Linear-scaling semiempirical quantum calculations for macromolecules
J. Chem. Phys. 105, 2744 (1996); doi:10.1063/1.472136
Issue Date: 15 August 1996
You are not logged in to this journal. Log in
A linear-scaling method to carry out semiempirical quantum mechanical calculations for large systems has been developed based on the density matrix version of the divide-and-conquer approach. The method has been tested and demonstrated to be accurate and efficient. With this implementation, semiempirical quantum mechanical calculations are made possible for large molecules over 9000 atoms on a typical workstation. For biological macromolecules, solvent effects are included with a dielectric continuum model. ©1996 American Institute of Physics.
| History: | Received 9 April 1996; accepted 6 May 1996 |
| Permalink: |
http://link.aip.org/link/?JCPSA6/105/2744/1 |
KEYWORDS and PACS
QUANTUM MECHANICS,
ELECTRONIC STRUCTURE,
DENSITY MATRIX,
CALCULATION METHODS,
MACROMOLECULES,
SOLVENT EFFECTS
- 31.10.+z
Electronic structure of atoms, molecules and their ions: theory Theory of electronic structure, electronic transitions, and chemical binding - 31.70.Dk
Electronic structure of atoms, molecules and their ions: theory Effects of atomic and molecular interactions on electronic structure Environmental and solvent effects - 87.15.By
Biological and medical physics Molecular biophysics Structure, bonding, conformation, configuration, and isomerism of biomolecules - YEAR: 1996
PUBLICATION DATA
0021-9606 (print)
1089-7690 (online)
REFERENCES (50)
For access to fully linked references, you need to log in.
For access to fully linked references, you need to Log in.
- J. P. Lewis, O. F. Sankey, and P. J. Ordejón, Phys. Rev. B (submitted).
- L. Y. Zhang and R. A. Friesner, J. Phys. Chem. 99, 16479 (1995).
- D. Bakowies, M. Bühl, and W. Thiel,
J. Am. Chem. Soc. 117, 10113 (1995 ). - W. Yang, Phys. Rev. Lett. 66, 438 (1991).
- W. Yang, Phys. Rev. A 44, 7823 (1991).
- G. Galli and M. Parrinello, Phys. Rev. Lett. 69, 3547 (1992).
- X.-P. Li, R. W. Nunes, and D. Vanderbilt, Phys. Rev. B 47, 10891 (1993).
- F. Mauri, G. Galli, and R. Car, Phys. Rev. B 47, 9973 (1993).
- P. Ordejón et al., Phys. Rev. B 48, 14646 (1993).
- E. B. Stechel, A. P. Williams, and P. J. Feibelman, Phys. Rev. B 49, 3898 (1993).
- S. Goedecker and L. Colombo,
Phys. Rev. B 73, 122 (1994 ). - J. M. Pérez-Jordá and W. Yang,
Chem. Phys. Lett. 247, 484 (1995 ). - J. M. Pérez-Jordá and W. Yang,
Chem. Phys. Lett. 241, 469 (1995 ). - J. M. Pérez-Jordá and W. Yang, J. Chem. Phys. 104, 8003 (1996).
- C. A. White et al.,
Chem. Phys. Lett. 230, 8 (1994 ). - M. C. Strain, G. E. Scuseria, and M. J. Frisch,
Science 271, 51 (1996 ). - J. J. P. Stewart, in Review in Computational Chemistry, Vol. 1, edited by K. B. Lipkowitz and D. B. Boyd (VCH, New York, 1990), Chap. 2.
- W. Thiel,
Tetrahedron 44, 7393 (1988 ). - J. J. P. Stewart, Abstract of the 211th ACS National meeting, Division of Computers in Chemistry.
- W. Yang and T.-S. Lee, J. Chem. Phys. 103, 5674 (1995).
- J. J. P. Stewart, MOPAC7 Version 2 Manual (QCPE, Bloomington, 1993).
- J. J. P. Stewart,
J. Comput.-aided Mol. Design 4, 1 (1990 ). - R. S. Mulliken, J. Chem. Phys. 23, 1833 (1955).
- P. D. Walker and P. G. Mezey,
J. Am. Chem. Soc. 115, 12423 (1993 ). - L. Massa, L. Huang, and J. Karle, J. Quantum Chem. 29, 371 (1995).
- Q. Zhao and W. Yang, J. Chem. Phys. 102, 9598 (1995).
- M. J. S. Dewar and V. Yamaguch,
Comput. Chem. 2, 25 (1978 ). - J. D. Head and M. C. Zerner,
Chem. Phys. Lett. 122, 264 (1985 ). - W. H. Press et al., Numerical Recipes in Fortran, 2nd ed. (Cambridge University Press, New York, 1992), p. 413.
- A. Klamt and G. Schüürmann, Perkin Trans. 2, 799 (1993).
- T. N. Troung and E. V. Stephanovich, J. Chem. Phys. 103, 3709 (1995).
- J. Andzelm, C. Kölmel, and A. Klamant, J. Chem. Phys. 103, 9312 (1995).
- D. York, T.-S. Lee, and W. Yang, Chem. Phys. Lett. (submitted).
- J. D. Jackson, Classical Electrodynamics (Wiley, New York, 1975).
- J. J. P. Stewart,
J. Comput. Chem. 10, 209 (1989 ). - J. J. P. Stewart,
J. Comput. Chem. 10, 221 (1989 ). - D. Fréchet et al.,
Biochemistry 33, 42 (1994 ). - M. M. Teeter, S. M. Roe, and N. H. Heo,
J. Mol. Biol. 230, 292 (1993 ). - J. Deisenhofer et al.,
Acta Crystallograph. B 31, 238 (1975 ). - D. York et al., Proc. Natl. Acad. Sci. 91, 7815 (1994).
- A. Woldawer, M. Miller, and M. Jaskólski,
Science 245, 616 (1989 ). - D. York, T. Darden, and L. Pedersen, J. Chem. Phys. 99, 8345 (1993).
- K. Harata, Acta Crystallograph. B 50, 250 (1994).
- E. F. Pai et al.,
EMBO J. 9, 2351 (1990 ). - J. L. Sussman et al.,
Science 253, 872 (1991 ). - H. Eklund, J.-P. Samama, and T. A. Jones,
Biochemistry 23, 5982 (1984 ). - H.-X. Deng et al.,
Science 261, 1047 (1993 ). - M. Newman et al.,
Science 269, 656 (1995 ). - L. Greengard,
Science 265, 909 (1994 ). - C. A. White et al.,
Chem. Phys. Lett. 230, 8 (1994 ).








