newanalysis.diffusion.msdCOM

newanalysis.diffusion.msdCOM(xyz, maxlen=None)

This function takes as input a three-dimensional coordinate array of the molecular centers of mass of a whole unfolded trajectory [timestep, molecule, xyz]. The optional parameter maxlen can be set to limit the length of the resulting MSD. This can be useful when dealing with very long trajectories, e.g. maxlen=n/2.

Usage:

msd = msdCOM(xyz)