Bridging the gap between long time trajectories and reaction pathways

Advances in Chemical Physics

Volumn 126, Issue , 2003, Pages 93-129

  Ron, Elber ^a   Cárdenas, Alfredo ^a   Avijit, Ghosh ^a   Stern, Harry A ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78751663166     PISSN: 00652385     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (24)

1. Y. Duan and P. A. Kollman, Pathways to a protein folding intermediate observed in a microsecond simulation in aqueous solution. Science 282, 740-744 (1998).
2. R. Elber, Reaction path studies of biological molecules, in Recent Developments in Theoretical Studies of Proteins, Ron Elber, ed., World Scientific, Singapore, 1996, pp. 65-136.
3. See, for instance, D. G. Truhlar and B. C. Garrett, Multidimensional transition state theory and the validity of Grote Hynes theory. J. Phys. Chem. B 104, 1069-1072 (2000).
4. R. Olender and R. Elber, Calculation of Classical Trajectories with a Very Large Time Step: Formalism and Numerical Examples. J. Chem. Phys. 105, 9299-9315 (1996).
5. R. Elber, J. Meller, and R. Olender, A stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide. J. Phys. Chem. B, 103, 899-911 (1999).
6. V. Zaloj and R. Elber, Parallel computations of molecular dynamics trajectories using stochastic path approach. Comput. Phys. Commun. 128, 118-127 (2000).
7. J. C. M. Uitdehaag, B. A. van der Veen, L. Dijkhuizen, R. Elber, and B. W. Dijkstra, The enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase. Proteins Struct. Funct. Genet. 43, 327-335 (2001).
8. L. Verlet, Computer experiments on classical fluids I. Thermodynamics properties of Lennard Jones molecules. Phys. Rev. 98, 159 (1967).
9. L. D. Landau and E. M. Lifshitz, Mechanics, Butterworth-Heinenann, Oxford, 1993.
10. P. F. Batcho, D. A. Case, and T. Schlick, Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. J. Chem. Phys. 115, 4003-4018 (2001).
11. R. H. Zhou, E. Harder, H. F. Xu, and B. J. Berne, Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems. J. Chem. Phys. 115, 2348-2358 (2001).
12. T. C. Bishop, R. D. Skeel, K. Schulten, Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics. J. Comp. Chem. 18, 1785-1791 (1997).
13. A. Ulitsky and R. Elber, The equilibrium of the time dependent Hartree and the locally enhanced sampling approximations: Formal properties, corrections, and computational studies of rare gas clusters. J. Chem. Phys. 98, 3380 (1993).
14. C. Lanczos, The Variational Principles of Mechanics, University of Toronto Press, 1970.
15. H. Kleinert, Path Integrals in Quantum Mechanics, Statistics and Polymer Physics, World Scientific, Singapore, 1995, Chapters 18.5 and 18.6.
16. R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker, C. Keasar, J. Zhang, and A. Ulitsky, Moil: A program for simulations of macromolecules. Comput. Phys. Commun. 91, 159-189 (1995).
17. J. M. Haile and S. Gupta, Extensions of the molecular dynamics simulation method 2. Isothermal systems. J. Chem. Phys. 79, 3067 (1983).
18. R. Elber, A. Ghosh, and A. Cárdenas, Account of Chemical Research 33, 396-403 (2002).
19. R. Czerminski and R. Elber, Self avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems. Int. J. Quant. Chem. 24, 167-186 (1990).
20. R. Elber, Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide. J. Chem. Phys. 93, 4312 (1990).
21. B. M. Mandelbort, The Fractal Geometry of Nature, Freeman, San Francisco, 1977.
22. A. Ulitsky and R. Elber, A new technique to calculate steepest descent paths in flexible polyatomic systems. J. Chem. Phys. 96, 1510 (1990).
23. See, for instance, R. J. Radmer and P. A. Kollman, Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes. J. Comp. Chem., 18, 902-919 (1997).
24. C. Dellago, P. G. Bolhuis, and D. Chandler, On the calculation of reaction rate constants in the transition path ensemble. J. Chem Phys. 110, 6617-6625 (1999).