Error when running Pairwise RMSD between two trajectories

[akashp...@gmail.com]

Hi all,

I wanted to calculate the Pairwise RMSD between two trajectories. I am getting an error when running the commands  in my notebook. Please find my code below:

GLY0 = mda.Universe(top, traj1)

GLY10 = mda.Universe(top, traj2)

prmsd = np.zeros((len(GLY0.trajectory),   # GLY0 on y-axis

                  len(GLY10.trajectory)))               # GLY10 on x-axis

from MDAnalysis.analysis import diffusionmap, align, rms

for i, frame_GLY0 in enumerate(GLY0.trajectory): 

    r = rms.RMSD(GLY10.trajectory, GLY0.trajectory,

                ref_frame=i).run()

    prmsd[i] = r.rmsd[:, -1]  

Error:

AttributeError Traceback (most recent call last) <ipython-input-14-331c3e3848f8> in <module> 5 6 for i, frame_GLY0 in enumerate(GLY0.trajectory): # assigns an index to each item in an iterable object that can be used to reference the item later ----> 7 r = rms.RMSD(GLY10.trajectory, GLY0.trajectory, 8 ref_frame=i).run() 9 prmsd[i] = r.rmsd[:, -1] # select 3rd column with RMSD values ~/opt/anaconda3/lib/python3.8/site-packages/MDAnalysis/analysis/rms.py in __init__(self, atomgroup, reference, select, groupselections, weights, weights_groupselections, tol_mass, ref_frame, **kwargs) 474 475 """ --> 476 super(RMSD, self).__init__(atomgroup.universe.trajectory, 477 **kwargs) 478 self.atomgroup = atomgroup AttributeError: 'DCDReader' object has no attribute 'universe'

Any guidance will be much appreciated.

Thanks,

Akash

[Oliver Beckstein]

Hi Akash,

Try passing atomgroups instead of trajectories

 R = rms.RMSD(GLY10, GLY0, ref_frame=i).run()

because the RMSD analysis class takes atomgroups or universes.

You also don’t have to iterate over GLY0.trajectory; you could just do `for i in range(GLY0.trajectory.n_frames)` to get the frame numbers.

Oliver

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Oliver Beckstein (he/his/him)

orbe...@gmail.com