Meaning	Description
Self-guided Langevin Dynamics	None	Method that accelerates low frequency motion to enhance conformational sampli…
Accelerated Molecular Dynamics	None	Method where a bias potential that reduces the height of local barriers, allo…
Gaussian Accelerated Molecular Dynamics	None	Method that adds a harmonic boost potential (following a Gaussian distributio…
Targeted Molecular Dynamics	None	Method that adds an additional term to the energy function based on the mass-…
Nudged Elastic Band Calculations	None	Method where the path for a conformational change is approximated with a seri…
Adaptive String Method	None	Method to find the Minimum Free Energy Path (MFEP) in the space of selected c…
LMOD method	None	Conformational search algorithm based on eigenvector following of low frequen…
DL-FIND Optimization	None	Method to search for potential energy stationary points along a chemical reac…
Thermodynamic Integration (TI)	None	Method to calculate ensemble-averaged energies “on-the-fly” along a path as t…
Linear Interaction Energies (LIE)	None	Method to compute binding free energies using the linear interaction energy m…
Replica Exchange Molecular Dynamics (REMD)	None	An expanded ensemble energy method that samples from an ensemble larger than …
Adaptively Biased Molecular Dynamics (ABMD)	None	Method for calculating free energy landscapes as a function of a small number…
Steered Molecular Dynamics (SMD)	None	Method that applies an external force onto a physical system, and drives a ch…
Umbrella Sampling	None	A method that enhances sampling of rare events by applying a biasing potentia…
Metadynamics	None	An enhanced sampling technique that adds a history-dependent bias to the pote…
Swarms of Trajectories String Method	None	A version of the string method, a path-finding algorithm that refines a punat…
Constant pH Molecular Dynamics	None	Method that uses Monte Carlo sampling of the Boltzmann distribution of discre…
Constant Redox Potential Molecular Dynamics	None	Method that uses Monte Carlo sampling of the Boltzmann distribution of discre…
Continuous Constant pH Molecular Dynamics	None	A method that is an alternative to the Monte-Carlo based constant pH methods …
NMR Refinement	None	Method to incorporate a variety of restraints (e
X-ray and CryoEM Refinement	None	Method to incorporate electron microscopy (EM) image information into macromo…
Locally Enhanced Sampling	None	A method to allow for multiple local copies of regions within a larger biomol…

Slots

Name	Description
simulation_method	Method used to perform simulation

Identifier and Mapping Information

Schema Source

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

LinkML Source

name: SimulationMethod
description: Options for simulation methods.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  Self-guided Langevin Dynamics:
    text: Self-guided Langevin Dynamics
    description: Method that accelerates low frequency motion to enhance conformational
      sampling.
    aliases:
    - Self-guided Langevin Dynamics
    - selfguided_langevin_dynamics
  Accelerated Molecular Dynamics:
    text: Accelerated Molecular Dynamics
    description: Method where a bias potential that reduces the height of local barriers,
      allowing the faster evolution of a calculation.
    aliases:
    - Accelerated Molecular Dynamics
    - accelerated_molecular_dynamics
  Gaussian Accelerated Molecular Dynamics:
    text: Gaussian Accelerated Molecular Dynamics
    description: Method that adds a harmonic boost potential (following a Gaussian
      distribution) to smooth the system potential energy surface.
    aliases:
    - Gaussian Accelerated Molecular Dynamics
    - Gaussian_accelerated_molecular_dynamics
  Targeted Molecular Dynamics:
    text: Targeted Molecular Dynamics
    description: Method that adds an additional term to the energy function based
      on the mass-wieghted root mean square deviation of a set of atoms in the current
      structure compared to a reference structure.
    aliases:
    - Targeted Molecular Dynamics
    - targeted_molecular_dynamics
  Nudged Elastic Band Calculations:
    text: Nudged Elastic Band Calculations
    description: Method where the path for a conformational change is approximated
      with a series of images describing the molecule at discrete points along the
      path.
    aliases:
    - Nudged Elastic Band Calculations
    - nudged_elastic_band_calculations
  Adaptive String Method:
    text: Adaptive String Method
    description: Method to find the Minimum Free Energy Path (MFEP) in the space of
      selected collective variables connecting initial and final stages of a given
      process.
    aliases:
    - Adaptive String Method
    - adaptive_string_method
  LMOD method:
    text: LMOD method
    description: Conformational search algorithm based on eigenvector following of
      low frequency vibrational modes.
    aliases:
    - LMOD method
    - LMOD_method
  DL-FIND Optimization:
    text: DL-FIND Optimization
    description: Method to search for potential energy stationary points along a chemical
      reaction in a QM/MM simulation.
    aliases:
    - DL-FIND Optimization
    - DLFind_optimization
  Thermodynamic Integration (TI):
    text: Thermodynamic Integration (TI)
    description: Method to calculate ensemble-averaged energies "on-the-fly" along
      a path as the simulation progresses between two states.
    aliases:
    - Thermodynamic Integration (TI)
    - thermodynamic_integration
  Linear Interaction Energies (LIE):
    text: Linear Interaction Energies (LIE)
    description: Method to compute binding free energies using the linear interaction
      energy model.
    aliases:
    - Linear Interaction Energies (LIE)
    - linear_interaction_energies
  Replica Exchange Molecular Dynamics (REMD):
    text: Replica Exchange Molecular Dynamics (REMD)
    description: An expanded ensemble energy method that samples from an ensemble
      larger than a typical statistical mechanical ensemble defined by the Hamiltonian
      governing the system.
    aliases:
    - Replica Exchange Molecular Dynamics (REMD)
    - replica_exchange_molecular_dynamics
  Adaptively Biased Molecular Dynamics (ABMD):
    text: Adaptively Biased Molecular Dynamics (ABMD)
    description: Method for calculating free energy landscapes as a function of a
      small number of collective variables.
    aliases:
    - Adaptively Biased Molecular Dynamics (ABMD)
    - adaptively_biased_molecular_dynamics
  Steered Molecular Dynamics (SMD):
    text: Steered Molecular Dynamics (SMD)
    description: Method that applies an external force onto a physical system, and
      drives a change in coordinates within a certain time. The moethod should be
      thought of as umbrella sampling where the center of the restraint is time-dependent.
    aliases:
    - Steered Molecular Dynamics (SMD)
    - steered_molecular_dynamics
  Umbrella Sampling:
    text: Umbrella Sampling
    description: A method that enhances sampling of rare events by applying a biasing
      potential to restrain the system along a chosen coordinate, allowing for the
      calculation of free energy profiles.
    aliases:
    - Umbrella Sampling
    - umbrella_sampling
  Metadynamics:
    text: Metadynamics
    description: An enhanced sampling technique that adds a history-dependent bias
      to the potential energy surface, encouraging the system to escape local minima
      and explore new configurations, often used to reconstruct free energy landscapes.
    aliases:
    - Metadynamics
    - metadynamics
  Swarms of Trajectories String Method:
    text: Swarms of Trajectories String Method
    description: A version of the string method, a path-finding algorithm that refines
      a punative transition pathway iteratively until the path is deemed to have been
      converged.
    aliases:
    - Swarms of Trajectories String Method
    - swarms_of_trajectories_string_method
  Constant pH Molecular Dynamics:
    text: Constant pH Molecular Dynamics
    description: Method that uses Monte Carlo sampling of the Boltzmann distribution
      of discrete protonation states concurrent with the molecular dynamics simulation.
    aliases:
    - Constant pH Molecular Dynamics
    - constant_pH_molecular_dynamics
  Constant Redox Potential Molecular Dynamics:
    text: Constant Redox Potential Molecular Dynamics
    description: Method that uses Monte Carlo sampling of the Boltzmann distribution
      of discrete redox sates concurrent with the molecular dynamics simulation.
    aliases:
    - Constant Redox Potential Molecular Dynamics
    - constant_redox_potential_molecular_dynamics
  Continuous Constant pH Molecular Dynamics:
    text: Continuous Constant pH Molecular Dynamics
    description: A method that is an alternative to the Monte-Carlo based constant
      pH methods where particles with fictitious mass and coordinates bound between
      0 (protonated) and 1 (deprotonated) are added to the system to present protonation
      states of titratable sites.
    aliases:
    - Continuous Constant pH Molecular Dynamics
    - continuous_constant_pH_molecular_dynamics
  NMR Refinement:
    text: NMR Refinement
    description: Method to incorporate a variety of restraints (e.g. NMR restraints
      derived from NOE and J-coupling data) into an optimization procedure.
    aliases:
    - NMR Refinement
    - NMR_refinement
  X-ray and CryoEM Refinement:
    text: X-ray and CryoEM Refinement
    description: Method to incorporate electron microscopy (EM) image information
      into macromolecular structure determination, by applying restraints for rigid
      and flexible fitting into EM maps.
    aliases:
    - X-ray and CryoEM Refinement
    - Xray_and_cryoEM_refinement
  Locally Enhanced Sampling:
    text: Locally Enhanced Sampling
    description: A method to allow for multiple local copies of regions within a larger
      biomolecule, e.g. to allow sidechains in a protein to be "disordered", while
      the backbone is represented as a single configuration.
    aliases:
    - Locally Enhanced Sampling
    - locally_enhanced_sampling