Charge Rescaling

In hybrid QC/MM simulations, when only a fragment of a residue is included in the QC region—such as part of a glutamate side chain—EasyHybrid automatically adjusts the partial charges of the remaining atoms in the MM portion of the residue to preserve a physically meaningful total charge.

Figure: Glutamic acid residue. The atoms shown in ball-and-stick represent the QC region, whereas those represented as lines correspond to the atoms that remain in the MM region.

Removing atoms from the MM region may leave the remaining MM atoms with a non-integer total charge (e.g., –0.73), which is incompatible with most QC/MM implementations in pDynamo that require the MM region to have an integer net charge. To correct this, EasyHybrid calculates the residual charge required to reach the nearest integer value,

where qi are the original partial charges of the N remaining MM atoms and Qtarget is the nearest integer (e.g., round(∑qi)). This residual charge is then uniformly redistributed across the remaining MM atoms by assigning each atom an additio'nal fraction:

so that each adjusted charge becomes qi′=qi+δq. Through this rescaling procedure, EasyHybrid ensures that the final total MM charge is an integer, maintaining consistency and compatibility with the requirements of the QC/MM framework in pDynamo.

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