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Quantitative harmonization of the three molecular orbital, valence bond, and broken symmetry approaches to the exchange coupling constant: Corrections and discussion
Three current methods, used to evaluate exchange coupling constants in molecular magnetism, i.e., the molecular orbital (MO) model [Hay et al., J. Am. Chem. Soc. 94, 4884 (1975)], the valence bond (VB...
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Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems

J. Chem. Phys. 113, 10512 (2000); doi:10.1063/1.1323257

Issue Date: 15 December 2000

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Arjan van der Vaart, Dimas Suárez, and Kenneth M. Merz, Jr.
Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802-6300
We present a detailed analysis of the performance of the semiempirical divide and conquer method as compared with standard semiempirical MO calculations. The influence of different subsetting schemes involving dual buffer regions on the magnitude of the errors in energies and computational cost of the calculations are discussed. In addition, the results of geometry optimizations on several protein systems (453 to 4088 atoms) driven by a quasi-Newton algorithm are also presented. These results indicate that the divide and conquer approach gives reliable energies and gradients and suggest that protein geometry optimization using semiempirical methods can be routinely feasible using current computational resources. ©2000 American Institute of Physics.
History: Received 4 August 2000; accepted 15 September 2000
Permalink: http://link.aip.org/link/?JCPSA6/113/10512/1
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KEYWORDS and PACS

Keywords
PACS
  • 31.15.Ct
    Electronic structure of atoms, molecules and their ions: theory Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations) Semi-empirical and empirical calculations (differential overlap, Hückel, PPP methods, etc.)
  • 87.15.By
    Biological and medical physics Biomolecules: structure and physical properties Structure and bonding
  • YEAR: 2000

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0021-9606 (print)   1089-7690 (online)
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REFERENCES (47)
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  1. S. Goedecker, Rev. Mod. Phys. 71, 1085 (1999).
  2. G. Galli, Phys. Status Solidi B 217, 231 (2000).
  3. P. Ordejón, Phys. Status Solidi B 217, 335 (2000).
  4. A. van der Vaart, V. Gogonea, S. L. Dixon, and K. M. Merz, Jr., J. Comput. Chem. (in press).
  5. X.-P. Li, R. W. Nunes, and D. Vanderbilt, Phys. Rev. B 47, 10891 (1993).
  6. R. W. Nunes and D. Vanderbilt, Phys. Rev. B 50, 17611 (1994).
  7. A. D. Daniels, J. M. Millam, and G. E. Scuseria, J. Chem. Phys. 107, 425 (1997).
  8. J. M. Millam and G. E. Scuseria, J. Chem. Phys. 106, 5569 (1997).
  9. M. Challacombe, J. Chem. Phys. 110, 2332 (1999).
  10. J. P. Stewart, J. Mol. Struct.: THEOCHEM 401, 195 (1997).
  11. J. J. P. Stewart, Int. J. Quantum Chem. 58, 133 (1996).
  12. W. Yang, Phys. Rev. Lett. 66, 1438 (1991).
  13. W. Yang and T.-S. Lee, J. Chem. Phys. 103, 5674 (1995).
  14. S. L. Dixon and K. M. Merz, Jr., J. Chem. Phys. 104, 6643 (1996).
  15. S. L. Dixon and K. M. Merz, Jr., J. Chem. Phys. 107, 879 (1997).
  16. R. McWeeny, Rev. Mod. Phys. 32, 335 (1960).
  17. J. J. Vincent, S. L. Dixon, and K. M. Merz, Jr., Theor. Chem. Acc. 99, 220 (1998).
  18. W. Pan, T.-S. Lee, and W. Yang, J. Comput. Chem. 19, 1101 (1998).
  19. T.-S. Lee and W. Yang, Int. J. Quantum Chem. 69, 397 (1998).
  20. M. D. Ermolaeva, A. van der Vaart, and K. M. J. Merz, J. Phys. Chem. 103, 1868 (1999).
  21. A. van der Vaart and K. M. Merz, Jr., J. Phys. Chem. A 103, 3321 (1999).
  22. V. Gogonea, L. M. Westerhoff, and K. M. Merz, Jr., J. Chem. Phys. 113, 1 (2000).
  23. A. D. Daniels, G. E. Scuseria, O. Farkas, and H. B. Schlegel, Int. J. Quantum Chem. 77, 82 (2000).
  24. S. L. Dixon, A. van der Vaart, V. Gogonea, J. J. Vincent, E. N. Brothers, D. Suárez, L. M. Westerhoff, and K. M. Merz, Jr., DIVLON 99, The Pennsylvania State University, 1999.
  25. M. J. S. Dewar and D. A. Liotard, J. Mol. Struct. 206, 123 (1990).
  26. Q. Zhao and W. Yang, J. Chem. Phys. 102, 9598 (1995).
  27. W. L. Jorgensen, J. Chandrasekhar, J. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
  28. G. Nadig, L. C. van Zant, S. L. Dixon, and K. M. Merz, Jr., J. Am. Chem. Soc. 120, 5593 (1998).
  29. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).
  30. D. C. Liu and J. Nocedal, Math. Program. 45, 503 (1989).
  31. J. Nocedal, Math. Comput. 35, 773 (1980).
  32. C. Baysal, H. Meirovitch, and I. M. Navon, J. Comput. Chem. 20, 354 (1999).
  33. E. N. Brothers and K. M. Merz, Jr. (unpublished).
  34. C. Schafmeister, W. S. Ross, and V. Romanovski, LEAP 10 (University of California, San Francisco, 1995).
  35. D. A. Case, D. A. Pearlman, J. W. Caldwell et al., AMBER 5.0 ed. (University of California, San Francisco, 1997).
  36. W. D. Cornell, P. Cieplak, C. I. Bayly et al., J. Am. Chem. Soc. 117, 5179 (1995).
  37. A. Cheng, R. S. Stanton, J. J. Vincent et al., ROAR 2.0 ed., The Pennsylvania State University, 1999.
  38. D. M. York, T.-S. Lee, and W. Yang, Phys. Rev. Lett. 80, 5011 (1998).
  39. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
  40. F. Sicheri and D. S. C. Yang, Nature (London) 375, 427 (1995).
  41. M. M. Teeter, S. M. Roe, and N. H. Heo, J. Mol. Biol. 230, 292 (1993).
  42. C. Van Alsenoy, Y. Ching-Hsing, A. Peeters, J. M. L. Martin, and L. Schäfer, J. Phys. Chem. A 102, 2245 (1998).
  43. G. J. Hoover, N. Menhart, A. Martin, S. Warder, and F. J. Castellino, Biochemistry 32, 10936 (1993).
  44. O. Farkas and H. B. Schlegel, J. Chem. Phys. 111, 10806 (1999).
  45. O. Farkas and H. B. Schlegel, J. Chem. Phys. 109, 7100 (1998).
  46. M. C. Vaney, S. Maignan, M. Ries-Kautt, and A. Ducruix, Acta Crystallogr., Sect. D: Biol. Crystallogr. 52, 505 (1996).
  47. D. E. Kuehner, J. Engmann, F. Fergg, M. Wernick, H. W. Blanch, and J. M. Prausnitz, J. Phys. Chem. B 103, 1368 (1999).

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