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## 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: Defining collective variables and Previous: Extended Lagrangian.   Contents   Index
vmd@ks.uiuc.edu