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:ANGLEATOMS=1,2,3the list of atoms involved in this collective variable (either 3 or 4 atoms).x:DISTANCEATOMS=1,2 METADthe pair of atom that we are calculating the distance between.ARG=compulsory keywordthe labels of the scalars on which the bias will actxPACE=100compulsory keywordthe frequency for hill additionSIGMA=0.1compulsory keywordthe widths of the Gaussian hillsHEIGHT=1.5the heights of the Gaussian hills.BIASFACTOR=5use well tempered metadynamics and use this bias factor.GRID_MIN=0the lower bounds for the gridGRID_MAX=10the upper bounds for the gridGRID_BIN=100the number of bins for the gridCALC_RCT( default=off ) calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct].ThisRCT_USTRIDE=50the update stride for calculating the c(t) reweighting factor.Thebias:REWEIGHT_METADTEMP=300the system temperature.hB:HISTOGRAM ...ARG=the quantities that are being used to construct the histogramaGRID_MIN=0.0compulsory keyword ( default=auto )the lower bounds for the gridGRID_MAX=picompulsory keyword ( default=auto )the upper bounds for the gridGRID_BIN=100the number of bins for the gridBANDWIDTH=0.1the bandwidths for kernel density esimtationLOGWEIGHTS=the logarithm of the quantity to use as the weights when calculating averagesbias... DUMPGRIDGRID=the grid you would like to print (can also use ARG for specifying what is being printed)hBFILE=histoBcompulsory keyword ( default=density )the file on which to write the grid.STRIDE=1compulsory keyword ( default=0 )the frequency with which the grid should be output to the file.FMT=%8.4fthe format that should be used to output real numbers

- 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 |