Next: Probability distributionrestraints
Up: Biasing and analysis methods
Previous: Adaptive Linear Bias/Experiment Directed
Contents
Index
Subsections
Multidimensional histograms
The histogram feature is used to record the distribution of a set of collective
variables in the form of a Ndimensional histogram.
It functions as a ``collective variable bias'', and is invoked by adding a
histogram block to the Colvars configuration file.
As with any other biasing and analysis method, when a histogram is applied to
an extendedsystem colvar (13.2.4), it accesses the value
of the fictitious coordinate rather than that of the ``true'' colvar.
A joint histogram of the ``true'' colvar and the fictitious coordinate
may be obtained by specifying the colvar name twice in a row
in the colvars parameter: the first instance will be understood as the
``true'' colvar, and the second, as the fictitious coordinate.
In addition to the common parameters name and colvars
described above, a histogram block may define the following parameter:

name: see definition of name (biasing and analysis methods)

colvars: see definition of colvars (biasing and analysis methods)

outputFreq
Frequency (in timesteps) at which the histogram files are refreshed
Context: histogram
Acceptable values: positive integer
Default value: colvarsRestartFrequency
Description: The histogram data are written to files at the given time interval.
A value of 0 disables the creation of these files (note: all data to continue a simulation are still included in the state file).

outputFile
Write the histogram to a file
Context: histogram
Acceptable values: UNIX filename
Default value: outputName.
name
.dat
Description: Name of the file containing histogram data (multicolumn format), which is written every outputFreq steps.
For the special case of 2 variables, Gnuplot may be used to visualize this file.

outputFileDX
Write the histogram to a file
Context: histogram
Acceptable values: UNIX filename
Default value: outputName.
name
.dat
Description: Name of the file containing histogram data (OpenDX format), which is written every outputFreq steps.
For the special case of 3 variables, VMD may be used to visualize this file.

gatherVectorColvars
Treat vector variables as multiple observations of a scalar variable?
Context: histogram
Acceptable values: UNIX filename
Default value: off
Description: When this is set to on, the components of a multidimensional colvar (e.g. one based on cartesian, distancePairs, or a vector of scalar numbers given by scriptedFunction) are treated as multiple observations of a scalar variable.
This results in the histogram being accumulated multiple times for each simulation step or iteration of cv update).
When multiple vector variables are included in histogram, these must have the same length because their components are accumulated together.
For example, if
,
and
are three variables of dimensions 5, 5 and 1, respectively, for each iteration 5 triplets
(
) are accumulated into a 3dimensional histogram.

weights
Treat vector variables as multiple observations of a scalar variable?
Context: histogram
Acceptable values: list of spaceseparated decimals
Default value: all weights equal to 1
Description: When gatherVectorColvars is on, the components of each multidimensional colvar are accumulated with a different weight.
For example, if
and
are two distinct cartesian variables defined on the same group of atoms, the corresponding 2D histogram can be weighted on a peratom basis: to compute an electron density map, it is possible to use weights [$sel get atomicnumber] in the definition of histogram.
Grid definition for multidimensional histograms
Like the ABF and metadynamics biases, histogram uses the parameters lowerBoundary, upperBoundary, and width to define its grid.
These values can be overridden if a configuration block histogramGrid { ...} is provided inside the configuration of histogram.
The options supported inside this configuration block are:

lowerBoundaries
Lower boundaries of the grid
Context: histogramGrid
Acceptable values: list of spaceseparated decimals
Description: This option defines the lower boundaries of the grid, overriding any values defined by the lowerBoundary keyword of each colvar.
Note that when gatherVectorColvars is on, each vector variable is automatically treated as a scalar, and a single value should be provided for it.

upperBoundaries: analogous to lowerBoundaries

widths: analogous to lowerBoundaries
Next: Probability distributionrestraints
Up: Biasing and analysis methods
Previous: Adaptive Linear Bias/Experiment Directed
Contents
Index
vmd@ks.uiuc.edu