Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials

Journal of Computational Chemistry

Volumn 26, Issue 7, 2005, Pages 699-707

  Olano, L Renee ^a   Rick, Steven W ^a  

^a UNIVERSITY OF NEW ORLEANS   (United States)

Author keywords

Extended Lagrangian; Fluctuating charge models; Molecular dynamics; Polarizable force fields

Indexed keywords

EXTENDED LAGRANGIAN; FLUCTUATING CHARGE MODELS; FLUCTUATING DYNAMICS; POLARIZABLE FORCE FIELDS;

ALGORITHMS; COMPUTER SIMULATION; GROUND STATE; INTEGRATION; LAGRANGE MULTIPLIERS; MATHEMATICAL MODELS;

MOLECULAR DYNAMICS;

EID: 18744395785     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20212     Document Type: Article

References (38)

1. Rick, S. W.; Stuart, S. J. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; Wiley; New York, 2002, p. 89.
2. Car, R.; Parrinello, M. Phys Rev Lett 1985, 55, 2471.
3. Vassilev, P.; Hartnig, C.; Koper, M. T. M.; Frechard, F.; van Santen, R. A. J Chem Phys 2001, 115, 9815.
4. Kolafa, J. J Comput Chem 2004, 25, 335.
5. Rick, S. W.; Stuart, S. J.; Berne, B. J. J Chem Phys 1994, 101, 6141.
6. Rick, S. W.; Berne, B. J. J Phys Chem B 1997, 101, 10488.
7. Rick, S. W.; Berne, B. J. J Am Chem Soc 1996, 118, 672.
8. Ribeiro, M. C. C.; Almeida, L. C. J. J Chem Phys 1999, 110, 11445.
9. Stern, H. A.; Rittner, F.; Berne, B. J.; Friesner, R. A. J Chem Phys 2001, 115, 2237.
10. Patel, S.; Brooks, III, C. L. J Comput Chem 2004, 25, 1.
11. Patel, S.; Mackerell, A. D.; Brooks, III, C. L. J Comput Chem 2004, 25, 1504.
12. Guilot, B.; Guissani, Y.; Bratos, S. J Chem Phys 1991, 95, 3643.
13. Guillot, B.; Guissani, Y. J Chem Phys 2001, 114, 6720.
14. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J Chem Phys 1994, 100, 9025.
15. Lüdemann, S.; Schreiber, H.; Abseher, R.; Steinhauser, O. J Chem Phys 1996, 104, 286.
16. Paschek, D. J Chem Phys 2004, 120, 10605.
17. Watanabe, K.; Klein, M. L. Chem Phys 1989, 131, 157.
18. Asthagiri, D.; Pratt, L. R.; Kress, J. D. Phys Rev E 2003, 68, 041505.
19. Grossman, J. C.; Schwegler, E.; Draegler, E. W.; Gygi, F.; Galli, G. J Chem Phys 2004, 120, 300.
20. Silvestrelli, P. L.; Parrinello, M. J Chem Phys 1999, 111, 3572.
21. Laasonen, K.; Sprik, M.; Parrinello, M.; Car, R. J Chem Phys 1993, 99, 9080.
22. Izvekov, S.; Voth, G. A. J Chem Phys 2002, 116, 10372.
23. Pastore, G.; Smargiassi, E.; Buda, F. Phys Rev A 1991, 44, 6334.
24. Tangney, P.; Scandolo, S. J Chem Phys 2002, 116, 14.
25. Toukmaji, A.; Sagui, C.; Board, J.; Darden, T. J Chem Phys 2000, 113, 10913.
26. Genzer, J.; Kolafa, J. J Mol Liq 2004, 109, 63.
27. Stuart, S. J.; Berne, B. J. J Phys Chem 1996, 100, 11934.
28. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J Chem Phys 1992, 97, 1990.
29. Rick, S. W.; Cachau, R. E. J Chem Phys 2000, 112, 5230.
30. Goldstein, H. Classical Mechanics, Second Edition; Addison-Wesley: Reading, MA, 1980.
31. Nosé, S. Mol Phys 1984, 52, 255.
32. Hoover, W. G. Phys Rev A 1985, 31, 1695.
33. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J Chem Phys 1994, 101, 4177.
34. Allen, L. C. Acc Chem Res 1990, 23, 175.
35. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madera, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. J. J Chem Phys 2004, 120, 9665.
36. Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. V. Numerical Recipes; Cambridge University Press: Cambridge, 1986.
37. Rick, S. W. J Chem Phys 2001, 114, 2276.
38. Stöckelmann, E.; Hentschke, R. J Chem Phys 1999, 110, 12097.