Biasing and analysis methods

A biasing or analysis method can be applied to existing collective variables by using the following configuration:

$<$ biastype$>$ {
  name $<$ name$>$
  colvars $<$ xi1$>$ $<$ xi2$>$ ...
  $<$ parameters$>$
}

The keyword $<$ biastype$>$ indicates the method of choice. There can be multiple instances of the same method, e.g. using multiple harmonic blocks allows defining multiple restraints.

All biasing and analysis methods implemented recognize the following options:

• name $\langle\,$ Identifier for the bias$\,\rangle$
  Context: colvar bias
  Acceptable values: string
  Default value: $<$ type of bias$><$ bias index$>$
  Description: This string is used to identify the bias or analysis method in the output, and to name some output files. Tip: because the default name depends on the order of definition, but the outcome of the simulation does not, it may be convenient to assign consistent names for certain biases; for example, you may want to name a moving harmonic restraint smd, so that it can always be identified regardless of the presence of other restraints.

• colvars $\langle\,$ Collective variables involved$\,\rangle$
  Context: colvar bias
  Acceptable values: space-separated list of colvar names
  Description: This option selects by name all the variables to which this bias or analysis will be applied.

• outputEnergy $\langle\,$ Write the current bias energy to the trajectory file$\,\rangle$
  Context: colvar bias
  Acceptable values: boolean
  Default value: off
  Description: If this option is chosen and colvarsTrajFrequency is not zero, the current value of the biasing energy will be written to the trajectory file during the simulation.

• outputFreq $\langle\,$ Frequency (number of steps) at which output files are written$\,\rangle$
  Context: colvar bias
  Acceptable values: positive integer
  Default value: colvarsRestartFrequency
  Description: If this bias produces aggregated data that needs to be written to disk (for example, a PMF), this number specifies the number of steps after which these data are written to files. A value of zero disables writing files for this bias during the simulation (except for outputEnergy, which is controlled by colvarsTrajFrequency). All output files are also written at the end of a simulation run, regardless of the value of this number. In VMD, this option has no effect.

• bypassExtendedLagrangian $\langle\,$ Apply bias to actual colvars, bypassing extended coordinates$\,\rangle$
  Context: colvar bias
  Acceptable values: boolean
  Default value: off
  Description: This option is implemented by the harmonicWalls and histogram biases. It is only relevant if the bias is applied to one or several extended-Lagrangian colvars (), for example within an eABF (13.6.3) simulation. Usually, biases use the value of the extended coordinate as a proxy for the actual colvar, and their biasing forces are applied to the extended coordinates as well. If bypassExtendedLagrangian is enabled, the bias behaves as if there were no extended coordinates, and accesses the value of the underlying colvars, applying any biasing forces along the gradients of those variables.

• stepZeroData $\langle\,$ Accumulate data starting at step 0 of a simulation run$\,\rangle$
  Context: colvar bias
  Acceptable values: boolean
  Default value: off
  Description: This option is meaningful for biases that record and accumulate data during a simulation, such as ABF (), metadynamics (), histograms () and in general any bias that accumulates free-energy samples with thermodynamic integration, or TI (). When this option is disabled (default), data will only be recorded into the bias after the first coordinate update: this is generally the correct choice in simulation runs. Biasing energy and forces will always be computed for all active biases, regardless of this option.