Generalized-ensemble algorithms for the isobaric-isothermal ensemble

Journal of the Physical Society of Japan

Volumn 79, Issue 7, 2010, Pages

  Mori, Yoshiharu ^a   Okamoto, Yuko ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Generalized ensemble algorithm; Isobaric isothermal ensemble; Molecular dynamics simulation; Monte Carlo simulation; Multibaric multithermal algorithm; Replicaexchange method; Simulated tempering

Indexed keywords

EID: 77956248445     PISSN: 00319015     EISSN: 13474073     Source Type: Journal    
DOI: 10.1143/JPSJ.79.074003     Document Type: Article

References (44)

1. A. Mitsutake, Y. Sugita, and Y. Okamoto: Biopolymers 60 (2001) 96.
2. B. A. Berg and T. Neuhaus: Phys. Lett. B 267 (1991) 249.
3. B. A. Berg and T. Neuhaus: Phys. Rev. Lett. 68 (1992) 9.
4. U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger: Chem. Phys. Lett. 259 (1996) 321.
5. N. Nakajima, H. Nakamura, and A. Kidera: J. Phys. Chem. B 101 (1997) 817.
6. K. Hukushima and K. Nemoto: J. Phys. Soc. Jpn. 65 (1996) 1604.
7. E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo: in Spin Glasses and Random Fields, ed. A. P. Young (World Scientific, Singapore, 1998) p. 59.
8. Y. Sugita and Y. Okamoto: Chem. Phys. Lett. 314 (1999) 141.
9. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov: J. Chem. Phys. 96 (1992) 1776.
10. E. Marinari and G. Parisi: Europhys. Lett. 19 (1992) 451.
11. A. Mitsutake and Y. Okamoto: Phys. Rev. E 79 (2009) 047701.
12. A. Mitsutake and Y. Okamoto: J. Chem. Phys. 130 (2009) 214105.
13. A. Mitsutake: J. Chem. Phys. 131 (2009) 094105.
14. H. Okumura and Y. Okamoto: Chem. Phys. Lett. 383 (2004) 391.
15. H. Okumura and Y. Okamoto: Phys. Rev. E 70 (2004) 026702.
16. H. Okumura and Y. Okamoto: Chem. Phys. Lett. 391 (2004) 248.
17. H. Okumura and Y. Okamoto: J. Comput. Chem. 27 (2006) 379.
18. T. Nishikawa, H. Ohtsuka, Y. Sugita, M. Mikami, and Y. Okamoto: Prog. Theor. Phys. Suppl. 138 (2000) 270.
19. T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami: Chem. Phys. Lett. 335 (2001) 435.
20. Y. Sugita and Y. Okamoto: in Lecture Notes in Computational Science and Engineering, ed. T. Schlick and H. H. Gan (Springer, Berlin, 2002) p. 303; cond-mat/0102296.
21. D. Paschek and A. E. García: Phys. Rev. Lett. 93 (2004) 238105.
22. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller: J. Chem. Phys. 21 (1953) 1087.
23. I. R. McDonald: Mol. Phys. 23 (1972) 41.
24. G. J. Martyna, D. J. Tobias, and M. L. Klein: J. Chem. Phys. 101 (1994) 4177.
25. S. Nosé: Mol. Phys. 52 (1984) 255.
26. S. Nosé: J. Chem. Phys. 81 (1984) 511.
27. W. G. Hoover: Phys. Rev. A 31 (1985) 1695.
28. H. C. Andersen: J. Chem. Phys. 72 (1980) 2384.
29. Y. Mori and Y. Okamoto: J. Phys. Soc. Jpn. 79 (2010) 074001.
30. Y. Sugita and Y. Okamoto: Chem. Phys. Lett. 329 (2000) 261.
31. A. Mitsutake and Y. Okamoto: Chem. Phys. Lett. 332 (2000) 131.
32. A. M. Ferrenberg and R. H. Swendsen: Phys. Rev. Lett. 63 (1989) 1195.
33. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg: J. Comput. Chem. 13 (1992) 1011.
34. J. W. Ponder and F. M. Richards: J. Comput. Chem. 8 (1987) 1016.
35. J. Wang, P. Cieplak, and P. A. Kollman: J. Comput. Chem. 21 (2000) 1049.
36. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein: J. Chem. Phys. 79 (1983) 926.
37. T. Darden, D. York, and L. Pedersen: J. Chem. Phys. 98 (1993) 10089.
38. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen: J. Chem. Phys. 103 (1995) 8577.
39. G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein: Mol. Phys. 87 (1996) 1117.
40. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen: J. Comput. Phys. 23 (1977) 327.
41. H. C. Andersen: J. Comput. Phys. 52 (1983) 24.
42. A. M. Ferrenberg and R. H. Swendsen: Phys. Rev. Lett. 61 (1988) 2635
43. [Errata; 63 (1989) 1658].
44. H. Okumura and Y. Okamoto: J. Phys. Chem. B 112 (2008) 12038.