Calculating average of each residues obtained for last 50ns

[Viswanath Vittaladevaram]

Hi,

How to calculate average of reach residues which is obtained during last 50ns?

I need an example of code that would be useful to relate to my  trajectory information obtained

Thanks,

Viswanath.V

[Hugo Macdermott-Opeskin]

Hi Viswanath.V

What kind of average do you want. The average position?

If so you will need to collect the positions in a numpy array and then average them using numpy.mean()

Something like this would work. 

positions = []

for ts in u.trajectory:

    positions.append(ts.positions)

# 3D array, atoms, xyz, time

positions_array = np.asarray(positions)

average = np.mean(positions_array, axis=-1)

You may need to double check i have the right axis for the mean etc.

Cheers

Hugo