Replica-exchange molecular dynamics simulations for various constant temperature algorithms

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

Andersen algorithm; Gaussian constraint method; Generalized ensemble algorithm; Langevin dynamics; Molecular dynamics simulation; Nos Hoover thermostat; Nos Poincar thermostat; Replica exchange method

Indexed keywords

EID: 77956249820     PISSN: 00319015     EISSN: 13474073     Source Type: Journal    
DOI: 10.1143/JPSJ.79.074001     Document Type: Article

References (23)

1. A. Mitsutake, Y. Sugita, and Y. Okamoto: Biopolymers 60 (2001) 96.
2. K. Hukushima and K. Nemoto: J. Phys. Soc. Jpn. 65 (1996) 1604.
3. 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.
4. Y. Sugita and Y. Okamoto: Chem. Phys. Lett. 314 (1999) 141.
5. W. G. Hoover: Phys. Rev. A 31 (1985) 1695.
6. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller: J. Chem. Phys. 21 (1953) 1087.
7. W. G. Hoover, A. J. C. Ladd, and B. Moran: Phys. Rev. Lett. 48 (1982) 1818.
8. D. J. Evans: J. Chem. Phys. 78 (1983) 3297.
9. D. J. Evans and G. P. Morriss: Phys. Lett. A 98 (1983) 433.
10. M. P. Allen and D. J. Tildesley: Computer Simulation of Liquids (Oxford University Press, New York, 1987) p. 259.
11. H. C. Andersen: J. Chem. Phys. 72 (1980) 2384.
12. S. D. Bond, B. J. Leimkuhler, and B. B. Laird: J. Comput. Phys. 151 (1999) 114.
13. G. J. Martyna, M. L. Klein, and M. Tuckerman: J. Chem. Phys. 97 (1992) 2635.
14. S. Nosé: Mol. Phys. 52 (1984) 255.
15. S. Nosé: J. Chem. Phys. 81 (1984) 511.
16. J. W. Ponder and F. M. Richards: J. Comput. Chem. 8 (1987) 1016.
17. J. Wang, P. Cieplak, and P. A. Kollman: J. Comput. Chem. 21 (2000) 1049.
18. F. Zhang: J. Chem. Phys. 106 (1997) 6102.
19. R. Mannella: Phys. Rev. E 69 (2004) 041107.
20. G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein: Mol. Phys. 87 (1996) 1117.
21. S. Nosé: J. Phys. Soc. Jpn. 70 (2001) 75.
22. H. Okumura, S. G. Itoh, and Y. Okamoto: J. Chem. Phys. 126 (2007) 084103.
23. W. Humphrey, A. Dalke, and K. Schulten: J. Mol. Graphics 14 (1996) 33.