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ChargeCalculator:Theoretical background

5 bytes removed, 15:27, 8 December 2014
EEM Cutoff Cover
To further enhance the time and memory efficiency of EEM, ACC implements an additional approximation with specific focus on large biomolecular complexes with hundreds of thousands of atoms. This additional approximation is applied to the ''EEM Cutoff'' method in order to reduce the number of EEM matrices that will be solved.
While in the ''EEM Cutoff'' method ACC generates one fragment for each atom in the molecule, this further approximation generates fragments only for a subset of atoms. The algorithm by which this subset of atoms is obtained ensures that each atom in the molecule will eventualy eventually contribute to at least one fragment. In other words, the entire volume of the molecule is covered, and the method is thus termed ''EEM Cutoff Cover''.
In ''EEM Cutoff Cover'', the subset of fragment generating atoms is obtained in such a way that:
The fragments for ''EEM Cutoff Cover'' are generated in the same way as for ''EEM Cutoff'', according to the ''cutoff radius''. Thus, the average size of the resulting EEM matrices will not differ. However, since fewer fragments are generated for ''EEM Cutoff Cover'', the final number of EEM matrices to be solved will be up to 4 times lower than for ''EEM Cutoff''.
''EEM Cutoff Cover'' has also proven robust and sufficiently accurate (RMSD less than 0.003e compared to the ''EEM Cutoff Cover'' of comparable cutoff radius), and is the method of choice for biomolecular complexes of tens of thousands of atoms and higher.

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