![]() In the conventional scheme, the position of the shells are minimized (Sangster and Dixon, 1976 Lindan and Gillan, 1993) at every MD step while keeping the core coordinates fixed. Molecular dynamics (MD) simulations with the shell model based MM force fields can be carried out in two ways. The shell model (Dick and Overhauser, 1958) (or the Drude oscillator model) is widely used to describe polarization of MM atoms. It was reported that inclusion of polarization of MM atoms has significant effects on various properties (Bakowies and Thiel, 1996 Illingworth et al., 2006 Geerke et al., 2007 Lu and Zhang, 2008 Boulanger and Thiel, 2014), for instance, free energy barriers of chemical reactions are affected by about 10% (Lu and Zhang, 2008 Boulanger and Thiel, 2014). Inclusion of polarization of MM atoms in QM/MM simulations demands usage of polarizable MM force fields, i.e., QM/polarized-MM (QM/p–MM) methods. However, such approaches cannot take into account the polarization of MM atoms due to the QM electrostatic potential. The QM/MM implementations with fixed charge MM models enable polarization of QM charge density due to MM electrostatic potential. Widely used MM force fields employ a fixed point charge model for accounting the electrostatic interactions between MM atoms. Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations offer a powerful way to bridge the length scales in a chemically complex system where a small region of the system of interest is treated by QM techniques, while the rest is described by computationally cheap MM force-fields. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. ![]() We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem.
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