Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer

Journal of Chemical Physics

Volumn 139, Issue 5, 2013, Pages

  Fujisaki, Hiroshi ^a,b   Shiga, Motoyuki ^c   Moritsugu, Kei ^b,d   Kidera, Akinori ^b,d  

^a NIPPON MEDICAL SCHOOL   (Japan)

^b RIKEN   (Japan)

^c JAPAN ATOMIC ENERGY AGENCY   (Japan)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BOLTZMANN WEIGHTS; CONVENTIONAL TRANSITIONS; COUPLING STRENGTHS; ENHANCED SAMPLINGS; LANGEVIN DYNAMICS; MOLECULAR SYSTEMS; ORIGINAL SYSTEMS; PATH SAMPLING METHOD;

PHYSICAL CHEMISTRY; PHYSICS;

HAMILTONIANS;

POLYMER;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS;

MOLECULAR DYNAMICS SIMULATION; POLYMERS;

EID: 84882283645     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4817209     Document Type: Article

References (60)

1. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford Science, Oxford, 1987).
2. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic Press, 2002).
3. J. L. Klepeis, K. Lindorff-Larsen, R. O. Dror, and D. E. Shaw, Curr. Opin. Struct. Biol. 19, 120-127 (2009); 10.1016/j.sbi.2009.03.004
4. R. O. Dror, R. M. Dirks, J. P. Grossman, H. Xu, and D. E. Shaw, Annu. Rev. Biophys. 41, 429 (2012). 10.1146/annurev-biophys-042910-155245
5. See http://ambermd.org/ for the Amber software.
6. See http://www.gromacs.org/ for the Gromacs software.
7. See http://www.charmm.org/ for the CHARMM software.
8. See http://www.ks.uiuc.edu/Research/namd/ for the NAMD software.
9. C. Dellago, P. G. Bolhuis, and P. L. Geissler, Adv. Chem. Phys. 123, 1-78 (2002). 10.1002/0471231509.ch1
10. C. Dellago and P. G. Bolhuis, Top. Curr. Chem. 268, 291-317 (2007). 10.1007/128-085
11. C. Dellago and P. G. Bolhuis, Adv. Polym. Sci. 221, 167 (2008).
12. S. Fuchigami, H. Fujisaki, Y. Matsunaga, and A. Kidera, Adv. Chem. Phys. 145, 35 (2011). 10.1002/9781118087817.ch2
13. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 118, 7762 (2003); 10.1063/1.1562614
14. T. S. van Erp and P. G. Bolhuis, J. Comput. Phys. 205, 157 (2005). 10.1016/j.jcp.2004.11.003
15. D. Moroni, T. S. van Erp, and P. G. Bolhuis, J. Chem. Phys. 120, 4055 (2004). 10.1063/1.1644537
16. T. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004); 10.1063/1.1738640
17. A. M. A. West, R. Elber, and D. Shalloway, J. Chem. Phys. 126, 145104 (2007). 10.1063/1.2716389
18. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124, 024102 (2006); 10.1063/1.2140273
19. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124, 194111 (2006). 10.1063/1.2198827
20. F. W. Wiegel, Introduction to Path-Integral Methods in Physics and Polymer Science (World Scientific, Singapore, 1986).
21. D. M. Zuckerman, Statistical Physics of Biomolecules: An Introduction (CRC Press, 2010).
22. R. Elber, A. Ghosh, and A. Cardenas, Acc. Chem. Res. 35, 396 (2002). 10.1021/ar010021d
23. P. Eastman, N. Gronbech-Jensen, and S. Doniach, J. Chem. Phys. 114, 3823 (2001). 10.1063/1.1342162
24. P. Faccioli, M. Sega, F. Pederiva, and H. Orland, Phys. Rev. Lett. 97, 108101 (2006); 10.1103/PhysRevLett.97.108101
25. M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, and H. Orland, Phys. Rev. Lett. 99, 118102 (2007); 10.1103/PhysRevLett.99.118102
26. E. Autieri, P. Faccioli, M. Sega, F. Pederiva, and H. Orland, J. Chem. Phys. 130, 064106 (2009). 10.1063/1.3074271
27. G. Mazzola, S. A. Beccara, P. Faccioli, and H. Orland, J. Chem. Phys. 134, 164109 (2011). 10.1063/1.3581892
28. H. Fujisaki, M. Shiga, and A. Kidera, J. Chem. Phys. 132, 134101 (2010). 10.1063/1.3372802
29. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996). 10.1143/JPSJ.65.1604
30. U. H. E. Hansmann, Chem. Phys. Lett. 281, 140-150 (1997). 10.1016/S0009-2614(97)01198-6
31. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141-151 (1999). 10.1016/S0009-2614(99)01123-9
32. K. Moritsugu, T. Terada, and A. Kidera, J. Chem. Phys. 133, 224105 (2010). 10.1063/1.3510519
33. E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Phys. Rev. Lett. 96, 028105 (2006); 10.1103/PhysRevLett.96.028105
34. P. Liu and G. A. Voth, J. Chem. Phys. 126, 045106 (2007). 10.1063/1.2408415
35. K. Moritsugu, T. Terada, and A. Kidera, J. Am. Chem. Soc. 134, 7094 (2012). 10.1021/ja3008402
36. K. Moritsugu, T. Terada, and A. Kidera, " Funnel landscape of protein-protein interaction. " (unpublished).
37. M. Iannuzzi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 90, 238302 (2003); 10.1103/PhysRevLett.90.238302
38. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168-175 (2006); 10.1016/j.cplett.2006.05.062
39. J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742-15757 (2008). 10.1021/jp805039u
40. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002). 10.1063/1.1472510
41. N. M. Toan, D. Marenduzzo, P. R. Cook, and C. Micheletti, Phys. Rev. Lett. 97, 178302 (2006). 10.1103/PhysRevLett.97.178302
42. C. Micheletti, G. Bussi, and A. Laio, J. Chem. Phys. 129, 074105 (2008). 10.1063/1.2969761
43. L. Onsager and S. Machlup, Phys. Rev. 91, 1505 (1953). 10.1103/PhysRev.91.1505
44. S. Machlup and L. Onsager, Phys. Rev. 91, 1512 (1953). 10.1103/PhysRev.91.1512
45. M. E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation (Oxford University Press, 2010).
46. Z. Hu, L. Cheng, and B. J. Berne, J. Chem. Phys. 133, 034105 (2010). 10.1063/1.3456556
47. B. W. Zhang, D. Jasnow, and D. M. Zuckerman, Proc. Natl. Acad. Sci. U.S.A. 104, 18043 (2007). 10.1073/pnas.0706349104
48. G. E. Crooks and D. Chandler, Phys. Rev. E 64, 026109 (2001). 10.1103/PhysRevE.64.026109
49. T. Terada, Y. Matsunaga, T. Furuta, K. Moritsugu, and A. Kidera, " μ2lib: A class library for multicopy and multiscale simulation. " (unpublished).
50. E. Vanden-Eijnden and M. Heymann, J. Chem. Phys. 128, 061103 (2008). 10.1063/1.2833040
51. T. F. Miller III and C. Predescu, J. Chem. Phys. 126, 144102 (2007). 10.1063/1.2712444
52. Y. Matsunaga, H. Fujisaki, T. Terada, and A. Kidera, " Application of the Onsager-Machlup action formalism to peptide systems. " (unpublished).
53. Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera, PLOS Comput. Biol. 8, e1002555 (2012). 10.1371/journal.pcbi.1002555
54. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 446, 182 (2007). 10.1016/j.cplett.2007.08.017
55. M. Miyazaki and T. Harada, J. Chem. Phys. 134, 085108 (2011). 10.1063/1.3516587
56. A. Apte, M. Hairer, A. M. Stuart, and J. Voss, Physica D 230, 50 (2007). 10.1016/j.physd.2006.06.009
57. D. Antoniou and S. D. Schwartz, J. Chem. Phys. 131, 224111 (2009). 10.1063/1.3272793
58. M. Shiga and H. Fujisaki, J. Chem. Phys. 136, 184103 (2012). 10.1063/1.4709723
59. S. A. Beccara, G. Garberoglio, and P. Faccioli, J. Chem. Phys. 135, 034103 (2011). 10.1063/1.3609244
60. L. Boninsegna and P. Faccioli, J. Chem. Phys. 136, 214111 (2012). 10.1063/1.4722213