In [ ]:
%matplotlib inline
from __future__ import print_function
import mdtraj as md

Use two files that are distributed with MDTraj examples

In [ ]:
crystal_fn = 'data/native.pdb'
trajectory_fn = 'data/frame0.xtc'

In [ ]:
crystal = md.load(crystal_fn)
trajectory = md.load(trajectory_fn, top=crystal)  # load the xtc. the crystal structure defines the topology

RMSD with exchangeable hydrogen atoms is generally not a good idea so let's take a look at just the heavy atoms

In [ ]:
rmsds_to_crystal = md.rmsd(trajectory, crystal, 0)
heavy_atoms = [atom.index for atom in crystal.topology.atoms if atom.element.symbol != 'H']
heavy_rmds_to_crystal = md.rmsd(trajectory, crystal, 0, atom_indices=heavy_atoms)

In [ ]:
from matplotlib import pyplot as plt
plt.plot(trajectory.time, rmsds_to_crystal, 'r', label='all atom')
plt.plot(trajectory.time, heavy_rmds_to_crystal, 'b', label='heavy atom')
plt.title('RMSDs to crystal')
plt.xlabel('simulation time (ps)')
plt.ylabel('RMSD (nm)')