@author: Ali Hashmi

a simple script to determine Mean-Squared Displacements (MSD) from multiple particle trajectories

a part of the MSD code is borrowed from: https://stackoverflow.com/questions/32988269/speedup-msd-calculation-in-python

How to compute from rawdata (rawdata as .txt files):

msd = MSDtraj("C:\\academic\\codes and scripts\\brownian simulation of nodal lefty\\3dcheck\\res",10,['t','x','y','z'],0.000001);

args are as follows: directory, number of files (trajectories), dimensions, smallest time-step, timeCMSD = 1000 (pts to consider))

msddata,stddata = msd.main()

msdplot = plt.plot(msddata)

plt.show(msdplot)

grad = np.polyfit(range(1,101),msddata[1:101], 1)[0] # using the first 100 values for computing gradient

print 'the effective diffusion coefficient is : ' + str(grad/(6*1e-6)) + ' um^2/sec' # effective diffusion coefficient `