CollectiveVariable class

class CollectiveVariable(cv_name, min_value, max_value, step_size, num_bins, min_spring_constant, max_spring_constant=None, max_shift=None, periodicity=None, units='')

This class represents a collective variable (CV or reaction coordinate). The name of the CV will give rise to the corresponding fields that are replaced in the MD input files. The minimal and maximal values determine the range in which the windows can be generated. The number of bins are used for the calculation of the PMF. The periodicity of the collective variables is used both for generating new windows and for the calculation of the PMF. The step size defines the distance between two neighboring windows. Finally the units are just used in the labels of the plots of the PMF.

Parameters:

• cv_name (str) – The name of the CV
• min_value (float) – The minimal value of the CV
• max_value (float) – The maximal value of the CV
• step_size (float) – The size of the step for this CV
• num_bins (int) – number of bins
• min_spring_constant – Minimal value of the spring constant to be used for this CV.
• max_spring_constant – Maximal value of the spring constant to be used for this CV.
• max_shift – Maximal value for the shift of this CV to compensate for free energy gradient.
• periodicity (float) – periodicity of the CV
• units (str) – the units of the CV