Bias

PLUMED allows you to run a number of enhanced sampling algorithms. The list of enhanced sampling algorithms contained in PLUMED is as follows:

ABMD | Adds a ratchet-and-pawl like restraint on one or more variables. |

BIASVALUE | Takes the value of one variable and use it as a bias |

EXTENDED_LAGRANGIAN | Add extended Lagrangian. |

EXTERNAL | Calculate a restraint that is defined on a grid that is read during start up |

LOWER_WALLS | Defines a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation. |

MAXENT | Add a linear biasing potential on one or more variables \(f_{i}\left(\boldsymbol{x}\right)\) satisfying the maximum entropy principle as proposed in Ref. [3] . |

METAD | Used to performed metadynamics on one or more collective variables. |

MOVINGRESTRAINT | Add a time-dependent, harmonic restraint on one or more variables. |

PBMETAD | Used to performed Parallel Bias metadynamics. |

RESTRAINT | Adds harmonic and/or linear restraints on one or more variables. |

UPPER_WALLS | Defines a wall for the value of one or more collective variables, which limits the region of the phase space accessible during the simulation. |

In addition to the keywords above, by enabling optional modules you can access to the following keywords:

CALIBER | (from PLUMED-ISDB module) Add a time-dependent, harmonic restraint on one or more variables. |

DRR | (from Extended-System Adaptive Biasing Force module) Used to performed extended-system adaptive biasing force(eABF) [75] method on one or more collective variables. This method is also called dynamic reference restraining(DRR) [138] . A detailed description of this module can be found at [38] . |

EDS | (from Experiment Directed Simulation module) Add a linear bias on a set of observables. |

FISST | (from FISST (Infinite Switch Simulated Tempering in Force) module) Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. |

FUNNEL | (from Funnel-Metadynamics (FM) module) Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. |

LOGMFD | (from Logarithmic Mean Force Dynamics module) Used to perform LogMFD, LogPD, and TAMD/d-AFED. |

MAZE_OPTIMIZER_BIAS | (from MAZE module) |

METAINFERENCE | (from PLUMED-ISDB module) Calculates the Metainference energy for a set of experimental data. |

OPES_EXPANDED | (from OPES (On-the-fly Probability Enhanced Sampling) module) On-the-fly probability enhanced sampling (OPES) with expanded ensembles target distribution (replica-exchange-like) [67]. |

OPES_METAD | (from OPES (On-the-fly Probability Enhanced Sampling) module) On-the-fly probability enhanced sampling (OPES) with metadynamics-like target distribution [66]. |

OPES_METAD_EXPLORE | (from OPES (On-the-fly Probability Enhanced Sampling) module) On-the-fly probability enhanced sampling (OPES) with well-tempered target distribution, exploration mode [future_paper] . |

RESCALE | (from PLUMED-ISDB module) Scales the value of an another action, being a Collective Variable or a Bias. |

VES_DELTA_F | (from Variationally Enhanced Sampling (VES code) module) Implementation of VES \(\Delta F\) method [65] (step two only). |

VES_LINEAR_EXPANSION | (from Variationally Enhanced Sampling (VES code) module) Linear basis set expansion bias. |

Methods, such as METAD or PBMETAD, that work by introducing a history dependent bias can be restarted using the RESTART keyword