메뉴 건너뛰기




Volumn 33, Issue 1-2, 2007, Pages 171-184

Ab initio quantum mechanical/molecular mechanical molecular dynamics using multiple-time-scale approach and perturbation theory

Author keywords

Ab initio; Molecular dynamics; QM MM; Water

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; HAMILTONIANS; MOLECULAR MECHANICS; PERTURBATION TECHNIQUES; QUANTUM THEORY;

EID: 33947414516     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020601052922     Document Type: Conference Paper
Times cited : (14)

References (51)
  • 1
    • 0017100947 scopus 로고
    • Theoretical studies of enzymatic reactions: Dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • A. Warshel, M. Levitt. Theoretical studies of enzymatic reactions: dielectric electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol., 227 (1976).
    • (1976) J. Mol. Biol , vol.227
    • Warshel, A.1    Levitt, M.2
  • 2
    • 84988053595 scopus 로고
    • - exchange reaction and gas phase protonation of polyethers
    • - exchange reaction and gas phase protonation of polyethers. J. Camput. Chem., 7, 718 (1986).
    • (1986) J. Camput. Chem , vol.7 , pp. 718
    • Singh, U.C.1    Kollman, P.A.2
  • 3
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • M.J. Field, P.A. Bash, M. Karplus. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Ghent., 11, 700 (1990).
    • (1990) J. Comput. Ghent , vol.11 , pp. 700
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 4
    • 84962367344 scopus 로고    scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • J. Gao. Methods and applications of combined quantum mechanical and molecular mechanical potentials. Rev. Comput. Chem., 7, 119 (1996).
    • (1996) Rev. Comput. Chem , vol.7 , pp. 119
    • Gao, J.1
  • 5
    • 0037098212 scopus 로고    scopus 로고
    • New challenges in quantum chemistry - quests for accurate calculations for large molecular systems
    • K. Morokuma. New challenges in quantum chemistry - quests for accurate calculations for large molecular systems. Phil. Trans. Roy. Land. Ser. A, 360, 1149 (2002).
    • (2002) Phil. Trans. Roy. Land. Ser. A , vol.360 , pp. 1149
    • Morokuma, K.1
  • 6
    • 0032711930 scopus 로고    scopus 로고
    • Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
    • G. Monard, K.M. Merz Jr. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res., 32, 904 (1999).
    • (1999) Acc. Chem. Res , vol.32 , pp. 904
    • Monard, G.1    Merz Jr., K.M.2
  • 8
    • 0033597059 scopus 로고    scopus 로고
    • Chemical reactivity studied by hybrid QM/MM methods
    • I.H. Hillier. Chemical reactivity studied by hybrid QM/MM methods. J. Mol. Struct. (Theochem), 463, 45 (1999).
    • (1999) J. Mol. Struct. (Theochem) , vol.463 , pp. 45
    • Hillier, I.H.1
  • 10
    • 0001753666 scopus 로고    scopus 로고
    • Combined quantum mechanical and molecular mechanical approaches
    • T. Mordasini, W. Thiel. Combined quantum mechanical and molecular mechanical approaches. Chimia, 52, 288 (1998).
    • (1998) Chimia , vol.52 , pp. 288
    • Mordasini, T.1    Thiel, W.2
  • 11
    • 0345713551 scopus 로고    scopus 로고
    • Hybrid models for combined quantum mechanical and molecular mechanical approaches
    • D. Bakowies, W. Thiel. Hybrid models for combined quantum mechanical and molecular mechanical approaches. J. Phys. Chem., 100, 10580 (1996).
    • (1996) J. Phys. Chem , vol.100 , pp. 10580
    • Bakowies, D.1    Thiel, W.2
  • 14
    • 0034269356 scopus 로고    scopus 로고
    • Structure optimization via free energy grandient method: Application to glycine zwitterion in aqueous solution
    • N. Okuyama-Yoshida, K. Kataoka, M. Nagaoka, T. Yamabe. Structure optimization via free energy grandient method: application to glycine zwitterion in aqueous solution. J. Chem. Phys., 113, 3519 (2000).
    • (2000) J. Chem. Phys , vol.113 , pp. 3519
    • Okuyama-Yoshida, N.1    Kataoka, K.2    Nagaoka, M.3    Yamabe, T.4
  • 15
    • 4644343956 scopus 로고    scopus 로고
    • A quantum chemical approach to the free energy calculations in condensed systems: The QM/MM method combined with the theory of energy representation
    • H. Takahashi, N. Matsubayashi, M. Nakahara, T. Nitta. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation. J. Chem. Phys., 121, 3989 (2004).
    • (2004) J. Chem. Phys , vol.121 , pp. 3989
    • Takahashi, H.1    Matsubayashi, N.2    Nakahara, M.3    Nitta, T.4
  • 16
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • M.E. Tuckerman, G.J. Martyna, B.J. Berne. Reversible multiple time scale molecular dynamics. J. Chem. Phys., 97, 1990 (1992).
    • (1992) J. Chem. Phys , vol.97 , pp. 1990
    • Tuckerman, M.E.1    Martyna, G.J.2    Berne, B.J.3
  • 17
    • 0000026966 scopus 로고    scopus 로고
    • Explicit reversible integrators for extended systems dynamics
    • G.J. Martyna, M.E. Tuckerman, D.J. Tobias, M.L. Klein. Explicit reversible integrators for extended systems dynamics. Mol. Phys., 87, 1117 (1996).
    • (1996) Mol. Phys , vol.87 , pp. 1117
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 18
    • 0037149116 scopus 로고    scopus 로고
    • Sampling phase space by a combined QM/MM ab initio Car-Parrinello molecular dynamics method with different (multiple) time steps in the quantum mechanical (qm) and molecular mechanical (mm) domains
    • T.K. Woo, P. Margl, P.R. Blöchl, T. Ziegler. Sampling phase space by a combined QM/MM ab initio Car-Parrinello molecular dynamics method with different (multiple) time steps in the quantum mechanical (qm) and molecular mechanical (mm) domains. J. Phys. Chem. A, 106, 1173 (2002).
    • (2002) J. Phys. Chem. A , vol.106 , pp. 1173
    • Woo, T.K.1    Margl, P.2    Blöchl, P.R.3    Ziegler, T.4
  • 19
    • 33751156482 scopus 로고
    • An examination of a Hartree-Fock/molecular mechanical coupled potential
    • R.V. Stanton, L.R. Little, K.M. Merz Jr. An examination of a Hartree-Fock/molecular mechanical coupled potential. J. Phys. Chem., 99, 17344 (1995).
    • (1995) J. Phys. Chem , vol.99 , pp. 17344
    • Stanton, R.V.1    Little, L.R.2    Merz Jr., K.M.3
  • 20
    • 84986517314 scopus 로고
    • An examination of a density functional/molecular mechanical coupled potential
    • R.V. Stanton, D.S. Hartsough, K.M. Merz Jr. An examination of a density functional/molecular mechanical coupled potential. J. Comput. Chem., 16, 113 (1995).
    • (1995) J. Comput. Chem , vol.16 , pp. 113
    • Stanton, R.V.1    Hartsough, D.S.2    Merz Jr., K.M.3
  • 21
    • 4244118545 scopus 로고    scopus 로고
    • A coupled density-functional-molecular mechanics Monte Carlo simulation method. The water molecule in liquid water
    • I. Tuñón, M.T.C. Martins-Costa, C. Millot, M.F. Ruiz-López, J.L. Rivail. A coupled density-functional-molecular mechanics Monte Carlo simulation method. The water molecule in liquid water. J. Comput. Chem., 17, 17 (1996).
    • (1996) J. Comput. Chem , vol.17 , pp. 17
    • Tuñón, I.1    Martins-Costa, M.T.C.2    Millot, C.3    Ruiz-López, M.F.4    Rivail, J.L.5
  • 22
    • 0000440811 scopus 로고    scopus 로고
    • On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanical coupling in a hybrid molecular dynamics simulation of liquid water
    • Y. Tu, A. Laaksonen. On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanical coupling in a hybrid molecular dynamics simulation of liquid water. J. Chem. Phys., 111, 7519 (1999).
    • (1999) J. Chem. Phys , vol.111 , pp. 7519
    • Tu, Y.1    Laaksonen, A.2
  • 23
    • 0034506648 scopus 로고    scopus 로고
    • Combined Hartree-Fock quantum mechanical and molecular mechanical molecular dynamics simulations of water at ambient and supercritical conditions
    • Y. Tu, A. Laaksonen. Combined Hartree-Fock quantum mechanical and molecular mechanical molecular dynamics simulations of water at ambient and supercritical conditions. J. Chem. Phys., 113, 11264 (2000).
    • (2000) J. Chem. Phys , vol.113 , pp. 11264
    • Tu, Y.1    Laaksonen, A.2
  • 24
    • 18744410128 scopus 로고    scopus 로고
    • Structure and ultrafast dynamics of liquid water: A quantum mechanics/molecular mechanics molecular dynamics simulations study
    • D. Xenides, B.R. Randolf, B.M. Rode. Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study. J. Chem, Phys., 122, 174506 (2005).
    • (2005) J. Chem, Phys , vol.122 , pp. 174506
    • Xenides, D.1    Randolf, B.R.2    Rode, B.M.3
  • 25
    • 2942639536 scopus 로고    scopus 로고
    • A quantum model for water: Equilibrium and dynamical properties
    • J. Lobaugh, G.A. Voth. A quantum model for water: equilibrium and dynamical properties. J. Chem. Phys., 106, 2400 (1997).
    • (1997) J. Chem. Phys , vol.106 , pp. 2400
    • Lobaugh, J.1    Voth, G.A.2
  • 26
    • 33947417733 scopus 로고    scopus 로고
    • Unfortunately, the Ewald sum technique for ab initio QM/MM simulations using localized Gaussian basis set has not been developed yet to our knowledge, while it is commonly used in semiempirical QM/MM simulations. See, J. Gao, C. Alhambra. A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations. J. Chem. Phys.,
    • Unfortunately, the Ewald sum technique for ab initio QM/MM simulations using localized Gaussian basis set has not been developed yet to our knowledge, while it is commonly used in semiempirical QM/MM simulations. See, J. Gao, C. Alhambra. A hybrid semiempirical quantum mechanical and lattice-sum method for electrostatic interactions in fluid simulations. J. Chem. Phys.,
  • 27
    • 19944369519 scopus 로고    scopus 로고
    • K. Nam, J. Gao, and D.M. York, An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations, J. Chem. Theor. Comput. 1, 2 (2005). 107, 1212 (1997).
    • K. Nam, J. Gao, and D.M. York, An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations, J. Chem. Theor. Comput. 1, 2 (2005). 107, 1212 (1997).
  • 28
    • 0041417956 scopus 로고    scopus 로고
    • QM/MMpol: A consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde, and acetone
    • M.A. Thompson. QM/MMpol: a consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde, and acetone. J. Phys. Chem., 100, 14492 (1996).
    • (1996) J. Phys. Chem , vol.100 , pp. 14492
    • Thompson, M.A.1
  • 29
    • 5244276541 scopus 로고    scopus 로고
    • Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent potential
    • J. Gao. Energy components of aqueous solution: insight from hybrid QM/MM simulations using a polarizable solvent potential. J. Comput. Chem., 18, 1061 (1997).
    • (1997) J. Comput. Chem , vol.18 , pp. 1061
    • Gao, J.1
  • 30
    • 0031582953 scopus 로고    scopus 로고
    • A solvation model using a hybrid quantum mechanical/molecular mechanical potential with fluctuating solvent charges
    • R.A. Bryce, R. Buesnel, I.H. Hillier, N.A. Burton. A solvation model using a hybrid quantum mechanical/molecular mechanical potential with fluctuating solvent charges. Chem. Phys, Lett., 279, 367 (1997).
    • (1997) Chem. Phys, Lett , vol.279 , pp. 367
    • Bryce, R.A.1    Buesnel, R.2    Hillier, I.H.3    Burton, N.A.4
  • 31
    • 0035138053 scopus 로고    scopus 로고
    • The effective fragment potential method: A QM-based MM approach to modelling environmental effects in chemistry
    • M.S. Gordon, M.A. Freitag, P. Bandyopadhyay, J.H. Jensen, V. Kairys, W.J. Stevens. The effective fragment potential method: a QM-based MM approach to modelling environmental effects in chemistry. J. Phys. Chem. A, 103, 293 (2001).
    • (2001) J. Phys. Chem. A , vol.103 , pp. 293
    • Gordon, M.S.1    Freitag, M.A.2    Bandyopadhyay, P.3    Jensen, J.H.4    Kairys, V.5    Stevens, W.J.6
  • 33
    • 33947404861 scopus 로고    scopus 로고
    • This correspond to predictor part in the Gear algorithm
    • This correspond to "predictor" part in the Gear algorithm.
  • 34
    • 0034662899 scopus 로고    scopus 로고
    • The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa
    • A.K. Soper. The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa. Chem. Phys., 258, 121 (2000).
    • (2000) Chem. Phys , vol.258 , pp. 121
    • Soper, A.K.1
  • 35
    • 0036703676 scopus 로고    scopus 로고
    • Water structure from scattering experiments and simulation
    • T. Head-Gordon, G. Hura. Water structure from scattering experiments and simulation. Chem. Rev., 102, 2651 (2002).
    • (2002) Chem. Rev , vol.102 , pp. 2651
    • Head-Gordon, T.1    Hura, G.2
  • 36
    • 0037162256 scopus 로고    scopus 로고
    • Car-Parrinello molecular dynamics simulation of liquid water: New results
    • S. Izvekov, G.A. Voth. Car-Parrinello molecular dynamics simulation of liquid water: new results. J. Chem. Phys., 116, 10372 (2002).
    • (2002) J. Chem. Phys , vol.116 , pp. 10372
    • Izvekov, S.1    Voth, G.A.2
  • 37
    • 0346934847 scopus 로고    scopus 로고
    • Free energy of liquid water on the basis of quasichemical theory and ab initio molecular dynamics
    • D. Asthagiri, L.R. Pratt, J.D. Kress. Free energy of liquid water on the basis of quasichemical theory and ab initio molecular dynamics. Phys. Rev. E, 68, 041505 (2003).
    • (2003) Phys. Rev. E , vol.68 , pp. 041505
    • Asthagiri, D.1    Pratt, L.R.2    Kress, J.D.3
  • 39
    • 0942288567 scopus 로고    scopus 로고
    • Towards an assessment of the accuracy of density functional theory for first principles simulations of water
    • J.C. Grossman, E. Schwegler, E.W. Draeger, F. Gygi, G. Galli. Towards an assessment of the accuracy of density functional theory for first principles simulations of water. J. Chem. Phys., 120, 300 (2004).
    • (2004) J. Chem. Phys , vol.120 , pp. 300
    • Grossman, J.C.1    Schwegler, E.2    Draeger, E.W.3    Gygi, F.4    Galli, G.5
  • 40
    • 4944230287 scopus 로고    scopus 로고
    • Towards an assessment of the accuracy of density functional theory for first principles simulations of water. II
    • E. Schwegler, J.C. Grossman, F. Gygi, G. Galli. Towards an assessment of the accuracy of density functional theory for first principles simulations of water. II. J. Chem. Phys., 121, 5400 (2004).
    • (2004) J. Chem. Phys , vol.121 , pp. 5400
    • Schwegler, E.1    Grossman, J.C.2    Gygi, F.3    Galli, G.4
  • 41
    • 22944439420 scopus 로고    scopus 로고
    • The influence of temperature and density functional models in ah initio molecular dynamics simulation of liquid water
    • J. VandeVondele, F. Mohamed, M. Krack, J. Hutter, M. Sprik, M. Parrinello. The influence of temperature and density functional models in ah initio molecular dynamics simulation of liquid water. J. Chem. Phys., 122, 014515 (2005).
    • (2005) J. Chem. Phys , vol.122 , pp. 014515
    • VandeVondele, J.1    Mohamed, F.2    Krack, M.3    Hutter, J.4    Sprik, M.5    Parrinello, M.6
  • 42
    • 33947413140 scopus 로고    scopus 로고
    • A.J. Sadlej's. pVTZ basis set was obtained from the extensible computational chemistry environment basis set database, version 02/25/04, Pacific Northwest Laboratory (http://www.emsl.pnl.gov/ forms/basisform.html).
    • A.J. Sadlej's. pVTZ basis set was obtained from the extensible computational chemistry environment basis set database, version 02/25/04, Pacific Northwest Laboratory (http://www.emsl.pnl.gov/ forms/basisform.html).
  • 45
    • 0001471456 scopus 로고    scopus 로고
    • Mixed quantum-classical calculations on the water molecule in liquid phase: Influence of a polarizable environment on electronic properties
    • G. Jansen, F. Colonna, J.G. Angyan. Mixed quantum-classical calculations on the water molecule in liquid phase: influence of a polarizable environment on electronic properties. Int. J. Quantum Chem., 58, 251 (1996).
    • (1996) Int. J. Quantum Chem , vol.58 , pp. 251
    • Jansen, G.1    Colonna, F.2    Angyan, J.G.3
  • 46
    • 0000228899 scopus 로고    scopus 로고
    • The electronic properties of water molecules in water clusters and liquid water
    • Y. Tu, A. Laaksonen. The electronic properties of water molecules in water clusters and liquid water. Chem. Phys. Lett., 329, 283 (2000).
    • (2000) Chem. Phys. Lett , vol.329 , pp. 283
    • Tu, Y.1    Laaksonen, A.2
  • 47
    • 18344379950 scopus 로고    scopus 로고
    • Water molecule dipole in the gas and in the liquid phase
    • P.L. Silvestrelli, M. Parrinello. Water molecule dipole in the gas and in the liquid phase. Phys. Rev. Lett., 82, 3308 (1999).
    • (1999) Phys. Rev. Lett , vol.82 , pp. 3308
    • Silvestrelli, P.L.1    Parrinello, M.2
  • 49
    • 37649028156 scopus 로고    scopus 로고
    • Quantum simulation of the heat capacity of water
    • W. Shinoda, M. Shiga. Quantum simulation of the heat capacity of water. Phys. Rev. E, 71, 041204 (2005).
    • (2005) Phys. Rev. E , vol.71 , pp. 041204
    • Shinoda, W.1    Shiga, M.2
  • 50
    • 26444460228 scopus 로고    scopus 로고
    • Calculation of heat capacities of light and heavy water by path-integral molecular dynamics
    • M. Shiga, W. Shinoda. Calculation of heat capacities of light and heavy water by path-integral molecular dynamics. J. Chem, Phys., 123, 134502 (2005).
    • (2005) J. Chem, Phys , vol.123 , pp. 134502
    • Shiga, M.1    Shinoda, W.2
  • 51
    • 0344103144 scopus 로고
    • Density, thermal expansivity, and compressibility of liquid water from 0° to 150° C: Correlations and tables for atmospheric pressure and saturation reviewed and expressed on 1968 temperature scale
    • G.S. Kell. Density, thermal expansivity, and compressibility of liquid water from 0° to 150° C: correlations and tables for atmospheric pressure and saturation reviewed and expressed on 1968 temperature scale. J. Chem. Eng. Data, 20, 97 (1975).
    • (1975) J. Chem. Eng. Data , vol.20 , pp. 97
    • Kell, G.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.