convert_to('PARMED') super slow

[fhh2626]

Expected behavior

The call of the method should be finished within a reasonable time scale

Actual behavior

For a 10k-atom system, this function call takes 2-3 min, and for a 60k-atom system, this takes > 15 min.

Code to reproduce the behavior

import MDAnalysis as mda
import parmed as pmd
prm = pmd.load_file('whatever.parm7', 'whatever.rst7')
u = mda.Universe(prm)
prot = u.select_atoms('all')
prm_u = prot.convert_to('PARMED')

....

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
  the latest conda version of MDAnalysis and parmed
• Which version of Python (python -V)?
  Python 3.7.8
• Which operating system?
  I tried both Windows 10 and Linux Mint 19

[IAlibay]

Just re-opening to confirm that sufficient work has been done here to address the issue.

@fhh2626 would you be able to confirm that the latest fix (#3029) alleviates your issue? (this would involve installing the developer version of MDAnalysis).

[fhh2626]

Yes, thanks for your nice work!