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Subsections


Multidimensional histograms

The histogram feature is used to record the distribution of a set of collective variables in the form of a N-dimensional 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 extended-system 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:


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:


next up previous contents index
Next: Probability distribution-restraints Up: Biasing and analysis methods Previous: Adaptive Linear Bias/Experiment Directed   Contents   Index
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