REWEIGHT_METAD
This is part of the bias module

Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.

This command allows you to use the reweighting algorithm discussed in [109] when constructing a histogram of the configurations visited during a metadynamics simulation.

Examples

In the following example there is a metadynamics bias acting on the distance between atoms 1 and 2. Clearly, this bias will have an effect on the region of phase space that will be sampled when an MD simulation is run using this variable. Consequently, when the histogram as a function of the angle, \(a\), is accumulated, we use reweighting into order to discount the effect of the bias from our final histogram. We do not use REWEIGHT_BIAS here, however, as the bias changes with time. We thus use the reweighting algorithm for metadynamics instead. Notice also that we have to specify how often we would like to calculate the c(t) reweighting factor and the grid over which we calculate c(t) in the input to the METAD command.

Click on the labels of the actions for more information on what each action computes
tested on master
a: ANGLE 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms).
=1,2,3 x: DISTANCE
ATOMS
the pair of atom that we are calculating the distance between.
=1,2 METAD
ARG
the input for this action is the scalar output from one or more other actions.
=x
PACE
compulsory keyword the frequency for hill addition
=100
SIGMA
compulsory keyword the widths of the Gaussian hills
=0.1
HEIGHT
the heights of the Gaussian hills.
=1.5
BIASFACTOR
use well tempered metadynamics and use this bias factor.
=5
GRID_MIN
the lower bounds for the grid
=0
GRID_MAX
the upper bounds for the grid
=10
GRID_BIN
the number of bins for the grid
=100
CALC_RCT
( default=off ) calculate the \f$c(t)\f$ reweighting factor and use that to obtain the normalized bias [rbias=bias-rct].This
RCT_USTRIDE
the update stride for calculating the \f$c(t)\f$ reweighting factor.The
=50 bias: REWEIGHT_METAD
TEMP
the system temperature.
=300 hB: HISTOGRAM ...
ARG
the input for this action is the scalar output from one or more other actions.
=a
GRID_MIN
compulsory keyword the lower bounds for the grid
=0.0
GRID_MAX
compulsory keyword the upper bounds for the grid
=pi
GRID_BIN
the number of bins for the grid
=100
BANDWIDTH
compulsory keyword the bandwidths for kernel density estimation
=0.1
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias ... DUMPGRID
GRID
compulsory keyword the action that creates the grid you would like to output
=hB
FILE
compulsory keyword ( default=density ) the file on which to write the grid.
=histoB
STRIDE
compulsory keyword ( default=0 ) the frequency with which the grid should be output to the file.
=1
FMT
the format that should be used to output real numbers
=%8.4f
Glossary of keywords and components
Compulsory keywords
ARG ( default=*.rbias ) the biases that must be taken into account when reweighting
Options
TEMP the system temperature. This is not required if your MD code passes this quantity to PLUMED