fix notebook so that it does not run out of filedescriptors

[orbeckst]

The code in the Li+ notebook

for i in sims:
    # make a protein Universe
    u = i.universe

    # select Li atoms
    ions = u.select_atoms('name LI')

    for ion in ions:
        # make radial distribution function
        df = pdbionsurvey.coordination.en(u, ion)
        
        # make directory if it doesn't exist
        i['coordination/LI/'].make()

        # store radial distribution function in .csv file
        df.to_csv(i['coordination/LI/{}.csv'.format(ion.number)].abspath)

will run out of open file descriptors if there are too many sims because the line

    u = i.universe

creates a MDAnalysis.Universe as a side effect and keeps it alive.

Instead do something like

u = mda.Universe(i.universedef.topology, i.universedef.filename)

This will ensure that the Universe is garbage-collected and with it the file descriptors will be released again.

Add a comment to the code and say why you're not using i.universe. It will also make it easier to make the code independent of MDS #13.