fake_traj.py

import pytraj as pt
import numpy as np

traj = pt.iterload('tz2.nc', 'tz2.parm7')
# note: use pt.load method if your trajectory is fit well to memory

c0 = pt.center_of_mass(traj, ':1-3')
c1 = pt.center_of_mass(traj, ':4-7')
c2 = pt.center_of_mass(traj, ':8-10')
c3 = pt.center_of_mass(traj, ':11-13')

# create a new array with shape=(n_frames, 4, 3)
xyz = np.hstack((c0, c1, c2, c3)).reshape(traj.n_frames, 4, 3)
print(xyz.shape)

# create a fake Topology with 4 atoms
fake_top = pt.tools.make_fake_topology(n_atoms=4)
# save to disk if using vmd
# fake_top.save('myfakeparm.parm7')
print(fake_top)

# write your fake trajectory
pt.write_traj('mytraj.nc', xyz, top=fake_top, overwrite=True)