References

1

J. DEISENHOFER and H. MICHEL, The Crystal Structure of the Photosynthetic Reaction Center from Rps. Viridis, in The Photosynthetic Bacterial Reaction Center: Structure and Dynamics, edited by J. BRETON and A. VERMEGLIO, pp. 1--3, London, 1988, Plenum Press.

2

R. HENDERSON, J. M. BALDWIN, T. A. CESKA, F. ZEMLIN, E. BECKMANN, and K. H. DOWNING, J. Molec. Biol. 213, 899 (1990).

3

M. LEVITT, J. Molec. Biol. 168, 621 (1983).

4

H. FRAUENFELDER, Biophys. J. 47, 35 (1985).

5

J. A. MCCAMMON and M. KARPLUS, Proc. Natl. Acad. Sci. USA 76, 3585 (1987).

6

M. LEVITT and S. LIFSON, J. Molec. Biol. 46, 269 (1969).

7

J. A. MCCAMMON, B. R. GELIN, and M. KARPLUS, Nature 267, 585 (1977).

8

H. S. CHAN and K. A. DILL, Ann. Rev. Biophys. Biophys. Chem. 20, 447 (1991).

9

J. E. MERTZ, D. J. TOBIAS, C. L. BROOKS, and U. C. SINGH, J. Comp. Chem. 12, 1270 (1991).

10

N. S. OSTLUND and R. A. WHITESIDE, A machine architecture for molecular dynamics: the systolic loop, in Macromolecular Structure and Specificity: Computer-Assisted Modeling and Applications, edited by B. VENKATARAGHAVAN and R. J. FELDMAN, pp. 195--208, Annals of the N. Y. Acad. of Sciences 439, New York, 1985.

11

H. HELLER, H. GRUBMÜLLER, and K. SCHULTEN, Molec. Sim. 5, 133 (1990).

12

B. R. BROOKS and M. HODOSCEK, Chem. Des. Autom. News 7, 16 (1992).

13

W. F. VAN GUNSTEREN and H. J. C. BERENDSEN, Angew. Chem. Int. Ed. Engl. 29, 992 (1990).

14

D. I. OKUNBOR, Canonical Integration Methods for Hamiltonian Dynamical Systems, PhD thesis, University of Illinois at Urbana-Champaign, Department of Computer Science, 1304 W. Springfield Avenue, Urbana, Il 61801-2987, 1992.

15

M. BUCHNER and B. M. LADANYI, Molec. Phys. 73, 1127 (1991).

16

J. TURNER, H. CHUN, V. LUPI, P. WEINER, S. GALLION, and C. SINGH, Chem. Des. Autom. News 7, 33 (1992).

17

R. D. RUTH, IEEE Trans. Nuc. Sci. 30, 2669 (1983).

18

J. BARNES and P. HUT, Nature 324, 446 (1986).

19

L. GREENGARD and V. ROKHLIN, Chem. Scr. 29A, 139 (1989).

20

S. J. AARSETH, Direct Methods for N-Body Simulations, pp. 378--418, Multiple Time Scales, Academic Press, 1st edition, 1985.

21

R. CHICON and E. MARTIN, American Journal of Physics 59, 759 (1991).

22

B. J. BERNE, Molecular Dynamics and Monte Carlo Simualtions of Rare Events, pp. 419--436, Multiple Time Scales, Academic Press, 1st edition, 1985.

23

B. R. BROOKS, R. E. BRUCCOLERI, B. D. OLAFSON, D. J. STATES, S. SWAMINATHAN, and M. KARPLUS, J. Comp. Chem. 4, 187 (1983).

24

H. GRUBMÜLLER, H. HELLER, A. WINDEMUTH, and K. SCHULTEN, Molec. Sim. 6, 121 (1991).

25

M. E. TUCKERMAN and B. J. BERNE, J. Chem. Phys. 95, 8362 (1991).

26

H. GRUBMüLLER, Molekulardynamik von Proteinen auf langen Zeitskalen, PhD thesis, Technische Universität München, München, 1994.

27

R. J. LONCHARICH and B. R. BROOKS, Proteins 6, 32 (1989).

28

W. F. VAN GUNSTEREN and H. J. C. BERENDSEN, Molec. Phys. 34, 1311 (1977).

29

BENNET, J. Comp. Phys. 19, 297 (1975).

30

METROPOLIS, J. Chem. Phys. 21, 1087 (1953).

31

PANGALI, Chem. Phys. Lett. 55, 413 (1978).

32

R. M. LEVY, M. KARPLUS, and J. A. MCCAMMON, Chem. Phys. Lett. 65, 4 (1979).

33

M. E. TUCKERMAN and B. J. BERNE, J. Chem. Phys. 95, 4389 (1991).

34

S. MIYAZAWA, Macromolecules 18, 534 (1985).

35

H. FRAUENFELDER, K. CHU, and R. PHILIPP, Physics from Proteins, in Biologically Inspired Physics, edited by L. PELITI, Plenum Press, New York, 1991.

36

L. VERLET, Phys. Rev. 159, 98 (1967).

37

K. D. GIBSON and H. A. SCHERAGA, J. Comp. Chem. 11, 468 (1990).

38

H. GRUBMüLLER and P. TAVAN, J. Comp. Chem. (1994), in preparation.

39

A. ANSARI et al., Biophysical Chemistry 26, 337 (1987).

40

G. U. NIENHAUS, J. R. MOURANT, and H. FRAUENFELDER, PNAS 89, 2902 (1992).

41

A. BRÜNGER, C. BROOKS, and M. KARPLUS, Proc. Natl. Acad. Sci. USA 82, 8458 (1985).

42

H. TREUTLEIN, K. SCHULTEN, A. BRÜNGER, M. KARPLUS, J. DEISENHOFER, and H. MICHEL, Proc. Natl. Acad. Sci. USA 89, 75 (1991).

43

S. SWAMINATHAN, T. ICHIYE, W. VAN GUNSTEREN, and M. KARPLUS, Biochemistry 21, 5230 (1982).

44

R. H. AUSTIN et al., Biochemistry 14, 5355 (1975).

45

A. ANSARI, J. BERENDZEN, S. F. BROWNE, H. FRAUENFELDER, I. E. T. IBEN, T. B. SAUKE, E. SHYAMSUNDER, and R. D. YOUNG, Proc. Natl. Acad. Sci. USA 82, 5000 (1985).

46

P. HäNGGI, P. TALKNER, and M. BORKOVEC, Rev. Mod. Phys. 62, 251 (1990).

47

B. R. BROOKS, R. W. PASTOR, and F. W. CARSON, Proc. Natl. Acad. Sci. USA 84, 4470 (1987).

48

R. CZERMINSKI and R. ELBER, Proc. Natl. Acad. Sci. USA 86, 6963 (1989).

49

R. ELBER, J. Chem. Phys. 93, 4312 (1990).

50

J. PLEISS and F. JäHNIG, Eur. Biophys. J. 21, 63 (1992).

51

J. P. VALLEAU and G. M. TORRIE, in Statistical Mechanics Part A: Equilibrium Techniques, edited by B. J. BERNE, p. 137, Plenum Press, New York, 1977.

52

J. CAO and B. J. BERNE, J. Chem. Phys. 92, 1980 (1990).

53

H. S. CHAN and K. A. DILL, J. Chem. Phys. 95, 3775 (1991).

54

J. D. HONEYCUTT and D. THIRUMALAI, Biopolymers 32, 695 (1992).

55

H. FRAUENFELDER, S. G. SLIGAR, and P. G. WOLYNES, Science 254, 1598 (1991).

56

W. DOSTER, S. CUSACK, and W. PETRY, Nature 337, 754 (1989).

57

W. NADLER, A. T. BRüNGER, K. SCHULTEN, and M. KARPLUS, Proc. Natl. Acad. Sci. USA 84, 7933 (1987).

58

D. E. SMITH and C. B. HARRIS, J. Chem. Phys. 92, 1304 (1990).

59

T. E. CREIGHTON, Proteins, W. H. Freeman and Company, San Francisco, 1984.

60

K. A. DILL, Biochemistry 29, 7133 (1990).

61

M. PRéVOST, S. J. WODAK, B. TIDOR, and M. KARPLUS, Proc. Natl. Acad. Sci. USA 88, 10880 (1991).

62

R. L. ORNSTEIN, J. Biol. Struct. Dyn. 7, 1019 (1990).

63

J. C. SMITH, Q. Rev. Biophys. 24, 227 (1991).

64

M. KURZYNSKI, Accounts of Chemical Research , submitted.

65

H. FRAUENFELDER, P. J. STEINBACH, and R. D. YOUNG, Chem. Scr. 29A, 145 (1989).

66

S. A. RICE and P. GRAY, The Statistical Mechanics of Simple Liquids, Interscience Publishers, John Wiley & Sons, Inc., New York, 1965.

67

R. ELBER and M. KARPLUS, Science 235, 318 (1987).

68

N. GO and T. NOGUTI, Chem. Scr. 29A, 151 (1989).

69

S. CHANDRASEKHAR, Rev. Mod. Phys. 15, 1 (1943).

70

H. A. KRAMERS, Physica 7, 284 (1940).