Ab initio molecular dynamics with born-oppenheimer and extended Lagrangian methods using atom centered basis functions

Bulletin of the Korean Chemical Society

Volumn 24, Issue 6, 2003, Pages 837-842

  Schlegel, H Bernhard ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

Ab initio molecular dynamics; ADMP; Born Oppenheimer dynamics; Direct classical trajectory calculations; Extended Lagrangian dynamics

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ATOM; BORN OPPENHEIMER METHOD; CALCULATION; COMPUTER SIMULATION; CONFERENCE PAPER; ELECTRONICS; ENERGY; LAGRANGIAN METHOD; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOTION;

EID: 0041565310     PISSN: 02532964     EISSN: None     Source Type: Journal    
DOI: 10.5012/bkcs.2003.24.6.837     Document Type: Conference Paper

References (84)

1. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, England, 1987.
2. Haile, J. M. Molecular Dynamics Simulation: Elementary Methods; Wiley: New York, 1992.
3. Thompson, D. L. Trajectory Simulations of Molecular Collisions: Classical treatment, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer III, H. F., Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 5, pp 3056-3073.
4. Advances in Classical Trajectory, Methods; Hase, W. L., Ed.; JAI Press: Greenwich, 1992.
5. Bunker, D. L. Meth. Compre. Phys. 1971, 10, 287.
6. Raff, L. M.; Thompson, D. L. The Classical Trajectory Approach to Reactive Scattering, in Theory of Chemical Reaction Dynamics; Baer, M., Ed.; CRC Press: Boca Raton, 1985.
7. Rapaport, D. C. The Art of Molecular Dynamics Simulation; Cambridge University Press: Cambridge: New York, 1995.
8. Frenkel, D.; Smit, B. Understanding Molecular Simulation: from Algorithms to Applications, 2nd ed.; Academic Press: San Diego, 2002.
9. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge Cambridgeshire, New York, 1987.
10. Gunsteren, W. F. v.; Weiner, P. K.; Wilkinson, A. J.; Alliant Computer Systems Corporation. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; ESCOM: Leiden, 1989.
11. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
12. Beveridge, D. L.; Dicapua, F. M. Annual Review of Biophysics and Biophysical Chemistry 1989, 18, 431-492.
13. Beveridge, D. L. Molecular Dynamics: DNA, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer III, H. F., Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 3, pp 1620-1628.
14. Auffinger, P.; Weshof, E. Molecular Dynamics: Simulation of Nucleic Acids, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T, Schaefer III, H. F., Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 3, pp 1628-1639.
15. Berendsen, H. J. C.; Tieleman, D. P. Molecular Dynamics: Studies of Lipid Bilayers, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer III, H. F., Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 3, pp 1639-1650.
16. Pedersen, L.; Darden, T Molecular Dynamics: Techniques and Applications to Proteins, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T, Schaefer III, H. F., Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 3, pp 1650-1659.
17. Schatz, G. C. Rev. Mod. Phys. 1989, 61, 669-688.
18. Schatz, G. C. The Analytical Representation of Potential Energy Surfaces for Chemical Reactions, in Advances in Molecular Electronic Structure Theory; Dunning, T. H., Ed.; JAI Press: London, 1990.
19. Bolton, K.; Hase, W. L.; Peslherbe, G. H. Direct Dynamics of Reactive Systems, in Modern Methods for Multidimensional Dynamics Computation in Chemistry; Thompson, D. L., Ed.; World Scientific: Singapore, 1998; pp 143-189.
20. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
21. Press, W. H. Numerical Recipes in FORTRAN: The Art of Scientific Computing. 2nd ed.; Cambridge University Press: Cambridge, England; New York, NY, 1992.
22. Helgaker, T.; Uggerud, E.; Jensen, H. J. A. Chem. Phys. Lett. 1990, 173, 145-150.
23. Uggerud, E.; Helgaker, T. J. Am. Chem. Soc. 1992, 114, 4265-4268.
24. Braten, S. M.; Helgaker, T.; Uggerud, E. Org. Mass Spectrom. 1993, 28, 1262-1269.
25. Bueker, H. H.; Uggerud, E. J. Phys. Chem. 1995, 99, 5945-5949.
26. Bueker, H. H.; Helgaker, T.; Ruud, K.; Uggerud, E. J. Phys. Chem. 1996, 100, 15388-15392.
27. Oiestad, A. M. L.; Uggerud, E. Int. J. Mass Spectrom. 1997, 167, 117-126.
28. Oiestad, E. L.; Uggerud, E. Int. J. Mass Spectrom. 1997, 165, 39-47.
29. Ruud, K.; Helgaker, T.; Uggerud, E. Theochem-J. Mol. Struct. 1997, 393, 59-71,
30. Uggerud, E. Mass Spectrom. Rev. 1999, 18, 285-308.
31. Chen, W.; Hase, W. L.; Schlegel, H. B. Chem. Phys. Lett. 1994, 228, 436-442.
32. Millam, J. M.: Bakken, V.; Chen, W.; Hase, W. L.; Schlegel, H. B. J. Chem. Phys. 1999, 111, 3800-3805.
33. Bakken, V.; Millam, J. M.; Schlegel, H. B. J. Chem. Phys. 1999, 111, 8773-8777.
34. Schlegel, H. B. Geometry Optimization, in Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer III, H. E, Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 2, pp 1136-1142.
35. Schlegel, H. B. Geometry Optimization on Potential Energy Surfaces, in Modern Electronic Structure Theory; Yarkony, D. R., Ed.: World Scientific Publishing: Singapore, 1995; pp 459-500.
36. Bofill, J. M. J. Comput. Chem. 1994, 15, 1-11.
37. Vreven, T; Bernardi, F.; Garavelli, M.; Olivucci, M.; Robb, M. A.; Schlegel, H. B. J. Am. Chem. Soc. 1997, 119, 12687-12688.
38. Bolton, K.; Hase, W. L.; Schlegel, H. B.; Song, K. Chem. Phys. Lett. 1998, 288, 621-627.
39. Bolton, K.; Schlegel, H. B.; Hase, W. L.; Song, K. Y. Phys. Chem. Chem. Phys. 1999, 1, 999-1011.
40. Sanchez-Galvez, A.; Hunt, P.; Robb, M. A.; Olivucci, M.; Vreven, T.; Schlegel, H. B. J. Am. Chem. Soc. 2000, 122, 2911-2924.
41. Li, X. S.; Millam, J. M.; Schlegel, H. B. J. Chem. Phys. 2000, 113, 10062-10067.
42. Bakken, V.; Danovich, D.; Shaik, S.; Schlegel, H. B. J. Am. Chem. Soc. 2001, 123, 130-134.
43. Li, X. S.; Millam, J. M.;: Schlegel, H. B. J. Chem. Phys. 2001, 114, 8897-8904.
44. Li, X. S.; Millam, J. M.; Schlegel, H. B. J. Chem. Phys. 2001, 115, 6907-6912.
45. Li, X. S.; Anand, S.; Millam, J. M.; Schlegel, H. B. Phys. Chem. Chem. Phys. 2002, 4, 2554-2559.
46. Anand, S.; Schlegel, H. B. J. Phys. Chem. A 2002, 106, 11623-11629.
47. Collins, M. A. Theor. Chem. Acc. 2002, 108, 313-324.
48. Ischtwan, J.; Collins, M. A. J. Chem. Phys. 1994, 100, 8080-8088.
49. Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 103, 9669-9675.
50. Thompson, K. C.; Collins, M. A. J. Chem. Soc.-Faraday Trans. 1997, 93, 871-878.
51. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302-8316.
52. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 564-578.
53. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816-826.
54. Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647-5657.
55. Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1996, 104, 4600-4610.
56. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1998, 109, 9728-9736.
57. Bettens, R. P. A.; Hansen, T. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 6322-6332.
58. Collins, M. A.; Zhang, D. H. J. Chem. Phys. 1999, 111, 9924-9931.
59. Fuller, R. O.; Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 2001, 114, 10711-10716.
60. Song, K. Y.: Collins, M. A. Chem. Phys. Lett. 2001, 335, 481-488.
61. Remler, D. K.; Madden, P. A. Mol. Phys. 1990, 70, 921-966.
62. Payne, M. C.; Teter, M. P.; Allan, D. C.; Arias, T. A.; Joannopoulos, J. D. Rev. Mol. Phys. 1992, 64, 1045-1097.
63. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Theory and Implementation, in Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John von Neumann Institute for Computing: Julich, 2000; Vol. 1, pp 301-449.
64. Tuckerman, M. E.; Parrinello, M. J. Chem. Phys. 1994, 101, 1302-1315.
65. Tuckerman, M. E.; Parrinello, M. J. Chem. Phys. 1994, 101, 1316-1329.
66. Rothlisberger, U. Computational Chemistry 2001, 6, 33-68.
67. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; Wiley: New York, 1986.
68. Foresman, J. B.; Frisch, A. Exploring Chemistry with Electronic Structure Methods, 2nd ed.; Gaussian Inc.: Pittsburgh, PA, 1996.
69. Jensen, F. Introduction to Computational Chemistry; Wiley: Chichester, New York, 1999.
70. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models; J. Wiley: West Sussex, England, New York, 2002.
71. Goedecker, S. Rev. Mod. Phys. 1999, 71, 1085-1123.
72. Scuseria, G. E. J. Phys. Chem. A 1999, 103, 4782-4790.
73. Li, X. P.; Nunes, W.; Vanderbilt, D. Phys. Rev. B 1993, 47, 10891-10894.
74. Schlegel, H. B.; Millam, J. M.; Iyengar, S. S.; Voth, G. A.; Daniels, A. D.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 2001, 114. 9758-9763.
75. Iyengar, S. S.; Schlegel, H. B.; Millam, J. M.; Voth, G. A.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 2001, 115, 10291-10302.
76. Schlegel, H. B.; Iyengar, S. S.; Li, X.; Millam, J. M.; Voth, G. A.; Scuseria, G. E.; Frisch, M. J. J. Chem. Phys. 2002, 177, 8694-8704.
77. Millam, J. M.; Scuseria, G. E. J. Chem. Phys. 1997, 106, 5569-5577.
78. McWeeny, R. Rev. Mod. Phys. 1960, 32, 335-339.
79. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649.
80. Hartke, B.; Carter, E. A. J. Chem. Phys. 1992, 97, 6569-6578.
81. Hartke, B.; Carter, E. A. Chem. Phys. Lett. 1992, 189, 358-362.
82. Gibson, D. A.; Carter, E. A. J. Phys. Chem. 1993, 97, 13429-13434.
83. Gibson, D. A.; Ionova, I. V.; Carter, E. A. Chem. Phys. Lett. 1995, 240. 261-267.
84. Tangney, P.; Scandolo, S. J. Chem. Phys. 2002, 116, 14-24.