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## Statistical analysis

Run-time calculations of statistical properties that depend explicitly on time can be performed for individual collective variables. Currently, several types of time correlation functions, running averages and running standard deviations are implemented. For run-time computation of histograms, please see the histogram bias ().

• 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: outputName. 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: outputName. name .runave.traj
Description: The running average and standard deviation are saved in this file.

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