Author: Tyler Reddy
The purpose of this Python module is to provide utility functions for analyzing the diffusion of particles in molecular dynamics simulation trajectories using either linear or anomalous diffusion models.
This function should fit anomalous diffusion data to Equation 1 in Kneller et al. (2011) J Chem Phys 135: 141105. It will assign an appropriate coefficient based on the specified degrees_of_freedom. The latter value defaults to 2 (i.e., a planar phospholipid bilayer). Input data should include arrays of MSD (in Angstroms) and time values (in ns). The results are returned in a tuple.
Parameters: | time_data_array : array_like
MSD_data_array : array_like
degrees_of_freedom : int
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Returns: | fractional_diffusion_coefficient
standard_deviation_fractional_diffusion_coefficient
alpha
standard_deviation_alpha
sample_fitting_data_X_values_nanoseconds
sample_fitting_data_Y_values_Angstroms
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Raises: | ValueError
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The linear (i.e., normal, random-walk) MSD vs. time diffusion constant calculation.
The results are returned in a tuple.
Parameters: | time_data_array : array_like
MSD_data_array : array_like
degrees_of_freedom : int
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Returns: | diffusion_constant
diffusion_constant_error_estimate
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Raises: | ValueError
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