Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling

Journal of Chemical Physics

Volumn 130, Issue 23, 2009, Pages

  Zheng, Lianqing ^a   Chen, Mengen ^a   Yang, Wei ^a,b  

^a FLORIDA STATE UNIVERSITY   (United States)

^b NANKAI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COLLECTIVE VARIABLES; ENERGY SCALING; ENSEMBLE METHODS; FREE ENERGY SIMULATIONS; GENERALIZED-ENSEMBLE SIMULATION; MODEL STUDY; ORDER PARAMETER; ORTHOGONAL SPACE; RANDOM WALK; RANDOM WALK STRATEGIES; SAMPLING EFFICIENCY; SYSTEM TEMPERATURE; TARGET SYSTEMS;

ENERGY BARRIERS;

FREE ENERGY;

ALANINE; DIPEPTIDE;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; PRESSURE; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; TEMPERATURE; THERMODYNAMICS;

ALANINE; COMPUTER SIMULATION; DIPEPTIDES; MODELS, CHEMICAL; PRESSURE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; THERMODYNAMICS;

EID: 67649114369     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3153841     Document Type: Article

References (21)

1. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 0959-440X 7, 181 (1997) 10.1016/S0959-440X(97)80023-1; U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1999); K. Tai, Biophys. Chem. 0301-4622 107, 213 (2004) 10.1016/j.bpc.2003.09.010; Y. Okamoto, J. Mol. Graphics Modell. 1093-3263 22, 425 (2004) 10.1016/j.jmgm.2003.12.009; S. A. Adcock and J. A. McCammon, Chem. Rev. (Washington, D.C.) 0009-2665 106, 1589 (2006) 10.1021/cr040426m; W. Yang, H. Nymeyer, H. -X. Zhou, B. A. Berg, and R. Brüschweiler, J. Comput. Chem. 0192-8651 29, 668 (2008). 10.1002/jcc.20819
2. B. A. Berg, J. Stat. Phys. 0022-4715 82, 323 (1996). 10.1007/BF02189233
3. U. H. E. Hansmann, Eur. Phys. J. B 1434-6028 12, 607 (1999) 10.1007/s100510051044; F. G. Wang and D. P. Landau, Phys. Rev. Lett. 0031-9007 86, 2050 (2001) 10.1103/PhysRevLett.86.2050; J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 0031-9007 97, 050601 (2006) 10.1103/PhysRevLett.97.050601; H. Li, D. Min, Y. Liu, and W. Yang, J. Chem. Phys. 0021-9606 127, 094101 (2007) 10.1063/1.2769356; C. Zhang and J. Ma, Phys. Rev. E 1063-651X 76, 036708 (2007) 10.1103/PhysRevE.76.036708; F. J. Martinez-Veracoechea and F. A. Escobedo, J. Phys. Chem. B 1089-5647 112, 8120 (2008) 10.1021/jp801688p; L. Zheng and W. Yang, J. Chem. Phys. 0021-9606 129, 014105 (2008) 10.1063/1.2949815; F. A. Escobedo and F. J. Martinez-Veracoechea, J. Chem. Phys. 0021-9606 129, 154107 (2008). 10.1063/1.2994717
4. C. Bartels and M. Karplus, J. Comput. Chem. 0192-8651 18, 1450 (1997) 10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I; T. Lelievre, M. Rousset, and G. Stoltz, J. Chem. Phys. 0021-9606 126, 134111 (2007) 10.1063/1.2711185; D. Min, Y. Liu, I. Carbone, and W. Yang, J. Chem. Phys. 0021-9606 126, 194104 (2007) 10.1063/1.2731769; L. Zheng, I. O. Carbone, A. Lugovskoy, B. A. Berg, and W. Yang, J. Chem. Phys. 0021-9606 129, 034105 (2008) 10.1063/1.2953321; T. Barducci, G. Bussi, and M. Parrinello, Phys. Rev. Lett. 0031-9007 100, 020603 (2008). 10.1103/PhysRevLett.100.020603
5. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 99, 12562 (2002). 10.1073/pnas.202427399
6. D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 0021-9606 91, 7831 (1989). 10.1063/1.457251
7. X. Huang, M. Hagen, B. Kim, R. A. Friesner, R. Zhou, and B. J. Berne, J. Phys. Chem. B 1089-5647 111, 5405 (2007). 10.1021/jp068826w
8. S. Trebst, D. A. Huse, and M. Troyer, Phys. Rev. E 1063-651X 70, 046701 (2004) 10.1103/PhysRevE.70.046701; H. G. Katzgraber, S. Trebst, D. A. Huse, and M. Troyer, J. Stat. Mech: Theory Exp., P03018 (2006) 10.1088/1742-5468/2006/03/ P03018 0021-9606; S. Trebst, M. Troyer, and U. H. Hansmann, J. Chem. Phys. 0021-9606 124, 174903 (2006) 10.1063/1.2186639; F. A. Escobedo and F. J. Martinez-Veracoechea, J. Chem. Phys. 0021-9606 127, 174103 (2007) 10.1063/1.2800320; L. Zheng and W. Yang, J. Chem. Phys. 129, 124107 (2008).; E. E. Borrero and F. A. Escobedo, J. Chem. Phys. 0021-9606 129, 024115 (2008). 10.1063/1.2953325
9. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. 0021-9606 96, 1776 (1992) 10.1063/1.462133; E. Marinari and G. Parisi, Europhys. Lett. 0295-5075 19, 451 (1992) 10.1209/0295-5075/19/6/002; A. Irback and F. Potthast, J. Chem. Phys. 0021-9606 103, 10298 (1995) 10.1063/1.469931; U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 1063-651X 54, 5863 (1996) 10.1103/PhysRevE.54.5863; U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 0192-8651 18, 920 (1997) 10.1002/(SICI)1096- 987X(199705)18:7<920::AID-JCC5>3.0.CO;2-T; E. Marinari, G. Parisi, and J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by, A. P. Young, (World Scientific, Singapore, 1998), pp. 59-98; A. Irback and E. Sandelin, J. Chem. Phys. 0021-9606 110, 12256 (1999). 10.1063/1.479164
10. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 0021-9606 113, 6042 (2000) 10.1063/1.1308516; H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 0021-9606 116, 9058 (2002) 10.1063/1.1472510; S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 0031-9007 91, 058305 (2003) 10.1103/PhysRevLett.91.058305; W. Kwak and U. H. E. Hansmann, Phys. Rev. Lett. 0031-9007 95, 138102 (2005) 10.1103/PhysRevLett.95.138102; P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 102, 13749 (2005). 10.1073/pnas. 0506346102
11. L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 20227 (2008). 10.1073/pnas.0810631106
12. X. J. Kong and C. L. Brooks, J. Chem. Phys. 0021-9606 105, 2414 (1996). 10.1063/1.472109
13. H. Li, M. Fajer, and W. Yang, J. Chem. Phys. 0021-9606 126, 024106 (2007) 10.1063/1.2424700; L. Zheng, H. Li, and W. Yang, in From Computational Biophysics to Systems Biology (CBSB08), NIC Series Vol. 36, edited by, U. H. E. Hansmann, J. Meinke, S. Mohanty, W. Nadler, O. Zimmermann, (Jülich, Germany, 2008), pp. 57-64.
14. D. Min, H. Li, B. A. Berg, M. O. Fenley, and W. Yang, Chem. Phys. Lett. 0009-2614 454, 391 (2008) 10.1016/j.cplett.2008.02.055; D. Min and W. Yang, J. Chem. Phys. 0021-9606 128, 094106 (2008). 10.1063/1.2834500
15. R. Marcus, J. Chem. Phys. 0021-9606 43, 679 (1965). 10.1063/1.1696792
16. G. King and A. Warshel, J. Chem. Phys. 0021-9606 93, 8682 (1990). 10.1063/1.459255
17. J. G. Kirkwood, J. Chem. Phys. 0021-9606 3, 300 (1935). 10.1063/1.1749657
18. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
19. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 0192-8651 4, 187 (1983). 10.1002/jcc.540040211
20. A. D. MacKerell, Jr., D. Bashford, M. Bellot, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 1089-5647 102, 3586 (1998). 10.1021/jp973084f
21. A. F. Voter, Phys. Rev. Lett. 0031-9007 78, 3908 (1997) 10.1103/PhysRevLett.78.3908; M. M. Steiner, P. A. Genilloud, and J. W. Wilkins, Phys. Rev. B 0163-1829 57, 10236 (1998) 10.1103/PhysRevB.57.10236; J. A. Rahman and J. C. Tully, J. Chem. Phys. 0021-9606 116, 8750 (2002) 10.1063/1.1469605; D. Hamelberg, J. Mongan, and J. A. McCammon, J. Chem. Phys. 0021-9606 120, 11919 (2004). 10.1063/1.1755656