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ChargeCalculator:Theoretical background

1,231 bytes added, 00:53, 29 November 2014
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=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 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''.
The atom selection algorithm In ''EEM Cutoff Cover', the subset of fragment generating atoms is ensures obtained in such a way that :* no two atoms in this subset are connected to each other* each atom in the molecule has at least one neighbor (within two bonds) included in this subset. The fragments for ''EEM Cutoff Cover'' are generated in the entire volume same way as for ''EEM Cutoff'', according to the ''cutoff radius''. Thus, the average size of the molecule is coveredresulting 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 method is thus termed ''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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