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 [105] 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

a: ANGLE 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms). 
=1,2,3  You cannot view the components that are calculated by each action for this input file. Sorry 
x: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2  You cannot view the components that are calculated by each action for this input file. Sorry 
METAD 
ARG
compulsory keyword 
the labels of the scalars on which the bias will act 
=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 c(t) reweighting factor and use that to obtain the
normalized bias [rbias=bias-rct].This 
 
RCT_USTRIDE
the update stride for calculating the c(t) reweighting factor.The 
=50  You cannot view the components that are calculated by each action for this input file. Sorry 
bias: REWEIGHT_METAD 
TEMP
the system temperature. 
=300  You cannot view the components that are calculated by each action for this input file. Sorry 
hB: HISTOGRAM ...
   
ARG
the quantities that are being used to construct the histogram 
=a 
   
GRID_MIN
compulsory keyword ( default=auto )
the lower bounds for the grid 
=0.0 
   
GRID_MAX
compulsory keyword ( default=auto )
the upper bounds for the grid 
=pi 
   
GRID_BIN
the number of bins for the grid 
=100 
   
BANDWIDTH
the bandwidths for kernel density esimtation 
=0.1 
   
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages 
=bias 
   
... You cannot view the components that are calculated by each action for this input file. Sorry 
DUMPGRID 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=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  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Description of components

This action calculates the logarithm of a weight for reweighting

Quantity	Description
.#!value	the weight to use for this frame to negate the effect the metadynamics bias

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