→EEM Cutoff Cover
''EEM Cutoff Cover'' has also proven robust and sufficiently accurate (RMSD less than 0.003e compared to the ''EEM Cutoff'' of comparable cutoff radius), and is the method of choice for biomolecular complexes of tens of thousands of atoms and higher.
The only notable issue which may arise with the ''EEM Cutoff Cover'' approach is when the molecular system contains atoms for which there are no EEM parameters. Unlike the ''full EEM'' and ''EEM Cutoff'' approaches, these atoms are not entirely ignored here. Specifically, they
contribute to the pivot selection step, and may be selected as pivots. This problem is enhanced when some atoms are missing (e.g., missing H atoms). At the end of the EEM Cover calculation, the atoms which appeared to be connected only to these problematic atoms will also not have atomic charges, even if they have EEM parameters, due to the nature of the EEM Cover approach. Anyway, the principle oriented solution would be to correct the pivot selection scheme so as to ignore the atoms without EEM parameters , consistent with the full EEM and EEM Cutoff approaches. However, this would mean full testing and benchmarking of the corrected algorithm, and I am not really looking forward to that :) Moreover, as David pointed out, this is unlikely to happen in cases where H are present, since it solely affects atoms which are connected only to atoms without EEM parameters, and not connected to any other atoms.