Defining collective variables

A collective variable is defined by the keyword colvar followed by its configuration options contained within curly braces:

colvar {
  name xi
  $<$ other options$>$
  function_name {
    $<$ parameters$>$
    $<$ atom selection$>$
  }
}

There are multiple ways of defining a variable:

• The simplest and most common way way is using one of the precompiled functions (here called ``components''), which are listed in section . For example, using the keyword rmsd (section ) defines the variable as the root mean squared deviation (RMSD) of the selected atoms.
• A new variable may also be constructed as a linear or polynomial combination of the components listed in section  (see for details).
• A user-defined Tcl function of the existing components (see list in section ), or of the atomic coordinates directly (see the cartesian keyword in ). The function is provided by a separate Tcl script, and referenced through the keyword scriptedFunction (see for details).

Choosing a component (function) is the only parameter strictly required to define a collective variable. It is also highly recommended to specify a name for the variable:

• name $\langle\,$ Name of this colvar$\,\rangle$
  Context: colvar
  Acceptable values: string
  Default value: ``colvar'' + numeric id
  Description: The name is an unique case-sensitive string which allows the Colvars module to identify this colvar unambiguously; it is also used in the trajectory file to label to the columns corresponding to this colvar.