Comparison of sampling efficiency between simulated tempering and replica exchange

Journal of Chemical Physics

Volumn 129, Issue 13, 2008, Pages

  Zhang, Cheng ^a   Ma, Jianpeng ^a,b  

^a Rice University   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SEPARATION;

ENERGY SPACES; PARTITION FUNCTIONS; REPLICA EXCHANGE; SAMPLING EFFICIENCY; SIMULATED TEMPERING; TEMPERATURE TRANSITIONS;

TEMPERING;

ALGORITHM; ARTICLE; COMPARATIVE STUDY; MONTE CARLO METHOD; TRANSITION TEMPERATURE;

ALGORITHMS; MONTE CARLO METHOD; TRANSITION TEMPERATURE;

EID: 53449094445     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2988339     Document Type: Article

References (11)

1. E. Marinari and G. Parisi, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/19/6/002 19, 451 (1992); A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.462133 96, 1776 (1991).
2. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986); C. J. Geyer, Proceedings of the 23rd Symposium on the Interface (American Statistical Association, New York, 1991); K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. JUPSAU 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996); U. H. E. Hansmann, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997).
3. S. Park and V. S. Pande, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.76.016703 76, 016703 (2007).
4. C. Zhang and J. P. Ma, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.76. 036708 76, 036708 (2007).
5. D. A. Kofke, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1507776 117, 6911 (2002).
6. A. Kone and D. A. Kofke, J. Chem. Phys. JCPSA6 0021-9606 122, 206101 (2005); D. J. Earl and M. W. Deem, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0376626 108, 6844 (2004); D. J. Earl and M. W. Deem, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b509983h 7, 3910 (2005); D. M. Zuckerman and E. Lyman, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct600297q 2, 1693 (2006); W. Nadler and U. H. E. Hansmann, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.76.065701 76, 065701 (R) (2007); S. Trebst, D. A. Huse, and M. Troyer, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.046701 70, 046701 (2004); S. Trebst, M. Troyer, and U. H. E. Hansmann, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2186639 124, 174903 (2006); H. G. Katzgraber, S. Trebst, D. A. Huse, and M. Troyer, J. Stat. Mech.: Theory Exp. ZZZZZZ 1742-5468 P03018 (2006); H. Nymeyer, IEEE Trans. Compon. Packag. Technol. ITCPFB 1521-3331 4, 626 (2008).
7. N. Rathore, M. Chopra, and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1831273 122, 024111 (2005); W. Nadler and U. H. E. Hansmann, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.75.026109 75, 026109 (2007).
8. S. Park, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.77.016709 77, 016709 (2008).
9. D. Sindhikara, Y. L. Meng, and A. E. Roitberg, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2816560 128, 024103 (2008).
10. M. J. Abraham and J. E. Gready, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct800016r 4, 1119 (2008).
11. M. E. J. Newman and G. T. Barkema, Monte Carlo Methods in Statistical Physics (Clarendon, Oxford University Press, Oxford, NY, 1999).