Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

Journal of Chemical Physics

Volumn 134, Issue 13, 2011, Pages

  Ferguson, Andrew L ^a,b   Panagiotopoulos, Athanassios Z ^a   Debenedetti, Pablo G ^a   Kevrekidis, Ioannis G ^a  

^a Princeton University   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DIPEPTIDES; DIFFUSION MAPS; ENERGY REGIONS; EXPLICIT SOLVENTS; FREE ENERGY LANDSCAPE; MOLECULAR SIMULATIONS; MOLECULAR SYSTEMS; NONLINEAR DIMENSIONALITY REDUCTION; PARAMETRIZATIONS; PHASE SPACES; UMBRELLA SAMPLING;

AMINO ACIDS; FREE ENERGY; NONLINEAR ANALYSIS; PEPTIDES; PHASE SPACE METHODS;

DIFFUSION BARRIERS;

ALANYLALANINE; DIPEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DIFFUSION; THERMODYNAMICS;

COMPUTER SIMULATION; DIFFUSION; DIPEPTIDES; MODELS, MOLECULAR; THERMODYNAMICS;

EID: 79954557298     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3574394     Document Type: Article

References (62)

1. S. S. Cho, Y. Levy, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 103, 586 (2006). 10.1073/pnas.0509768103 (Pubitemid 43153069)
2. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005). 10.1021/jp045546c (Pubitemid 40552537)
3. A. E. Garca, Phys. Rev. Lett. 68, 2696 (1992). 10.1103/PhysRevLett.68. 2696
4. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins: Struct., Funct., Genet. 17, 412 (1993). 10.1002/prot.340170408 (Pubitemid 23358549)
5. R. Hegger, A. Altis, P. H. Nguyen, and G. Stock, Phys. Rev. Lett. 98, 028102 (2007). 10.1103/PhysRevLett.98.028102 (Pubitemid 46135131)
6. P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, Proc. Natl. Acad. Sci. U.S.A. 103, 9885 (2006). 10.1073/pnas.0603553103 (Pubitemid 43993592)
7. H. Stamati, C. Clementi, and L. E. Kavraki, Proteins: Struct. Funct. Bioinf. 78, 223 (2009). 10.1002/prot.22526
8. P. I. Zhuravlev, C. K. Materese, and G. A. Papoian, J. Phys. Chem. B 113, 8800 (2009). 10.1021/jp810659u
9. A. L. Ferguson, A. Z. Panagiotopoulos, P. G. Debenedetti, and I. G. Kevrekidis, Proc. Natl. Acad. Sci. U.S.A. 107, 13597 (2010). 10.1073/pnas.1003293107
10. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, New York, 2001).
11. G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 118, 10762 (2003). 10.1063/1.1574777
12. B. E. Sonday, M. Haataja, and I. G. Kevrekidis, Phys. Rev. E 80, 031102 (2009). 10.1103/PhysRevE.80.031102
13. A. L. Ferguson, S. Zhang, I. Dikiy, A. Z. Panagiotopoulos, P. G. Debenedetti, and A. J. Link, Biophys. J. 99, 3056 (2010). 10.1016/j.bpj.2010.08. 073
14. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977). 10.1016/0021-9991(77)90121-8
15. R. Du, V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich, J. Chem. Phys. 108, 334 (1998). 10.1063/1.475393
16. M. Belkin and P. Niyogi, Neural Comput. 15, 1373 (2003). 10.1162/089976603321780317 (Pubitemid 37049796)
17. J. B. Tenenbaum, V. de Silva, and J. C. Langford, Science 290, 2319 (2000). 10.1126/science.290.5500.2319 (Pubitemid 32041577)
18. S. T. Roweis and L. K. Saul, Science 290, 2323 (2000). 10.1126/science.290.5500.2323 (Pubitemid 32041578)
19. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker, Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005). 10.1073/pnas.0500334102 (Pubitemid 40740988)
20. R. R. Coifman and S. Lafon, Appl. Comput. Harmon. Anal. 21, 5 (2006). 10.1016/j.acha.2006.04.006 (Pubitemid 43947619)
21. D. S. Chekmarev, T. Ishida, and R. M. Levy, J. Phys. Chem. B 108, 19487 (2004). 10.1021/jp048540w (Pubitemid 40011200)
22. A. Singer, R. Erban, I. G. Kevrekidis, and R. R. Coifman, Proc. Natl. Acad. Sci. U.S.A. 106, 16090 (2009). 10.1073/pnas.0905547106
23. R. Erban, T. A. Frewen, X. Wang, T. C. Elston, R. Coifman, B. Nadler, and I. G. Kevrekidis, J. Chem. Phys. 126, 155103 (2007). 10.1063/1.2718529 (Pubitemid 46644962)
24. E. Plaku, H. Stamati, C. Clementi, and L. E. Kavraki, Proteins: Struct., Funct., Bioinf., 67, 897 (2007). 10.1002/prot.21337 (Pubitemid 46753937)
25. A. Kentsis, T. Gindin, M. Mezei, and R. Osman, PLoS ONE, 2, e446 (2007). 10.1371/journal.pone.0000446
26. R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, IEEE Trans. Image Process. 17, 1891 (2008). 10.1109/TIP.2008.2002305
27. B. Nadler, S. Lafon, R. R. Coifman, and I. G. Kevrekidis, in Advances in Neural Information Processing Systems, edited by, Y. Weiss, B. Schlkopf, and, J. Platt, Neural Information Processing Systems (NIPS) (MIT Press, Cambridge, MA, 2006), Vol. 18, pp. 955-962.
28. K. Y. Sanbonmatsu and A. E. Garca, Proteins: Struct., Funct., Genet., 46, 225 (2002). 10.1002/prot.1167 (Pubitemid 34052076)
29. A. L. Ferguson, P. G. Debenedetti, and A. Z. Panagiotopoulos, J. Phys. Chem. B 113, 6405 (2009). 10.1021/jp811229q
30. T. F. Miller, E. Vanden-Eijnden, and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 104, 14559 (2007). 10.1073/pnas.0705830104 (Pubitemid 350003183)
31. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic, San Diego, 2002).
32. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
33. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. 13, 1011 (1992). 10.1002/jcc.540130812
34. B. Roux, Comput. Phys. Commun. 91, 275 (1995). 10.1016/0010-4655(95) 00053-I
35. B. Peters and B. L. Trout, J. Chem. Phys. 125, 054108 (2006). 10.1063/1.2234477 (Pubitemid 44192324)
36. B. Peters, G. T. Beckham, and B. L. Trout, J. Chem. Phys. 127, 034109 (2007). 10.1063/1.2748396 (Pubitemid 47133785)
37. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Modeling. 7, 306 (2001).
38. 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 (Pubitemid 43076182)
39. W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc. 110, 1657 (1988). 10.1021/ja00214a001
40. G. A. Kaminski, R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). 10.1021/jp003919d (Pubitemid 35339015)
41. 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
42. A. W. Schttelkopf and D. M.F. van Aalten, Acta Crystallogr. 60, 1355 (2004). 10.1107/S0907444904011679 (Pubitemid 41079731)
43. 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
44. S. Nosé, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
45. W. G. Hoover, Phys. Rev. A 31, 1695 (1985). 10.1103/PhysRevA.31.1695
46. M. Parinello and A. Rahman, J. Appl. Phys. 52, 7182 (1981). 10.1063/1.328693 (Pubitemid 12456820)
47. D. A. Case, T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr, A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods, J. Comput. Chem. 26, 1668 (2005). 10.1002/jcc.20290 (Pubitemid 43076180)
48. B. R. Brooks, C. L. Brooks, III, A. D. Mackerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus, J. Comput. Chem. 30, 1545 (2009). 10.1002/jcc.21287
49. K. J. Maschhoff and D. C. Sorensen, in Third International Workshop on Applied Parallel Computing, Industrial Computation and Optimization, Lecture Notes in Computer Science, Vol. 1184, edited by, J. Wasniewski, J. Dongarra, K. Madsen, and, D. Olesen, (Springer, New York, 1996), pp. 478-486.
50. J. Apostolakis, P. Ferrara, and A. Caflisch, J. Chem. Phys. 110, 2099 (1999). 10.1063/1.477819
51. T. A. Frewen, G. Hummer, and I. G. Kevrekidis, J. Chem. Phys. 131, 134104 (2009). 10.1063/1.3207882
52. M. B. Kubitzki and B. L. De Groot, Biophys. J. 92, 4262 (2007). 10.1529/biophysj.106.103101 (Pubitemid 46910542)
53. C. A. F. de Oliveira, D. Hamelberg, and J. A. McCammon, J. Chem. Phys. 127, 175105 (2007). 10.1063/1.2794763 (Pubitemid 350075555)
54. E. Vanden-Eijnden and M. Venturoli, J. Chem. Phys. 130, 194103 (2009). 10.1063/1.3130083
55. M. Bonomi, A. Barducci, and M. Parrinello, J. Comput. Chem. 30, 1615 (2009). 10.1002/jcc.21305
56. C. Velez-Vega, E. E. Borrero, and F. A. Escobedo, J. Chem. Phys. 130, 225101 (2009). 10.1063/1.3147465
57. P. G. Bolhuis, C. Dellago, and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 97, 5877 (2000). 10.1073/pnas.100127697 (Pubitemid 30367492)
58. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006). 10.1063/1.2212942 (Pubitemid 44088333)
59. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997). 10.1002/(SICI)1096-987X(199709)18:121450::AID-JCC33.0.CO;2-I
60. J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. 126, 155101 (2007). 10.1063/1.2714538 (Pubitemid 46644960)
61. See supplementary material at http://dx.doi.org/10.1063/1.3574394 E-JCPSA6-134-011114 for eigenvalue spectra and additional diffusion map embeddings pertaining to the application of the umbrella bootstrapped diffusion map approach to alanine dipeptide, and a local principal component analysis of a selected isomerization pathway identified by the approach.
62. P. Liu, Q. Shi, E. Lyman, and G. A. Voth, J. Chem. Phys. 129, 114103 (2008). 10.1063/1.2976663