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Link molecule method for quantum mechanical/molecular mechanical hybrid simulations. (English) Zbl 1147.82325

Summary: We present a new coupling method for hybrid simulations in which the system is partitioned into covalently linked quantum mechanical (QM) and molecular mechanical (MM) regions. Our method, called the “link molecule method (LMM),” is substantially different from the link atom methods in that LMM is free from the delicate issue of how to remove the additional degrees of freedom with respect to the position of the virtual atoms linking the QM and the MM regions. The force acting on the atom at the regional boundary is obtained in a simple form based on the total energy conservation. The accuracy of LMM is demonstrated in detail using a system of silicon partitioned into the QM and the MM region at the (1 0 0) boundary plane. This condition has been difficult to simulate by conventional methods employing the link atoms because of the strong repulsion between the nearby link atoms.

MSC:

82B21 Continuum models (systems of particles, etc.) arising in equilibrium statistical mechanics
82B10 Quantum equilibrium statistical mechanics (general)
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[2] Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M., A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields, J. Chem. Phys., 110, 10452-10467 (1999)
[3] Laio, A.; VandeVondele, J.; Rothlisberger, U., A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations, J. Chem. Phys., 116, 6941-6947 (2002)
[4] Bernstein, N.; Hess, D. W., Lattice trapping barriers to brittle fracture, Phys. Rev. Lett., 91, 025501 (2003)
[5] Ogata, S.; Shimojo, F.; Kalia, R. K.; Nakano, A.; Vashishta, P., Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids, Comput. Phys. Commum., 149, 30-38 (2002)
[6] Csányi, G.; Albaret, T.; Payne, M. C.; De Vita, A., Learn on the fly”: a hybrid classical and quantum-mechanical molecular dynamics simulation, Phys. Rev. Lett., 93, 175503 (2004)
[7] Nakamura, Y.; Takahashi, N.; Uda, T.; Ohno, T., Multiregional hybrid method and its application: formation of an atomic protrusion at an atomic force microscope tip apex, Phys. Rev. Lett., 97, 086103 (2006)
[8] Zhang, Y.; Lee, T. S.; Yang, W., A pseudobond approach to combining quantum mechanical and molecular mechanical methods, J. Chem. Phys., 110, 46-54 (1999)
[9] Zhang, Y., Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods, J. Chem. Phys., 122, 024114 (2005)
[10] DiLabio, G. A.; Hurley, M. M.; Christiansen, P. A., Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules, J. Chem. Phys., 116, 9578 (2002)
[11] DiLabio, G. A.; Wolkow, P. A.; Johnson, E. R., Efficient silicon surface and cluster modeling using quantum capping potentials, J. Chem. Phys., 122, 044708 (2005)
[12] Poteau, R.; Ortega, I.; Alary, F.; Solis, A. R.; Barthelat, J. C.; Daudey, J. P., Effective group potentials 1., Method J. Phys. Chem. A, 105, 198-205 (2001)
[13] Troullier, N.; Martins, J. L., Efficient pseudopotentials for plane-wave calculations, Phys. Rev. B, 43, 1993-2006 (1991)
[14] T. Uda, M. Okamoto, QM/MM hybrid simulations on semiconductor surfaces, in: Proceedings of the 5th Asian Workshop on First-principles Electronic Calculations, 2002, p. 57.; T. Uda, M. Okamoto, QM/MM hybrid simulations on semiconductor surfaces, in: Proceedings of the 5th Asian Workshop on First-principles Electronic Calculations, 2002, p. 57.
[15] Okamoto, M.; Uda, T.; Betsuyaku, K.; Nishikawa, N.; Terakura, K., QM/MM hybrid simulations on silicon surfaces, (Proceedings of the 26th International Conference on the Physics of Semiconductors (2002), World Scientific: World Scientific Edinburgh, Singapore), CD-ROM
[16] Perdew, J. P.; Wang, Y., Accurate and simple analytic representation of the electron-gas correlation energy, Phys. Rev. B, 45, 13244 (1992)
[17] Stillinger, F. H.; Weber, T. A., Computer simulation of local order in condensed phases of silicon, Phys. Rev. B, 31, 5262-5271 (1985)
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