PMF class¶
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class
PMF(points, values, cv_list, max_E)¶ Parameters: - points (
numpy.array) – values of the CVs at which the PMF is found in values. - values (
numpy.array) – Free energy corresponding to CV values in points - cv_list (
list(CollectiveVariable)) – List of the CVs
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GetCurvatures(point, steps)¶
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GetValue(point)¶ Free energy at a certain position on the free energy surface.
Parameters: point – values of the CV for which we want the free energy.
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Plot(outputdir, filename, n_levels=None, max_E=None, windows=None, energy_units='')¶ Plot the PMF.
Parameters: - outputdir – Output directory to which the plot is saved
- filename – name of the file to which the plot is saved (”.png” will be added)
- n_levels – for 2D plots, the number of isoenergy curves used in the plot
- max_E – Maximal free energy, everything above will be shown at this level.
- windows – If a list of windows is passed, arrows showing the exploration will be plotted
- energy_units – Units displayed for the energy axis
- points (