Module: bias

Description	Usage
bias potentials that can be used to force rare events to occur in MD simulations
Authors: The PLUMED core developers

Details

This module contains various methods for adding bias potentials.
These bias potentials are the core of the enhanced sampling algorithms that allow you to force rare events to occur on the short timescales that are accessible on the molecular dynamics timescale.

In addition, the module also contains tools such as REWEIGHT_BIAS, REWEIGHT_METAD and REWEIGHT_TEMP_PRESS. These actions allow you to extract "unbiased" free energy surfaces from biased simulations and to thus extract free energy differences from your enhanced sampling calculations.

Actions

The following actions are part of this module

BIAS: bias potentials that can be used to force rare events to occur in MD simulations REWEIGHTING: actions for computing weights that can be used when calculating the unbiased distribution

Name	Description	Tags
ABMD	Adds a ratchet-and-pawl like restraint on one or more variables.	BIAS
BIASVALUE	Takes the value of one variable and use it as a bias	BIAS
EXTENDED_LAGRANGIAN	Add extended Lagrangian.	BIAS
EXTERNAL	Calculate a restraint that is defined on a grid that is read during start up	BIAS
LOWER_WALLS	Defines a wall for the value of one or more collective variables,	BIAS
MAXENT	Add a linear biasing potential on one or more variables that satisfies a maximum entropy principle.	BIAS
METAD	Used to performed metadynamics on one or more collective variables.	BIAS
MOVINGRESTRAINT	Add a time-dependent, harmonic restraint on one or more variables.	BIAS
PBMETAD	Used to performed Parallel Bias metadynamics.	BIAS
RESTRAINT	Adds harmonic and/or linear restraints on one or more variables.	BIAS
REWEIGHT_BIAS	Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored	REWEIGHTING
REWEIGHT_METAD	Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.	REWEIGHTING
REWEIGHT_TEMP_PRESS	Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation.	REWEIGHTING
UPPER_WALLS	Defines a wall for the value of one or more collective variables,	BIAS