Attempting to run a simulation of chloroform with the GROMACS inputs page. On the concatenation and aligning of trajectory step, getting this error:
ValueError Traceback (most recent call last)
in <cell line: 49>()
47 # print(rms.rmsd(u1.select_atoms('name CA').positions, u2.select_atoms('name CA').positions, superposition=False))
48
---> 49 align.AlignTraj(u1, u2, select='name CA', in_memory=True).run()
50
51 nw = u1.select_atoms("not (resname HOH)")
Attempting to run a simulation of chloroform with the GROMACS inputs page. On the concatenation and aligning of trajectory step, getting this error: ValueError Traceback (most recent call last)
3 frames /usr/local/lib/python3.10/site-packages/MDAnalysis/analysis/base.py in run(self, start, stop, step, frames, verbose, progressbar_kwargs) 446 self.frames[i] = ts.frame 447 self.times[i] = ts.time --> 448 self._single_frame() 449 logger.info("Finishing up") 450 self._conclude()
/usr/local/lib/python3.10/site-packages/MDAnalysis/analysis/align.py in _single_frame(self) 700 mobile_com = self.mobile_atoms.center(self._weights) 701 mobile_coordinates = self.mobile_atoms.positions - mobile_com --> 702 mobile_atoms, self.results.rmsd[index] = _fit_to( 703 mobile_coordinates, 704 self._ref_coordinates,
/usr/local/lib/python3.10/site-packages/MDAnalysis/analysis/align.py in _fit_to(mobile_coordinates, ref_coordinates, mobile_atoms, mobile_com, ref_com, weights) 342 weights=weights) 343 --> 344 mobile_atoms.translate(-mobile_com) 345 mobile_atoms.rotate(R) 346 mobile_atoms.translate(ref_com)
/usr/local/lib/python3.10/site-packages/MDAnalysis/core/groups.py in translate(self, t) 1424 vector = np.asarray(t) 1425 # changes the coordinates in place -> 1426 atomgroup.universe.trajectory.ts.positions[atomgroup.indices] += vector 1427 return self 1428
ValueError: operands could not be broadcast together with shapes (2500,3) (0,3) (2500,3)