Simulating rare events using a weighted ensemble-based string method

Journal of Chemical Physics

Volumn 138, Issue 4, 2013, Pages

  Adelman, Joshua L ^a   Grabe, Michael ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE REFINEMENT; BRUTE FORCE; COLLECTIVE VARIABLES; CONFORMATIONAL CHANGE; EFFICIENT SAMPLING; ELASTIC NETWORK MODELS; HIGH DIMENSIONAL PHASE SPACE; NONEQUILIBRIUM SYSTEM; ORDER PARAMETER; PATH SAMPLING; PATH SAMPLING METHOD; PROTEIN CONFORMATIONAL CHANGES; RARE EVENT; REACTION PATHWAYS; REGULATORY PROTEIN; STRING METHODS; TWO DIMENSIONAL MODEL; VORONOI TESSELLATIONS;

BROWNIAN MOVEMENT; PHASE SPACE METHODS;

TWO DIMENSIONAL;

NITROGEN REGULATORY PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; PII NITROGEN REGULATORY PROTEINS; PROTEIN CONFORMATION;

MLCS; MLOWN;

EID: 84873594876     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4773892     Document Type: Article

References (57)

1. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, " Transition path sampling and the calculation of rate constants.," J. Chem. Phys. 108, 1964-1977 (1998). 10.1063/1.475562
2. T. Woolf, " Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations.," Chem. Phys. Lett. 289, 433-441 (1998). 10.1016/S0009-2614(98)00427-8
3. T. S. van Erp, D. Moroni, and P. G. Bolhuis, " A novel path sampling method for the calculation of rate constants.," J. Chem. Phys. 118, 7762-7774 (2003). 10.1063/1.1562614
4. A. K. Faradjian and R. Elber, " Computing time scales from reaction coordinates by milestoning.," J. Chem. Phys. 120, 10880-10889 (2004). 10.1063/1.1738640
5. R. J. Allen, P. B. Warren, and P. R. Ten Wolde, " Sampling rare switching events in biochemical networks.," Phys. Rev. Lett. 94, 018104 (2005). 10.1103/PhysRevLett.94.018104
6. A. Warmflash, P. Bhimalapuram, and A. R. Dinner, " Umbrella sampling for nonequilibrium processes.," J. Chem. Phys. 127, 154112 (2007). 10.1063/1.2784118
7. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, " Transition path sampling: throwing ropes over rough mountain passes, in the dark.," Annu. Rev. Phys. Chem. 53, 291-318 (2002). 10.1146/annurev. physchem.53.082301.113146
8. C. Dellago and P. G. Bolhuis, " Transition path sampling and other advanced simulation techniques for rare events.," in Advanced Computer Simulation Approaches for Soft Matter Sciences III, Advances in Polymer Science Vol. 221, edited by, C. Holm, and, K. Kremer, (Springer, Berlin, 2009), pp. 167-233.
9. M. C. Zwier and L. T. Chong, " Reaching biological timescales with all-atom molecular dynamics simulations.," Curr. Opin. Pharmacol. 10, 745-752 (2010). 10.1016/j.coph.2010.09.008
10. R. Elber and M. Karplus, " A method for determining reaction paths in large molecules: Application to myoglobin.," Chem. Phys. Lett. 139, 375-380 (1987). 10.1016/0009-2614(87)80576-6
11. S. Fischer and M. Karplus, " Conjugate peak refinement: An algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom.," Chem. Phys. Lett. 194, 252-261 (1992). 10.1016/0009-2614(92)85543-J
12. G. Henkelman and H. Jónsson, " Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points.," J. Chem. Phys. 113, 9978-9985 (2000). 10.1063/1.1323224
13. W. E, W. Ren, and E. Vanden-Eijnden, " String method for the study of rare events.," Phys. Rev. B 66, 052301 (2002). 10.1103/PhysRevB.66. 052301
14. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, " String method in collective variables: Minimum free energy paths and isocommittor surfaces.," J. Chem. Phys. 125, 024106 (2006). 10.1063/1.2212942
15. W. E, W. Ren, and E. Vanden-Eijnden, " Finite temperature string method for the study of rare events.," J. Phys. Chem. B 109, 6688-6693 (2005). 10.1021/jp0455430
16. A. C. Pan, D. Sezer, and B. Roux, " Finding transition pathways using the string method with swarms of trajectories.," J. Phys. Chem. B 112, 3432-3440 (2008). 10.1021/jp0777059
17. A. C. Pan and B. Roux, " Building Markov state models along pathways to determine free energies and rates of transitions.," J. Chem. Phys. 129, 064107 (2008). 10.1063/1.2959573
18. E. Vanden-Eijnden and M. Venturoli, " Revisiting the finite temperature string method for the calculation of reaction tubes and free energies.," J. Chem. Phys. 130, 194103 (2009). 10.1063/1.3130083
19. A. Dickson, A. Warmflash, and A. R. Dinner, " Nonequilibrium umbrella sampling in spaces of many order parameters.," J. Chem. Phys. 130, 074104 (2009). 10.1063/1.3070677
20. J. Rogal, W. Lechner, J. Juraszek, B. Ensing, and P. G. Bolhuis, " The reweighted path ensemble.," J. Chem. Phys. 133, 174109 (2010). 10.1063/1.3491817
21. M. E. Johnson and G. Hummer, " Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.," J. Phys. Chem. B 116, 8573-8583 (2012). 10.1021/jp212611k
22. B. M. Dickson, H. Huang, and C. B. Post, " Unrestrained computation of free energy along a path.," J. Phys. Chem. B 116, 11046-11055 (2012). 10.1021/jp304720m
23. W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E, " Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.," J. Chem. Phys. 123, 134109 (2005). 10.1063/1.2013256
24. T. F. Miller III, E. Vanden-Eijnden, and D. Chandler, " Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain.," Proc. Natl. Acad. Sci. U.S.A. 104, 14559-14564 (2007). 10.1073/pnas.0705830104
25. V. Ovchinnikov, M. Cecchini, E. Vanden-Eijnden, and M. Karplus, " A conformational transition in the myosin VI converter contributes to the variable step size.," Biophys. J. 101, 2436-2444 (2011). 10.1016/j.bpj.2011.09.044
26. D. Bhatt and D. M. Zuckerman, " Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.," J. Chem. Theory Comput. 6, 3527-3539 (2010). 10.1021/ct100406t
27. J. L. Adelman, A. L. Dale, M. C. Zwier, D. Bhatt, L. T. Chong, D. M. Zuckerman, and M. Grabe, " Simulations of the alternating access mechanism of the sodium symporter Mhp1.," Biophys. J. 101, 2399-2407 (2011). 10.1016/j.bpj.2011.09.061
28. G. A. Huber and S. Kim, " Weighted-ensemble Brownian dynamics simulations for protein association reactions.," Biophys. J. 70, 97-110 (1996). 10.1016/S0006-3495(96)79552-8
29. B. W. Zhang, D. Jasnow, and D. M. Zuckerman, " Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.," Proc. Natl. Acad. Sci. U.S.A. 104, 18043-18048 (2007). 10.1073/pnas.0706349104
30. B. W. Zhang, D. Jasnow, and D. M. Zuckerman, " The 'weighted ensemble' path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.," J. Chem. Phys. 132, 054107 (2010). 10.1063/1.3306345
31. D. Bhatt, B. W. Zhang, and D. M. Zuckerman, " Steady-state simulations using weighted ensemble path sampling.," J. Chem. Phys. 133, 014110 (2010). 10.1063/1.3456985
32. A. Rojnuckarin, D. R. Livesay, and S. Subramaniam, " Bimolecular reaction simulation using weighted ensemble Brownian dynamics and the University of Houston Brownian Dynamics program.," Biophys. J. 79, 686-693 (2000). 10.1016/S0006-3495(00)76327-2
33. A. Rojnuckarin, S. Kim, and S. Subramaniam, " Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond.," Proc. Natl. Acad. Sci. U.S.A. 95, 4288-4292 (1998). 10.1073/pnas.95.8.4288
34. +/18-crown-6 ether.," J. Chem. Theory Comput. 7, 1189-1197 (2011). 10.1021/ct100626x
35. A. Dickson, A. Warmflash, and A. R. Dinner, " Separating forward and backward pathways in nonequilibrium umbrella sampling.," J. Chem. Phys. 131, 154104 (2009). 10.1063/1.3244561
36. F. Zhu and G. Hummer, " Pore opening and closing of a pentameric ligand-gated ion channel.," Proc. Natl. Acad. Sci. U.S.A. 107, 19814-19819 (2010). 10.1073/pnas.1009313107
37. S. Lettieri, M. C. Zwier, C. A. Stringer, E. Suarez, L. T. Chong, and D. M. Zuckerman, " Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories.," preprint arXiv:1210.3094 [physics.bio-ph] (2012).
38. E. Vanden-Eijnden and M. Venturoli, " Exact rate calculations by trajectory parallelization and tilting.," J. Chem. Phys. 131, 044120 (2009). 10.1063/1.3180821
39. A. Dickson, M. Maienschein-Cline, A. Tovo-Dwyer, J. Hammond, and A. Dinner, " Flow-dependent unfolding and refolding of an RNA by nonequilibrium umbrella sampling.," J. Chem. Theory Comput. 7, 2710-2720 (2011). 10.1021/ct200371n
40. See http://chong.chem.pitt.edu/WESTPA for the WESTPA software package.
41. A. Dickson, A. Warmflash, and A. R. Dinner, " Erratum: 'Nonequilibrium umbrella sampling in spaces of many order parameters' [J. Chem. Phys. 130, 074104 (2009)].," J. Chem. Phys. 136, 229901 (2012). 10.1063/1.4729744
42. A. Dickson, A. Warmflash, and A. R. Dinner, " Erratum: 'Separating forward and backward pathways in nonequilibrium umbrella sampling' [J. Chem. Phys. 131, 154104 (2009)].," J. Chem. Phys. 136, 239901 (2012). 10.1063/1.4730937
43. A. Damjanović, B. García-Moreno E, and B. R. Brooks, " Self-guided Langevin dynamics study of regulatory interactions in NtrC.," Proteins 76, 1007-1019 (2009). 10.1002/prot.22439
44. M. Lei, J. Velos, A. Gardino, A. Kivenson, M. Karplus, and D. Kern, " Segmented transition pathway of the signaling protein nitrogen regulatory protein C.," J. Mol. Biol. 392, 823-836 (2009). 10.1016/j.jmb.2009.06.065
45. J. L. Adelman, J. D. Chodera, I.-F. W. Kuo, T. F. Miller III, and D. Barsky, " The mechanical properties of PCNA: Implications for the loading and function of a DNA sliding clamp.," Biophys. J. 98, 3062-3069 (2010). 10.1016/j.bpj.2010.03.056
46. E. Lyman, J. Pfaendtner, and G. A. Voth, " Systematic multiscale parameterization of heterogeneous elastic network models of proteins.," Biophys. J. 95, 4183-4192 (2008). 10.1529/biophysj.108.139733
47. L. Yang, G. Song, A. Carriquiry, and R. L. Jernigan, " Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.," Structure 16, 321-330 (2008). 10.1016/j.str.2007.12.011
48. D. Kern, B. F. Volkman, P. Luginbühl, M. J. Nohaile, S. Kustu, and D. E. Wemmer, " Structure of a transiently phosphorylated switch in bacterial signal transduction.," Nature (London) 402, 894-898 (1999). 10.1038/47273
49. D. L. Theobald, " Rapid calculation of RMSDs using a quaternion-based characteristic polynomial.," Acta Crystallogr. A 61, 478-480 (2005). 10.1107/S0108767305015266
50. J. Chodera, W. Swope, J. Pitera, C. Seok, and K. Dill, " Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations.," J. Chem. Theory Comput. 3, 26-41 (2007). 10.1021/ct0502864
51. M. R. Shirts and J. D. Chodera, " Statistically optimal analysis of samples from multiple equilibrium states.," J. Chem. Phys. 129, 124105 (2008). 10.1063/1.2978177
52. R. Du, V. Pande, A. Grosberg, T. Tanaka, and E. Shakhnovich, " On the transition coordinate for protein folding.," J. Chem. Phys. 108, 334 (1998). 10.1063/1.475393
53. P. Geissler, C. Dellago, and D. Chandler, " Kinetic pathways of ion pair dissociation in water.," J. Phys. Chem. B 103, 3706-3710 (1999). 10.1021/jp984837g
54. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, " Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.," Proc. Natl. Acad. Sci. U.S.A. 106, 19011-19016 (2009). 10.1073/pnas.0905466106
55. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schütte, and F. Noé, " Markov models of molecular kinetics: Generation and validation.," J. Chem. Phys. 134, 174105 (2011). 10.1063/1.3565032
56. L. Maragliano, E. Vanden-Eijnden, and B. Roux, " Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials.," J. Chem. Theory Comput. 5, 2589-2594 (2009). 10.1021/ct900279z
57. B. Peters, A. Heyden, A. T. Bell, and A. Chakraborty, " A growing string method for determining transition states: Comparison to the nudged elastic band and string methods.," J. Chem. Phys. 120, 7877-7886 (2004). 10.1063/1.1691018