Adaptive single replica multiple state transition interface sampling

Journal of Chemical Physics

Volumn 139, Issue 4, 2013, Pages

  Du, Wei Na ^a   Bolhuis, Peter G ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DIPEPTIDES; EXPLICIT WATER; LENNARD-JONES CLUSTER; META-STABLE STATE; MULTIPLE STATE; REPLICA EXCHANGE; SAMPLING ALGORITHM; WALKING THROUGH;

AMINO ACIDS; ISOMERIZATION; ISOMERS;

INTERFACE STATES;

EID: 84903362810     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4813777     Document Type: Article

References (53)

1. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. 28, 578 (1974). 10.1016/0009-2614(74)80109-0
2. E. Carter, G. Ciccotti, J. T. Hynes, and R. Kapral, Chem. Phys. Lett. 156, 472 (1989). 10.1016/S0009-2614(89)87314-2
3. T. Huber, A. Torda, and W. van Gunsteren, J. Comput.-Aided Mol. Des. 8, 695 (1994). 10.1007/BF00124016
4. H. Grubmüller, Phys. Rev. E 52, 2893 (1995). 10.1103/PhysRevE.52. 2893
5. A. F. Voter, J. Chem. Phys. 106, 4665 (1997). 10.1063/1.473503
6. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002). 10.1073/pnas.202427399
7. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001). 10.1063/1.1410978
8. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999). 10.1016/S0009-2614(99)01123-9
9. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992). 10.1209/0295-5075/19/6/002
10. L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008). 10.1073/pnas.0810631106
11. Y. Q. Gao, J. Chem. Phys. 128, 064105 (2008). 10.1063/1.2825614
12. C. H. Bennett, in Algorithms for Chemical Computations, ACS Symposium Series Vol. 46, edited by, R. Christofferson, (American Chemical Society, Washington, DC, 1977).
13. D. Chandler, J. Chem. Phys. 68, 2959 (1978). 10.1063/1.436049
14. G. Henkelman and H. Jónsson, J. Chem. Phys. 113, 9978 (2000). 10.1063/1.1323224
15. R. Elber, A. Cardenas, A. Ghosh, and H. A. Stern, Adv. Chem. Phys. 126, 93 (2003). 10.1002/0471428019.ch3
16. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006). 10.1063/1.2212942
17. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998). 10.1063/1.475562
18. C. Dellago and P. G. Bolhuis, Adv. Polym. Sci. 221, 167 (2009). 10.1007/978-3-540-87706-6-3
19. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 118, 7762 (2003). 10.1063/1.1562614
20. A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004). 10.1063/1.1738640
21. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124, 024102 (2006). 10.1063/1.2140273
22. F. Cérou, A. Guyader, T. Lelièvre, and D. Pommier, J. Chem. Phys. 134, 054108 (2011). 10.1063/1.3518708
23. A. Warmflash, P. Bhimalapuram, and A. R. Dinner, J. Chem. Phys. 127, 154112 (2007). 10.1063/1.2784118
24. J. T. Berryman and T. Schilling, J. Chem. Phys. 133, 244101 (2010). 10.1063/1.3525099
25. G. Huber and S. Kim, Biophys. J. 70, 97 (1996). 10.1016/S0006-3495(96) 79552-8
26. T. S. van Erp, Phys. Rev. Lett. 98, 268301 (2007). 10.1103/PhysRevLett. 98.268301
27. P. G. Bolhuis, J. Chem. Phys. 129, 114108 (2008). 10.1063/1.2976011
28. J. Rogal and P. G. Bolhuis, J. Chem. Phys. 129, 224107 (2008). 10.1063/1.3029696
29. J. Rogal, W. Lechner, J. Juraszek, B. Ensing, and P. G. Bolhuis, J. Chem. Phys. 133, 174109 (2010). 10.1063/1.3491817
30. D. Swendson and P. G. Bolhuis, " Multiple state replica exchange transition interface sampling.," J. Chem. Phys., (to be published).
31. M. Hagen, B. Kim, P. Liu, R. A. Friesner, and B. J. Berne, J. Phys. Chem. B 111, 1416 (2007). 10.1021/jp064479e
32. W. Lechner, C. Dellago, and P. G. Bolhuis, J. Chem. Phys. 135, 154110 (2011). 10.1063/1.3651367
33. E. E. Borrero and C. Dellago, J. Chem. Phys. 133, 134112 (2010). 10.1063/1.3496376
34. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
35. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992). 10.1002/jcc.540130812
36. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001). 10.1103/PhysRevLett.86.2050
37. F. Wang and D. P. Landau, Phys. Rev. E 64, 056101 (2001). 10.1103/PhysRevE.64.056101
38. D. J. Wales and R. S. Berry, J. Chem. Phys. 92, 4283 (1990). 10.1063/1.457788
39. D. Moroni, " Efficient sampling of rare event pathways.," Ph.D. thesis (Universiteit van Amsterdam, 2005).
40. B. Leimkuhler, E. Noorizadeh, and F. Theil, J. Stat. Phys. 135, 261 (2009). 10.1007/s10955-009-9734-0
41. F. Spear, Am. Mineral. 65, 1291 (1980).
42. E. E. Borrero, M. Weinwurm, and C. Dellago, J. Chem. Phys. 134, 244118 (2011). 10.1063/1.3601919
43. W.-N. Du, K. A. Marino, and P. G. Bolhuis, J. Chem. Phys. 135, 145102 (2011). 10.1063/1.3644344
44. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 10.1021/ct700301q
45. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291
46. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001). 10.1007/s008940100045
47. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, Comput. Phys. Commun. 91, 43 (1995). 10.1016/0010-4655(95)00042-E
48. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995). 10.1021/ja00124a002
49. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
50. T. Darden, D. York, and L. G. Pedersen, J. Comput. Chem. 98, 10089 (1993). 10.1063/1.464397
51. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995). 10.1063/1.470117
52. G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126, 014101 (2007). 10.1063/1.2408420
53. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schütte, and F. Noé, J. Chem. Phys. 134, 174105 (2011). 10.1063/1.3565032