  The charge transfer effect is an important component in the physical
description of realistic proteins. In the hybrid quantum mechanical-molecular
mechanical (QM/MM) simulations, the significant charge transfer between the
QM/MM boundaries could lead to the slow convergence problem with very large QM
regions. In this work, we will discuss how community structure in complex
network (electronic structure topology associated domain) can be used to
measure QM/MM boundary effects and how it can provide a different perspective
on well established concepts in available QM/MM simulations. The graph theory
is employed to provide an useful solution to distinguish the significant charge
transfer regions between the core active site and the surrounding protein
environment in the QM/MM simulations. According to community detection
algorithm for complex network, the charge transfer topology associated domain
(ctTAD) is suggested to provide an alternative tool for systematically
minimizing the charge transfer effects of QM/MM boundary with minor
computational costs.
