Building an average model from MD snapshots
This is possible with the Python package MDTraj. Assuming you have your trajectory saved as trajectory.dcd and topology in topology.pdb:

import mdtraj as md
from mdtraj.geometry.alignment import compute_average_structure

traj = md.load('trajectory.dcd', top='topology.pdb')
average = compute_average_structure(traj.xyz)


I believe it will RMSD align the trajectory first, but you may need to specify that explicitly first.

You might also want to check out MDAnalysis as well, it may have similar functionality. I've used both packages and both are still actively maintained.