Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

Journal of Chemical Physics

Volumn 141, Issue 21, 2014, Pages

  Wu, Hao ^a   Mey, Antonia S J S ^a   Rosta, Edina ^b   Noé, Frank ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HAMILTONIANS; SPACE FLIGHT; THERMODYNAMIC PROPERTIES; TRAJECTORIES;

CONFIGURATION SPACE; DISCRETE TRANSITIONS; MARKOV STATE MODELS; MAXIMUM LIKELIHOOD ESTIMATE; STATE-SPACE TRAJECTORIES; SUITABLE CONDITIONS; THERMODYNAMIC STATE; WEIGHTED HISTOGRAM ANALYSIS METHOD;

MAXIMUM LIKELIHOOD ESTIMATION;

ION CHANNEL; PROTEIN;

CHEMISTRY; MOLECULAR DYNAMICS; PROBABILITY; STATISTICAL MODEL; THERMODYNAMICS;

ION CHANNELS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MOLECULAR DYNAMICS SIMULATION; PROTEINS; THERMODYNAMICS;

EID: 84915746596     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4902240     Document Type: Article

References (43)

1. C. G. Greyer, in Proceedings of the 23rd Symposium of the Interface on Computing Science and Statistics, Interface Foundation, Fairfax (American Statistical Association, New York, 1991), pp. 156-163.
2. K. Hukushimi and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996). 10.1143/JPSJ.65.1604
3. U. H. Hansmann, Chem. Phys. Lett. 281, 140 (1997). 10.1016/S0009-2614(97)01198-6
4. Y. Sugita and Y. Okamato, Chem. Phys. Lett. 314, 141 (1999). 10.1016/S0009-2614(99)01123-9
5. E. Marinari and G. Parisi, Euro. Phys. Lett. 19, 451 (1992). 10.1209/0295-5075/19/6/002
6. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977). 10.1016/0021-9991(77)90121-8
7. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
8. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992). 10.1002/jcc.540130812
9. M. Souaille and B. Roux, Comput. Phys. Commun. 135, 40 (2001). 10.1016/S0010-4655(00)00215-0
10. M. R. Shirts and J. D. Chodera, J. Chem. Phys. 129, 124105 (2008). 10.1063/1.2978177
11. S. Sriraman, I. G. Kevrekidis, and G. Hummer, J. Phys. Chem. B 109, 6479 (2005). 10.1021/jp046448u
12. D. D. L. Minh and J. D. Chodera, J. Chem. Phys. 131, 134110 (2009). 10.1063/1.3242285
13. J. D. Chodera, W. C. Swope, F. Noé, J.-H. Prinz, and V. S. Pande, J. Phys. Chem. 134, 244107 (2011). 10.1063/1.3592152
14. J.-H. Prinz, J. D. Chodera, V. S. Pande, W. C. Swope, J. C. Smith, and F. Noé, J. Chem. Phys. 134, 244108 (2011). 10.1063/1.3592153
15. W. Du and P. G. Bolhuis, J. Chem. Phys. 139, 044105 (2013). 10.1063/1.4813777
16. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997). 10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I
17. S. Sakuraba and A. Kitao, J. Comput. Chem. 30, 1850 (2009). 10.1002/jcc.21186
18. H. Wu and F. Noé, SIAM Multiscale Model. Simul. 12, 25 (2014). 10.1137/120895883
19. A. S. J. S. Mey, H. Wu, and F. Noé, Phys. Rev. X 4, 041018 (2014). 10.1103/PhysRevX.4.041018
20. E. Rosta and G. Hummer, " Free energies from dynamic weighted histogram analysis using unbiased Markov state model," J. Chem. Theory Comput. (submitted).
21. M. Shirts and V. S. Pande, Science 290, 1903 (2000). 10.1126/science.290.5498.1903
22. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. Weikl, Proc. Natl. Acad. Sci. U.S.A. 106, 19011 (2009). 10.1073/pnas.0905466106
23. I. Buch, T. Giorgino, and G. de Fabritiis, Proc. Natl. Acad. Sci. U.S.A. 108, 10184 (2011). 10.1073/pnas.1103547108
24. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002). 10.1073/pnas.202427399
25. H. Grubmüller, Phys. Rev. E 52, 2893 (1995). 10.1103/PhysRevE.52.2893
26. C. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard, J. Comput. Phys. 151, 146 (1999). 10.1006/jcph.1999.6231
27. W. C. Swope, J. W. Pitera, and F. Suits, J. Phys. Chem. B 108, 6571 (2004). 10.1021/jp037421y
28. N. Singhal and V. S. Pande, J. Chem. Phys. 123, 204909 (2005). 10.1063/1.2116947
29. F. Noé, I. Horenko, C. Schütte, and J. C. Smith, J. Chem. Phys. 126, 155102 (2007). 10.1063/1.2714539
30. J. D. Chodera, K. A. Dill, N. Singhal, V. S. Pande, W. C. Swope, and J. W. Pitera, J. Chem. Phys. 126, 155101 (2007). 10.1063/1.2714538
31. N. V. Buchete and G. Hummer, J. Phys. Chem. B 112, 6057 (2008). 10.1021/jp0761665
32. 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
33. M. Sarich, F. Noé, and C. Schütte, SIAM Multiscale Model. Simul. 8, 1154 (2010). 10.1137/090764049
34. Z. Tan, J. Stat. Plan. Inf. 138, 1967 (2008). 10.1016/j.jspi.2007.07.013
35. Z. Tan, E. Gallicchio, M. Lapelosa, and R. M. Levy, J. Chem. Phys. 136, 144102 (2012). 10.1063/1.3701175
36. F. Zhu and G. Hummer, J. Comput. Chem. 33, 453 (2012). 10.1002/jcc.21989
37. F. Noé, J. Chem. Phys. 128, 244103 (2008). 10.1063/1.2916718
38. G. R. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande, J. Chem. Phys. 131, 124101 (2009). 10.1063/1.3216567
39. J. R. Norris, Markov Chains, Cambridge Series in Statistical and Probabilistic Mathematics Vol. 2 (Cambridge University Press, Cambridge, 1998).
40. E. Gallicchio, M. Andrec, A. K. Felts, and R. M. Levy, J. Phys. Chem. B 109, 6722 (2005). 10.1021/jp045294f
41. J.-B. Hiriart-Urruty and C. Lemaréchal, Convex Analysis and Minimization Algorithms I: Fundamentals (Springer, Heidelberg, 1993).
42. J.-B. Hiriart-Urruty and C. Lemaréchal, Convex Analysis and Minimization Algorithms II: Advanced Theory and Bundle Methods (Springer, Heidelberg, 1993).
43. S. Boyd and L. Vandenberghe, Convex Optimization (Cambridge University Press, 2004).