Editing ChargeCalculator:Theoretical background (section)

=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 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:
* 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 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''. The charge on each atom in the molecule is then computed as the sum of its charge contributions from each fragment. Further, each atomic charge is corrected in such a way that the sum of all atomic charges equals the total molecular charge. ''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, these atoms are included in the subset of atoms used in the fragment generation step. In extremely rare cases, the molecular system might contain atoms which are only connected to atoms without EEM parameters and which have been included in the fragment generation step. In this case, ''EEM Cutoff Cover'' will not be able to calculate charges for these uniquely bonded atoms, even when EEM parameters are available for them. This problem is very unlikely to arise if H atoms are present, and will only affect a small number of charges even if it does. 



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