Editing ChargeCalculator:Job submission (section)

==Pick computation method==
[[File:ACC FirstTimeUserGuide 09.jpg|thumb|right|650px| In addition to classical EEM, '''ACC''' offers two time and memory efficient EEM implementations. Please use ''EEM Cutoff'' for systems with tens of thousands of atoms, and ''EEM Cutoff Cover'' for larger systems, in both cases with a ''Cutoff Radius'' parameter of at least 8.]]

The default computation includes all atoms in the system and solves the entire EEM matrix in double precision. For very large systems you may need to resort to one of the time and memory efficient EEM implementations specifically tailored for such systems (check the [[ChargeCalculator:Theoretical_background | Theoretical background ]] for more details). By default, '''ACC''' tries to suggest a computation method suitable for the molecule(s) you uploaded.

You may change the method chosen by default, and ''add'' one or more methods of your choice using the ''Add'' button at the top of the ''Computation Methods'' section. Note that each unique method configuration added to the list will result in an additional '''ACC''' job, or set of jobs.

Even for molecules containing several thousands of atoms, our implementation of EEM is very time efficient, and you may use the method labeled as ''Full EEM''. For systems with tens of thousands of atoms, you will probably need to pick ''EEM Cutoff'', and a reasonable value for the ''Cutoff Radius'' parameter (we recommend a minimum of 10). A biomolecular complex with hundreds of thousands of atoms makes good use of the method ''EEM Cutoff Cover'' with a ''Cutoff Radius'' of 8 and ''single Precision''.

If your system is solvated or includes a few key water molecules, you may want to run parallel calculations with and without the water molecules (tick the ''Ignore Waters'' option), to see how water can affect the charge distribution in the biomolecule.  Note that '''ACC''' identifies water atoms if they are annotated by a residue name typically associated with water (HOH, WAT, H2O). Other residue names sometimes associated with water, such as SOL and TIP, are not considered here because the Protein Data Bank contains instances of such residues which are chemical components different from water. Thus, if you wish to ignore water which is annotated in your file as SOL or TIPx, you will need to remove these records before submitting to '''ACC'''.

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