Rugged Metropolis sampling with simultaneous updating of two dynamical variables

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 72, Issue 1, 2005, Pages

  Berg, Bernd A ^a,b   Zhou, Huan Xiang ^a,b  

^a Florida State University   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIHEDRAL ANGLES; RUGGED METROPOLIS (RM) ALGORITHM;

ALGORITHMS; CORRELATION METHODS; SAMPLING;

FREE ENERGY;

METENKEPHALIN; PEPTIDE;

ALGORITHM; ANIMAL; BIOPHYSICS; BRAIN; CHEMICAL MODEL; CHEMISTRY; COMPUTER; COMPUTER SIMULATION; CONFORMATION; HUMAN; METABOLISM; MONTE CARLO METHOD; PROCEDURES; PROTEIN CONFORMATION; PROTEIN FOLDING; STATISTICAL MODEL; TEMPERATURE; THEORETICAL MODEL; THERMODYNAMICS; TIME;

ALGORITHMS; ANIMALS; BIOPHYSICS; BRAIN; COMPUTER SIMULATION; COMPUTERS; ENKEPHALIN, METHIONINE; HUMANS; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; MONTE CARLO METHOD; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; TEMPERATURE; THERMODYNAMICS; TIME FACTORS;

EID: 27244461072     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.72.016712     Document Type: Article

References (26)

1. B. A. Berg, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90. 180601 90, 180601 (2003).
2. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 84, 7524 (1987).
3. W. K. Hastings, Biometrika BIOKAX 0006-3444 57, 97 (1970).
4. A. D. Bruce, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/18/14/009 18, L873 (1985).
5. A. Milchev, D. W. Heermann, and K. Binder, J. Stat. Phys. JSTPBS 0022-4715 10.1007/BF01011906 44, 749 (1986).
6. M. W. Deem and J. S. Bader, Mol. Phys. MOPHAM 0026-8976 10.1080/00268979650026785 87, 1245 (1996).
7. G. Favrin, A. Irbäck, and F. Sjunnesson, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1364637 114, 8154 (2001).
8. J. P. Ulmschneider and W. L. Jorgensen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1542611 118, 4261 (2003).
9. A. Bazavov and B. A. Berg, Phys. Rev. D PRVDAQ 0556-2821 10.1103/PhysRevD.71.114506 71, 114506 (2005).
10. G. La Penna, S. Morante, A. Perico, and G. C. Rossi, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1795694 121, 10725 (2004);
11. B. Berg, H. Noguchi, and Y. Okamoto, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.036126 68, 036126 (2003);
12. U. H. E. Hansmann, Physica A PHYADX 0378-4371 10.1016/S0378-4371(02) 01764-8 321, 152 (2003);
13. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers BIPMAA 0006-3525 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F 60, 96 (2001).
14. N. Go and H. A. Scheraga, Macromolecules MAMOBX 0024-9297 3, 178 (1970).
15. Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 85, 6611 (1987).
16. U. H. Hansmann, M. Masuya, and Y. Okamoto, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.20.10652 94, 10652 (1997).
17. N. A. Alves and U. H. Hansmann, Int. J. Mod. Phys. C IJMPEO 0129-1831 10.1142/S0129183100000274 11, 301 (2000).
18. B. A. Berg, Markov Chain Monte Carlo Simulations and Their Statistical Analysis (World Scientific, Singapore, 2004).
19. M. J. Sippl, G. Nemethy, and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 88, 6231 (1984) and references given therein.
20. F. Eisenmenger, U. H. Hansmann, S. Hayryan, and C.-K. Hu, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/S0010-4655(01)00197-7 138, 192 (2001).
21. G. E. Schultz and R. H. Schirmer, Principle of Protein Structure (Springer, New York, 1979).
22. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic Press, San Diego, 1996).
23. B. A. Berg and H.-P. Hsu, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.69.026703 69, 026703 (2004).
24. Y. Peng, U. H. Hansmann, and N. A. Alves, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1532348 118, 2374 (2003);
25. Y. Peng and U. H. Hansmann, Biophys. J. BIOJAU 0006-3495 82, 3269 (2003).
26. D. Bouzida, S. Kumar, and R. Swendsen, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.45.8894 45, 8894 (1992).