--- search: boost: 2.0 --- # Enum: SimulationMethod _Options for simulation methods._
URI: [https://CCPBioSim.ac.uk/biosim-schema/SimulationMethod](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](../slots/simulation_method.md) | Method used to perform simulation | ## Identifier and Mapping Information ### Schema Source * from schema: https://CCPBioSim.ac.uk/biosim-schema/ ## LinkML Source ```yaml 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 ```