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 [111] 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 The ANGLE action with label a calculates a single scalar value
x: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label x calculates a single scalar value
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 The METAD action with label 
bias: REWEIGHT_METAD 
TEMP
the system temperature. 
=300 The REWEIGHT_METAD action with label bias calculates a single scalar value
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 
   
...The HISTOGRAM action with label hB
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 The DUMPGRID action with label 

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