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) [70] method on one or more collective variables. This method is also called dynamic reference restraining(DRR) [127] . A detailed description of this module can be found at [37] . 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_METAD (from OPES (On-the-fly Probability Enhanced Sampling) module) On-the-fly probability enhanced sampling (OPES) with metadynamics-like target distribution [62]. 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 [61] (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