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ChargeCalculator:Theoretical background

369 bytes removed, 18:12, 4 March 2015
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 in 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 included in the end subset of atoms used in the EEM Cover calculationfragment generation step. In extremely rare cases, the molecular system might contain atoms which appeared to be are only connected only to these problematic atoms will also not have atomic charges, even if they have without EEM parametersand which have been included in the fragment generation step. In this case, due to the nature of the ''EEM Cutoff Cover approach. Anyway, the principle oriented solution would '' will not be able to correct the pivot selection scheme so as to ignore the calculate charges for these uniquely bonded atoms without , even when EEM parameters, consistent with the full EEM and EEM Cutoff approachesare available for them. 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 This problem is very unlikely to happen in cases where arise if H atoms are present, since and will only affect a small number of charges even if it solely affects atoms which are connected only to atoms without EEM parameters, and not connected to any other atomsdoes.  

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