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Subsections

Defining collective variables and their properties

In the configuration file each colvar is defined by the keyword colvar, followed by its configuration options within curly braces: colvar { ... }. One of these options is the name of a colvar component: for example, including rmsd { ... } defines the colvar as a RMSD function. In most applications, only one component is used, and the component is equal to the colvar.

The full list of colvar components can be found in Section 10.4, with the syntax to select atoms in Section 10.3. The following section lists several options to control the behavior of a single colvar, regardless of its type.

General options for a collective variable

The following options are not required by default; however, the first four are very frequently used:
• name Name of this colvar
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 Colvar fluctuation scale, or resolution for grid-based methods
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 (10.5.4) 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 (10.5.7) and ABF biases (10.5.1) interpret it as the grid spacing in the direction of this variable. Metadynamics (10.5.3) 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 Lower boundary of the colvar
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 Upper boundary of the colvar
Context: colvar
Acceptable Values: decimal
Description: Similarly to lowerBoundary, defines the highest possible or allowed value.

• hardLowerBoundary Whether the lower boundary is the physical lower limit
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 10.4 for the physical ranges of values of each component.

• hardUpperBoundary Whether the upper boundary is the physical upper limit of the colvar's values
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: Analogous to hardLowerBoundary.

• expandBoundaries Allow to expand the two boundaries if needed
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 (10.5.3) 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 Do not include biasing forces in the total force for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: If the colvar supports total force calculation (see 10.4.3), 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.

Artificial boundary potentials (walls)

The following options are useful to define restraints (confining potentials) for this colvar. To apply moving restraints, or restraints to more than one colvar simultaneously, a more convenient option is to use the harmonic bias (10.5.4).

• lowerWallConstant Lower wall force constant (kcal/mol/U )
Context: colvar
Acceptable Values: positive decimal
Description: Defines the force constant for a confining restraint on the colvar, in the form of a half-harmonic'' potential. The potential starts at lowerWall if it is defined, or lowerBoundary otherwise. The energy unit of the constant is kcal/mol, while the spatial unit U is that of the colvar.

• lowerWall Position of the lower wall
Context: colvar
Acceptable Values: decimal
Default Value: lowerBoundary
Description: Defines the value below which a confining restraint on the colvar is applied, in the form of a half-harmonic'' potential. Allows to use a different position of the wall than lowerBoundary.

• upperWallConstant Upper wall force constant (kcal/mol/U )
Context: colvar
Acceptable Values: positive decimal
Description: Analogous to lowerWallConstant.

• upperWall Position of the upper wall
Context: colvar
Acceptable Values: decimal
Default Value: upperBoundary
Description: Analogous to lowerWall.

Trajectory output

• outputValue Output a trajectory for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: on
Description: If colvarsTrajFrequency is non-zero, the value of this colvar is written to the trajectory file every colvarsTrajFrequency steps in the column labeled  name ''.

• outputVelocity Output a velocity trajectory for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, the finite-difference calculated velocity of this colvar are written to the trajectory file under the label v_ name ''.

• outputEnergy Output an energy trajectory for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: This option applies only to extended Lagrangian colvars. If colvarsTrajFrequency is defined, the kinetic energy of the extended degree and freedom and the potential energy of the restraining spring are are written to the trajectory file under the labels Ek_ name '' and Ep_ name ''.

• outputTotalForce Output a total force trajectory for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, the total force on this colvar (i.e. the projection of all atomic total forces onto this colvar -- see equation (53) in section 10.5.1) are written to the trajectory file under the label fs_ name ''. For extended Lagrangian colvars, the total force'' felt by the extended degree of freedom is simply the force from the harmonic spring. Note: not all components support this option. The physical unit for this force is kcal/mol, divided by the colvar unit U.

• outputAppliedForce Output an applied force trajectory for this colvar
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: If colvarsTrajFrequency is defined, the total force applied on this colvar by biases and confining potentials (walls) within the Colvars module are written to the trajectory under the label fa_ name ''. For extended Lagrangian colvars, this force is actually applied to the extended degree of freedom rather than the geometric colvar itself. The physical unit for this force is kcal/mol divided by the colvar unit.

Extended Lagrangian.

The following options enable extended-system dynamics, where a colvar is coupled to an additional degree of freedom (fictitious particle) by a harmonic spring. All biasing and confining forces are then applied to the extended degree of freedom. The actual'' geometric colvar (function of Cartesian coordinates) only feels the force from the harmonic spring. This is particularly useful when combined with an ABF bias (10.5.1) to perform eABF simulations (10.5.2).

• extendedLagrangian Add extended degree of freedom
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: Adds a fictitious particle to be coupled to the colvar by a harmonic spring. The fictitious mass and the force constant of the coupling potential are derived from the parameters extendedTimeConstant and extendedFluctuation, described below. Biasing forces on the colvar are applied to this fictitious particle, rather than to the atoms directly. This implements the extended Lagrangian formalism used in some metadynamics simulations [39]. The energy associated with the extended degree of freedom is reported under the MISC title in NAMD's energy output.

• extendedFluctuation Standard deviation between the colvar and the fictitious particle (colvar unit)
Context: colvar
Acceptable Values: positive decimal
Description: Defines the spring stiffness for the extendedLagrangian mode, by setting the typical deviation between the colvar and the extended degree of freedom due to thermal fluctuation. The spring force constant is calculated internally as , where is the value of extendedFluctuation.

• extendedTimeConstant Oscillation period of the fictitious particle (fs)
Context: colvar
Acceptable Values: positive decimal
Default Value: 200
Description: Defines the inertial mass of the fictitious particle, by setting the oscillation period of the harmonic oscillator formed by the fictitious particle and the spring. The period should be much larger than the MD time step to ensure accurate integration of the extended particle's equation of motion. The fictitious mass is calculated internally as , where is the period and is the typical fluctuation (see above).

• extendedTemp Temperature for the extended degree of freedom (K)
Context: colvar
Acceptable Values: positive decimal
Default Value: thermostat temperature
Description: Temperature used for calculating the coupling force constant of the extended variable (see extendedFluctuation) and, if needed, as a target temperature for extended Langevin dynamics (see extendedLangevinDamping). This should normally be left at its default value.

• extendedLangevinDamping Damping factor for extended Langevin dynamics (ps )
Context: colvar
Acceptable Values: positive decimal
Default Value: 1.0
Description: If this is non-zero, the extended degree of freedom undergoes Langevin dynamics at temperature extendedTemp. The friction force is minus extendedLangevinDamping times the velocity. This is useful because the extended dynamics coordinate may heat up in the transient non-equilibrium regime of ABF. Use moderate damping values, to limit viscous friction (potentially slowing down diffusive sampling) and stochastic noise (increasing the variance of statistical measurements). In doubt, use the default value.

Statistical analysis of collective variables

When the global keyword analysis is defined in the configuration file, run-time calculations of statistical properties for individual colvars can be performed. At the moment, several types of time correlation functions, running averages and running standard deviations are available.

• corrFunc Calculate a time correlation function?
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: Whether or not a time correlaction function should be calculated for this colvar.

• corrFuncWithColvar Colvar name for the correlation function
Context: colvar
Acceptable Values: string
Description: By default, the auto-correlation function (ACF) of this colvar, , is calculated. When this option is specified, the correlation function is calculated instead with another colvar, , which must be of the same type (scalar, vector, or quaternion) as .

• corrFuncType Type of the correlation function
Context: colvar
Acceptable Values: velocity, coordinate or coordinate_p2
Default Value: velocity
Description: With coordinate or velocity, the correlation function  = is calculated between the variables and , or their velocities. is the scalar product when calculated between scalar or vector values, whereas for quaternions it is the cosine between the two corresponding rotation axes. With coordinate_p2, the second order Legendre polynomial, , is used instead of the cosine.

• corrFuncNormalize Normalize the time correlation function?
Context: colvar
Acceptable Values: boolean
Default Value: on
Description: If enabled, the value of the correlation function at  = 0 is normalized to 1; otherwise, it equals to .

• corrFuncLength Length of the time correlation function
Context: colvar
Acceptable Values: positive integer
Default Value: 1000
Description: Length (in number of points) of the time correlation function.

• corrFuncStride Stride of the time correlation function
Context: colvar
Acceptable Values: positive integer
Default Value: 1
Description: Number of steps between two values of the time correlation function.

• corrFuncOffset Offset of the time correlation function
Context: colvar
Acceptable Values: positive integer
Default Value: 0
Description: The starting time (in number of steps) of the time correlation function (default:  = 0). Note: the value at  = 0 is always used for the normalization.

• corrFuncOutputFile Output file for the time correlation function
Context: colvar
Acceptable Values: UNIX filename
Default Value: name .corrfunc.dat
Description: The time correlation function is saved in this file.

• runAve Calculate the running average and standard deviation
Context: colvar
Acceptable Values: boolean
Default Value: off
Description: Whether or not the running average and standard deviation should be calculated for this colvar.

• runAveLength Length of the running average window
Context: colvar
Acceptable Values: positive integer
Default Value: 1000
Description: Length (in number of points) of the running average window.

• runAveStride Stride of the running average window values
Context: colvar
Acceptable Values: positive integer
Default Value: 1
Description: Number of steps between two values within the running average window.

• runAveOutputFile Output file for the running average and standard deviation
Context: colvar
Acceptable Values: UNIX filename
Default Value: name .runave.dat
Description: The running average and standard deviation are saved in this file.

Next: Selecting atoms for colvars: Up: Collective Variable-based Calculations (Colvars)1 Previous: General parameters and input/output   Contents   Index
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