convert_to('PARMED') super slow #3028
Description
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