Calculation of classical trajectories with boundary value formulation

Lecture Notes in Physics

Volumn 703, Issue , 2006, Pages 435-451

  Elber, Ron ^a  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33947203112     PISSN: 00758450     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-35273-2_12     Document Type: Article

References (20)

1. L. Verlet (1967) Computer experiments on classical fluids I. Thermodynamics properties of Lennard Jones molecules. Phys. Rev. 98, p. 159
2. D. Chandler (1978) Statistical mechanics of isomerization dynamics in liquids and transition-state approximation. J. Chem. Phys. 68, pp. 2959-2970
3. C. Dellago, P. G. Bolhuis, and D. Chandler (1999) On the calculation of reaction rates in the transition path ensemble. J. Chem. Phys. 110, pp. 6617-6625
4. L. D. Landau and E. M. Lifshitz (2000) Mechanics, third edition, Butterworth-Heinenann, Oxford, Chap. 1
5. L. D. Landau and E. M. Lifshitz (2000) Mechanics, third edition, Butterworth-Heinenann, Oxford, pp. 140-142
6. R. Olender and R. Elber (1996) Calculation of classical trajectories with a very large time step: Formalism and numerical examples. J. Chem. Phys. 105, pp. 9299-9315
7. R. Elber, J. Meller and R. Olender (1999) A stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide. J. Phys. Chem. B 103, pp. 899-911
8. K. Siva and R. Elber (2003) Ion permeation through the gramicidin channel: Atomically detailed modeling by the stochastic difference equation. Proteins, Structure, Function and Genetics 50, pp. 63-80
9. A. Ulitksy and R. Elber (1990) A new technique to calculate the steepest descent paths in flexible polyatomic systems. J. Chem. Phys. 96, p. 1510
10. E. Weinan, R. Weiqing, and E. Vanden-Eijnden (2002) String method for the study of rare events. Physical Review B 66, p. 52301
11. H. Jonsson, G. Mills, and K. W. Jacobsen (1998) Nudge Elastic Band Method for Finding Minimum Energy Paths of Transitions, in Classical and Quantum Dynamics in Condensed Phase Simulations. Edited by B.J. Berne, G. Ciccotti, D.F. Coker, World Scientific, p. 385.
12. C. Lanczos (1970) The variational principles of mechanics. University of Toronto Press
13. L. Onsager and S. Machlup (1953) Phys. Rev. 91, p. 1505
14. ibid. (1953); 91, p. 1512
15. J. C. M. Uitdehaag, B. A. van der Veen, L. Dijkhuizen, R. Elber, and B. W. Dijkstra (2001) Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase. Proteins Structure Function and Genetics 43, pp. 327-335
16. K. Siva and R. Elber (2003) Ion permeation through the gramicidin channel: Atomically detailed modeling by the Stochastic Difference Equation. Proteins Structure Function and Genetics 50, pp. 63-80
17. D. Bai and R. Elber, Calculation of point-to-point short time and rare trajectories with boundary value formulation. J. Chemical Theory and Computation, 2, 484-494(2006)
18. A. Ghosh, R. Elber, and H. Scheraga (2002) An atomically detailed study of the folding pathways of Protein A with the Stochastic Difference Equation. Proc. Natl. Acad. Sci. 99, pp. 10394-10398
19. A. Cárdenas and R. Elber (2003) Kinetics of Cytochrome C Folding: Atomically Detailed Simulations. Proteins, Structure Function and Genetics 51, pp. 245-257
20. A. Cárdenas and R. Elber (2003) Atomically detailed simulations of helix formation with the stochastic difference equation. Biophysical Journal, 85, pp. 2919-2939