Extracting effective normal modes from equilibrium dynamics at finite temperature

Journal of Chemical Physics

Volumn 125, Issue 14, 2006, Pages

  Martinez, M ^a   Gaigeot, M P ^a,b   Borgis, D ^b   Vuilleumier, R ^a  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EQUILIBRIUM DYNAMICS; LIQUID WATER; PRINCIPAL MODE ANALYSIS (PMA); TIME-CORRELATION FUNCTIONS;

COMPUTER SIMULATION; CORRELATION METHODS; EXTRACTION; FOURIER TRANSFORMS; FUNCTIONS; PHASE EQUILIBRIA;

MOLECULAR DYNAMICS;

EID: 33750027973     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2346678     Document Type: Article

References (45)

1. R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985).
2. P. L. Silvestrelli, M. Bernasconi, and M. Parrinello, Chem. Phys. Lett. 277, 478 (1997).
3. V. Dubois, P. Umari, and A. Pasquarello, Chem. Phys. Lett. 390, 193 (2004).
4. J.-W. Handgraaf, E. J. Meijer, and M.-P. Gaigeot, J. Chem. Phys. 121, 10111 (2004).
5. D. E. Bikiel, F. D. Salvo, M. C. G. Lebrero, F. Doctorovich, and D. A. Estrin, Inorg. Chem. 44, 5286 (2005).
6. M. Gaigeot, R. Vuilleumier, M. Sprik, and D. Borgis, J. Chem. Theory Comput. 1, 772 (2005).
7. M.-P. Gaigeot and M. Sprik, J. Phys. Chem. B 108, 7458 (2004).
8. M.-P. Gaigeot and M. Sprik, J. Phys. Chem. B 107, 10344 (2003).
9. R. Iftimie and M. E. Tuckerman, J. Chem. Phys. 122, 214508 (2005).
10. M. Nonella, G. Mathias, and P. Tavan, J. Phys. Chem. A 107, 8638 (2003).
11. A. Putrino, D. Sebastiani, and M. Parrinello, J. Chem. Phys. 113, 7102 (2000).
12. A. Putrino and M. Parrinello, Phys. Rev. Lett. 88, 176401 (2002).
13. R. Resta, Phys. Rev. Lett. 80, 1800 (1998).
14. R. Kubo, M. Toda, and N. Hashitsume, Statistical Physics, 2nd ed. (Springer, Berlin, 1991), Vol. II.
15. J. M. Bowman, X. Zhang, and A. Brown, J. Chem. Phys. 119, 646 (2003).
16. M. Kaledin, A. Brown, A. Kaledin, and J. M. Bowman, J. Chem. Phys. 121, 5646 (2004).
17. J. Kohanoff, Comput. Mater. Sci. 2, 221 (1994).
18. G. Onida, W. Andreoni, J. Kohanoff, and M. Parrinello, Chem. Phys. Lett. 219, 1 (1994).
19. M. C. G. Lebrero, L. L. Perissinotti, and D. A. Estrin, J. Phys. Chem. A 109, 9598 (2005).
20. R. M. Stratt, Acc. Chem. Res. 28, 201 (1995).
21. M. Buchner, B. Ladanyi, and R. M. Stratt, J. Chem. Phys. 97, 8522 (1992).
22. M. Cho, G. R. Fleming, S. Saito, I. Ohmine, and R. M. Stratt, J. Chem. Phys. 100, 6672 (1994).
23. R. E. Larsen and R. M. Stratt, J. Chem. Phys. 110, 1036 (1999).
24. M. Nonella, G. Mathias, M. Eichinger, and P. Tavan, J. Phys. Chem. B 107, 316 (2003).
25. L. Pejov, D. Spangberg, and K. Hermansson, J. Phys. Chem. A 109, 5144 (2005).
26. R. M. Levy, O. de la Luz Rojas, and R. A. Friesner, J. Phys. Chem. 88, 4233 (1984).
27. R. A. Wheeler, H. Dong, and S. E. Boesch, ChemPhysChem 4, 382 (2003).
28. R. A. Wheeler and H. Dong, ChemPhysChem 4, 1227 (2003).
29. B. R. Brooks, D. Janezic, and M. Karplus, J. Comput. Chem. 16, 1522 (1995).
30. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins: Struct., Funct., Genet. 17, 412 (1993).
31. F. Tama, F. X. Gadea, O. Marques, and Y.-H. Sanejouand, Proteins: Struct., Funct., Genet. 41, 1 (2000).
32. F. Tama and Y.-H. Sanejouand, Protein Eng. 14, 1 (2001).
33. M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12247 (2004).
34. M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12233 (2004).
35. A. Strachan, J. Chem. Phys. 120, 1 (2004).
36. D. J. Evans, O. G. Jepps, and G. Ayton, Phys. Rev. E 62, 4757 (2000).
37. E. B. Wilson, J. Decius, and P. C. Cross, Molecular Vibrations (Dover, New York, 1955).
38. B. Butler, G. Ayton, O. G. Jepps, and D. J. Evans, J. Chem. Phys. 109, 6519 (1998).
39. C. Eckart, Phys. Rev. 47, 552 (1935).
40. A. D. Becke, Phys. Rev. A 38, 3098 (1988).
41. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
42. N. Troullier and J. L. Martins, Phys. Rev. B 43, 1993 (1991).
43. L. Kleinman and D. M. Bylander, Phys. Rev. Lett. 48, 1425 (1982).
44. CPMD, IBM Corp., 1990-2001/MPI für Festkörperforschung Stuttgart, 1997-2004.
45. M. Sharma, R. Resta, and R. Car, Phys. Rev. Lett. 95, 187401 (2005).