String method in collective variables: Minimum free energy paths and isocommittor surfaces

Journal of Chemical Physics

Volumn 125, Issue 2, 2006, Pages

  Maragliano, Luca ^a   Fischer, Alexander ^a   Vanden Eijnden, Eric ^a   Ciccotti, Giovanni ^b  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITÀ DI ROMA LA SAPIENZA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DIHEDRAL ANGLES; ISOCOMMITTOR SURFACES; ISOMERIZATION TRANSITION; STRING METHOD;

CONFORMAL MAPPING; COSTS; FREE ENERGY; SAMPLING; STATISTICAL METHODS; THEOREM PROVING;

COMPUTATION THEORY;

EID: 33746255471     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2212942     Document Type: Article

References (34)

1. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001).
2. L. Rosso, P. Mináry, S. Shou, and M. E. Tuckerman, J. Chem. Phys. 116, 4389 (2001).
3. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002).
4. P. G. Bolhuis, C. Dellago, P. L. Geissler, and D. Chandler, Annu. Rev. Phys. Chem. 54, 20 (2002).
5. R. Elber, A. Ghosh, and A. Cardenas, Acc. Chem. Res. 35, 396 (2002).
6. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 52301 (2002).
7. W. E and E. Vanden-Eijnden, J. Stat. Phys. (in press).
8. W. E, W. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 413, 242 (2005).
9. W. E and E. Vanden-Eijnden, in Multiscale Modelling and Simulation, edited by S. Attinger and P. Koumoutsakos (Springer-Verlag, Berlin, 2004).
10. E. Vanden-Eijnden, in Computer Simulations in Condensed Matter: From Materials to Chemical Biology, edited by M. Ferrario, G. Ciccotti, and K. Binder (Springer-Verlag, Berlin, in press).
11. G. Hummer, J. Chem. Phys. 120, 516 (2004).
12. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005).
13. E. A. Carter, G. Ciccotti, J. T. Hynes, and R. Kapral, Chem. Phys. Lett. 156, 472 (1989).
14. W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E, J. Chem. Phys. 123, 134109 (2005).
15. B. M. Pettitt and M. Karplus, Chem. Phys. Lett. 121, 194 (1985).
16. R. Czerminski and R. Elber, J. Chem. Phys. 92, 5580 (1990).
17. T. Lazaridis, D. J. Tobias, C. L. Brooks III, and M. E. Paulaitis, J. Chem. Phys. 95, 7612 (1991).
18. D. J. Tobias and C. L. Brooks III, J. Phys. Chem. 96, 3864 (1992).
19. C. L. Brooks III and D. A. Case, Chem. Rev. (Washington, D.C.) 93, 2487 (1993).
20. P. G. Bolhuis, C. Dellago, and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 97, 5877 (2000).
21. G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 118, 10762 (2003).
22. R. Durrett, Stochastic Calculus (CRC, Washington, DC, 1996).
23. M. I. Freidlin and A. D. Wentzell, Random Perturbations of Dynamical Systems (Springer, New York/Verlag, Berlin, 1984).
24. C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences (Springer, New York, 1997).
25. S. Nosé, Mol. Phys. 57, 187 (1986).
26. G. Henkelman and H. Jonsson, J. Chem. Phys. 113, 9978 (2000).
27. W. Ren, Commun. Math. Sci. 1, 5877 (2003).
28. H. Jonsson, G. Mills, and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker, (World Scientific, Singapore, 1998).
29. M. Buck and M. Karplus, J. Am. Chem. Soc. 121, 9645 (1999).
30. A. S. MacKerell, Jr., D. Bashford, M. Bellott et al., J. Phys. Chem. B 102, 3586 (1998).
31. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
32. B. Oksendal, Stochastic Differential Equations (Springer, New York/Verlag, Berlin, 1984).
33. M. Kac, Probability and Related Topics in Physical Sciences. Lectures in Applied Mathematics (Interscience, New York, 1959).
34. G. Ciccotti, R. Kapral, and E. Vanden-Eijnden, ChemPhysChem 6, 1809 (2005).