Improve example runtime

[mattwthompson]

Description
The examples currently take anywhere between 11 and 40 (!) minutes to run in GitHub Actions. When I run them locally and give it 10 workers, its runtime it also less than desirable:

$ python -m pytest -x -c pyproject.toml --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
          --ignore=examples/deprecated/ \
          --ignore=examples/experimental/ \
          --ignore=examples/lammps/
============================================================== test session starts ===============================================================
platform darwin -- Python 3.12.0, pytest-8.4.2, pluggy-1.6.0
rootdir: /Users/mattthompson/software/openff-interchange
configfile: pyproject.toml
plugins: anyio-4.11.0, xdist-3.8.0, nbval-0.11.0, cov-7.0.0
10 workers [127 items]
......................................................................................s.......^R
 .^R
..s.....................s.......            [100%]
================================================================ warnings summary ================================================================
examples/host-guest/host_guest.ipynb: 1 warning
examples/openmm-import/protein-ligand.ipynb: 1 warning
examples/vectorized_representations/vectorized_representations.ipynb: 1 warning
examples/conformer_energies/conformer_energies.ipynb: 1 warning
examples/packed_box/packed_box.ipynb: 1 warning
examples/protein_ligand/protein_ligand.ipynb: 1 warning
examples/ligand_in_water/ligand_in_water.ipynb: 1 warning
examples/virtual_sites/virtual_sites.ipynb: 1 warning
examples/amber/amber.ipynb: 1 warning
examples/openmm/openmm.ipynb: 1 warning
  /Users/mattthompson/mamba/envs/interchange-examples-env/lib/python3.12/site-packages/coverage/control.py:946: CoverageWarning: No data was collected. (no-data-collected); see https://coverage.readthedocs.io/en/7.11.0/messages.html#warning-no-data-collected
    self._warn("No data was collected.", slug="no-data-collected")

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================= tests coverage =================================================================
________________________________________________ coverage: platform darwin, python 3.12.0-final-0 ________________________________________________

Coverage XML written to file coverage.xml
============================================================== slowest 20 durations ==============================================================
172.74s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 19
83.56s call     examples/protein_ligand/protein_ligand.ipynb::Cell 7
76.32s call     examples/protein_ligand/protein_ligand.ipynb::Cell 23
64.77s call     examples/openmm/openmm.ipynb::Cell 0
61.66s call     examples/amber/amber.ipynb::Cell 0
55.80s call     examples/protein_ligand/protein_ligand.ipynb::Cell 19
52.56s call     examples/packed_box/packed_box.ipynb::Cell 6
51.52s call     examples/packed_box/packed_box.ipynb::Cell 7
46.62s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 14
40.82s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 18
39.28s call     examples/virtual_sites/virtual_sites.ipynb::Cell 0
38.34s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 0
36.89s call     examples/protein_ligand/protein_ligand.ipynb::Cell 27
35.01s call     examples/protein_ligand/protein_ligand.ipynb::Cell 2
34.37s call     examples/packed_box/packed_box.ipynb::Cell 0
34.34s call     examples/protein_ligand/protein_ligand.ipynb::Cell 0
33.76s call     examples/conformer_energies/conformer_energies.ipynb::Cell 0
33.65s call     examples/vectorized_representations/vectorized_representations.ipynb::Cell 0
33.56s call     examples/openmm-import/protein-ligand.ipynb::Cell 0
33.52s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 6
============================================ 124 passed, 3 skipped, 10 warnings in 446.27s (0:07:26) =============================================

From a quick pass, the slowest cells appear to be (roughly in descending order):

• Running a ligand in TIP4P in GROMACS
• Getting the protein-ligand single-point energies in all three supported engines
• Getting the protein single-point energies in all three supported engines
• Assigning partial charges to large ligands
• Running short (5-10 ps) simulations
• Writing to Amber files
• Loading a PDB file file with a protein and other components
• Loading a PDB file file with a protein
• Creating openmm.app.Simulation objects
• Energy-minimizing condensed-phase systems

Some of these can be worked around by updating the examples themselves, others are probably sore spots for users.