General options for a collective variable

The following options are not required by default; however, the first four are very frequently used:

• 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.

• width $\langle\,$ Colvar fluctuation scale, or resolution for grid-based methods$\,\rangle$
  Context: colvar
  Acceptable values: positive decimal
  Default value: 1.0
  Description: This number has the same physical unit as the colvar value and defines an effective colvar unit. Biasing algorithms use it for different purposes. Harmonic restraints (13.5.4) use it to set the physical unit of the force constant, which is useful for multidimensional restraints involving colvars with different units or scale which may then be defined by a single, scaled force constant. Histogram (13.5.7) and ABF biases (13.5.1) interpret it as the grid spacing in the direction of this variable. Metadynamics (13.5.3) uses it to set the width of newly added hills. In other cases, it is simplest to keep the default value of 1, so that harmonic force constants are provided in their usual physical unit. When a non-unity width is required by the application, the optimal value is application-dependent, but can often be thought of as a user-provided estimate of the fluctuation amplitude for the colvar. In those cases, it should generally be set smaller than or equal to the standard deviation of the colvar during a very short simulation run.

• lowerBoundary $\langle\,$ Lower boundary of the colvar$\,\rangle$
  Context: colvar
  Acceptable values: decimal
  Description: Defines the lowest end of the interval of ``relevant'' values for the colvar. This number can be either a true physical boundary, or a user-defined number. Together with upperBoundary and width, it is used to define a grid of values along the colvar (not available for colvars based on distanceDir, distanceVec, and orientation). This option does not affect dynamics: to confine a colvar within a certain interval, the options lowerWall and lowerWallConstant should be used.

• upperBoundary $\langle\,$ Upper boundary of the colvar$\,\rangle$
  Context: colvar
  Acceptable values: decimal
  Description: Similarly to lowerBoundary, defines the highest possible or allowed value.

• hardLowerBoundary $\langle\,$ Whether the lower boundary is the physical lower limit$\,\rangle$
  Context: colvar
  Acceptable values: boolean
  Default value: off
  Description: This option does not affect simulation results, but enables some internal optimizations. Depending on its mathematical definition, a colvar may have ``natural'' boundaries: for example, a distance colvar has a ``natural'' lower boundary at 0. Setting this option instructs the Colvars module that the user-defined lower boundary is ``natural''. See Section 13.4 for the physical ranges of values of each component.

• hardUpperBoundary $\langle\,$ Whether the upper boundary is the physical upper limit of the colvar's values$\,\rangle$
  Context: colvar
  Acceptable values: boolean
  Default value: off
  Description: Analogous to hardLowerBoundary.

• expandBoundaries $\langle\,$ Allow to expand the two boundaries if needed$\,\rangle$
  Context: colvar
  Acceptable values: boolean
  Default value: off
  Description: If defined, biasing and analysis methods may keep their own copies of lowerBoundary and upperBoundary, and expand them to accommodate values that do not fit in the initial range. Currently, this option is used by the metadynamics bias (13.5.3) to keep all of its hills fully within the grid. This option cannot be used when the initial boundaries already span the full period of a periodic colvar.

• subtractAppliedForce $\langle\,$ Do not include biasing forces in the total force for this colvar$\,\rangle$
  Context: colvar
  Acceptable values: boolean
  Default value: off
  Description: If the colvar supports total force calculation (see 13.4.3), all forces applied to this colvar by biases will be removed from the total force. This keyword allows to recover some of the ``system force'' calculation available in the Colvars module before version 2016-08-10. Please note that removal of all other external forces (including biasing forces applied to a different colvar) is no longer supported, due to changes in the underlying simulation engines (primarily NAMD). This option may be useful when continuing a previous simulation where the removal of external/applied forces is essential. For all new simulations, the use of this option is not recommended.