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.
Multiple time stepping
By setting a STRIDE different from 1, you change how frequently an action is calculated. In the case of actions such as PRINT, this just means how frequently you dump some quantity on the disk. Notice that variables are only computed when necessary. Thus, if a variable is only appearing as the argument of a PRINT statement with STRIDE=10, it will be computed every 10 steps.
In a similar fashion, the STRIDE keyword can be used in a bias potential so as to apply the bias potential every few steps. In this case, forces from this bias potential are scaled up by a factor equal to STRIDE.
This technique can allow your simulation to run faster if you need the apply a bias potential on some very expensive collective variable. Consider the following input:
c1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-1000 c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1001-2000 d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=d HEIGHTthe heights of the Gaussian hills=1 SIGMAthe widths of the Gaussian hills=0.1 BIASFACTORuse well tempered metadynamics and use this bias factor=5 PACEthe frequency for hill addition=500
This performs a METAD simulation biasing the distance between two centers of mass. Since computing these centers requires a lot of atoms to be imported from the MD engine, it could slow down significantly the simulation. Notice that whereas the bias is changed every PACE=500 steps, it is applied every STRIDE step, where STRIDE=1 by default. The following input could lead to a significantly faster simulation at the price of a negligible systematic error
c1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-1000 c2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1001-2000 d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=d HEIGHTthe heights of the Gaussian hills=1 SIGMAthe widths of the Gaussian hills=0.1 BIASFACTORuse well tempered metadynamics and use this bias factor=5 PACEthe frequency for hill addition=500 STRIDEthe frequency with which the forces due to the bias should be calculated=2
Similarly, the STRIDE keyword can be used with other biases (e.g. RESTRAINT).
The technique is discussed in details in the paper cited below. See also EFFECTIVE_ENERGY_DRIFT.
Actions
The following actions are part of this module
| 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 |
References
More information about this module is available in the following articles: