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Statistical analysis of collective variables
When the global keyword analysis is defined in the
configuration file, runtime 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 autocorrelation 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