Biomodeling: DNA-binding proteins (PCNA)




Diffusion of PCNA in MD simulations


PCNA in MD simulations

In the Dropbox folder (PCNA), you can find a trajectory file.

Mean-Squared Displacement (MSD) and Diffusion Coefficient

For a 1D diffusion case, the diffusion coefficient is defined as MSD(∆ t)= 2D∆.t

A Python example.

import numpy as np

# calculate COM of PCNA and put the z coordinates to zdata array.

r = np.sqrt(zdata**2) 

diff = np.diff(r) #this calculates r(t + dt) - r(t)

diff_sq = diff**2

MSD = np.mean(diff_sq)

Rotation and Tilt angles of PCNA