import numpy as np import matplotlib.pyplot as plt from tqdm import tqdm import MDAnalysis as md from density import Density from potential import Potential u = md.Universe('trj/md128_280k.tpr', 'trj/md128_280k.xtc') h2o = u.select_atoms('name OW or name HW1 or name HW2') pot = Potential(u) for _ in tqdm(u.trajectory, total=len(u_trajectory)): pot.potential_matrix() ''' plt.plot(t, np.mean(rot, axis=1), 'o') plt.plot(ref[:,0], ref[:,2]/512, '-') plt.xlim((0, 0.2)) plt.show() '''