Journal of Chemical Physics
The Journal of Chemical Physics
Search:
   
 
 
 
Previous Article
Energy switching approach to potential surfaces. II. Two-valued function for the water molecule
A recently proposed energy switching scheme is used to improve the two-valued many-body expansion potential energy surface of Murrell, Carter, Mills, and Guest [Mol. Phys. 42, 605 (1981)] for H2O by m...
Next Article
The Cotton-Mouton effect of liquid water. Part I: The dielectric continuum model
We present a gauge-origin independent method for calculating the electric-field dependence of the molecular magnetizability—that is, the hypermagnetizability, related to the Cotton–Mouton Ef...

Fast, accurate semiempirical molecular orbital calculations for macromolecules

J. Chem. Phys. 107, 879 (1997); doi:10.1063/1.474386

Issue Date: 15 July 1997

You are not logged in to this journal. Log in

Steven L. Dixon and Kenneth M. Merz, Jr.
Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
A detailed review of the semiempirical divide-and-conquer (D&C) method is given, including a new approach to subsetting, which involves dual buffer regions. Comparisons are drawn between this method and other semiempirical macromolecular schemes. D&C calculations are carried out using a basic 32 Mbyte memory workstation on a variety of peptide systems, including proteins containing up to 1960 atoms. Aspects of storage and SCF convergence are addressed, and parallelization of the D&C algorithm is discussed. ©1997 American Institute of Physics.
History: Received 28 January 1997; accepted 9 April 1997
Permalink: http://link.aip.org/link/?JCPSA6/107/879/1
BUY THIS ARTICLE   (US$24)
Download PDF (229 kB) View Cart

KEYWORDS and PACS

Keywords
PACS
  • 36.20.-r
    Studies of special atoms, molecules, and their ions; clusters Macromolecules and polymer molecules
  • 31.15.Ne
    Electronic structure of atoms, molecules and their ions: theory Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations) Self-consistent-field methods
  • 87.15.-v
    Biological and medical physics Molecular biophysics
  • YEAR: 1996-97

PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
Publisher:
AIP is a member of CrossRef AIP

REFERENCES (37)

For access to fully linked references, you need to log in. For access to fully linked references, you need to Log in.
  1. M. J. S. Dewar and W. Thiel, J. Am. Chem. Soc. 99, 4899 (1977).
  2. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).
  3. J. J. P. Stewart, J. Comput. Chem. 10, 221 (1989).
  4. J. J. P. Stewart, in Reviews in Computational Chemistry, edited by K. B. Lipkowitz and D. B. Boyd (VCH, New York, 1990), Chap. 2.
  5. S. L. Dixon and K. M. Merz, Jr., J. Chem. Phys. 104, 6643 (1996).
  6. W. Yang and T.-S. Lee, J. Chem. Phys. 103, 5674 (1995).
  7. T.-S. Lee, D. M. York, and W. Yang, J. Chem. Phys. 105, 2744 (1996).
  8. M. J. S. Dewar, The Molecular Orbital Theory of Organic Chemistry (McGraw-Hill, New York, 1969).
  9. W. J. Hehre, L. Radom, P. v. R. Schleyer, and J. A. Pople, Ab Initio Molecular Orbital Theory (Wiley, New York, 1986).
  10. D. A. Pearlman, D. A. Case, J. C. Caldwell, G. L. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman, AMBER 4.0, University of California, San Francisco, 1991.
  11. W. Yang, Phys. Rev. Lett. 66, 1438 (1991).
  12. For a residue-based cutoff, if any two atoms located in separate amino acid units are within the cutoff, then all pairs of atoms in both residues are considered for interactions.
  13. J. J. J. P. Stewart, Int. J. Quantum Chem. 58, 133 (1996).
  14. C. A. White, B. G. Johnson, P. M. W. Gill, and M. Head-Gordon, Chem. Phys. Lett. 230, 8 (1994).
  15. M. S. Daw, Phys. Rev. B 47, 10 895 (1993).
  16. A. Gibson, R. Haydock, and J. P. LaFemina, Phys. Rev. B 47, 9229 (1993).
  17. X.-P. Li, R. W. Nunes, and D. Vanderbilt, Phys. Rev. B 47, 10 891 (1993).
  18. P. Ordejón and D. A. Drabold, Phys. Rev. B 48, 14 646 (1993).
  19. W. Kohn, Int. J. Quantum Chem. 56, 229 (1995).
  20. C. C. J. Roothaan, Rev. Mod. Phys. 23, 69 (1951).
  21. G. H. Golub and C. F. Van Loan, Matrix Computations (The Johns Hopkins University Press, Baltimore, 1983).
  22. P. Badziag and F. Solms, Comput. Chem. 12, 233 (1988).
  23. A. V. Mitin, J. Comput. Chem. 9, 107 (1988).
  24. P. Pulay, Chem. Phys. Lett. 73, 393 (1980).
  25. R. N. Camp and H. F. King, J. Chem. Phys. 75, 268 (1981).
  26. A. L. Lehninger, Biochemistry (Worth, New York, 1978), Chap. 6.
  27. J. J. P. Stewart, MOPAC 7.0, Quantum Chemistry Program Exchange, Program 455, Indiana University, Bloomington, Indiana, 1993.
  28. J. Bentz, D. Alford, and H. Ellens, in The Structure of Biological Membranes (Chemical Rubber, Boca Raton, 1992), Chap. 20.
  29. H. Hope, Acta Crystallogr. B 44, 22 (1988).
  30. A. Wlodawer, J. Deisenhofer, and R. Huber, J. Mol. Biol. 193, 145 (1987).
  31. R. J. Almassy, J. C. Fontecilla-Camps, F. L. Suddath, and C. E. Bugg, J. Mol. Biol. 170, 497 (1983).
  32. J. Sevcik, E. J. Dodson, and G. G. Dodson, Acta Crystallogr. B 47, 240 (1991).
  33. J. Koepke, M. Maslowska, U. Heineman, and W. Saenger, J. Biol. Chem. 263, 15 358 (1988).
  34. A. C. M. Young, R. F. Tilton, and J. C. Dewan, J. Mol. Biol. 235, 302 (1994).
  35. J. J. Vincent, S. L. Dixon, and K. M. Merz, Jr. (in preparation).
  36. A. van der Vaart, S. L. Dixon, and K. M. Merz, Jr. (in preparation).
  37. M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids (Oxford University Press, New York, 1994).

CITING ARTICLES

For access to citing articles, you need to log in.
For access to citing articles, you need to Log in.