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. [2] . |

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:

DRR | (from Extended-System Adaptive Biasing Force module) Used to performed extended-system adaptive biasing force(eABF) [60] methodon one or more collective variables. This method is alsocalled dynamic reference restraining(DRR) [98] . |

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

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

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

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