Bibliography

1

M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Clarendon Press, Oxford, New York, 1987.
Reprinted in paperback in 1989 with corrections.

2

T. W. Allen, S. Kuyucak, and S. Chung.
Molecular dynamics study of the KcsA potassium channel.
Biophysics Journal, 77:2502-2516, 1999.

3

A. Amadei, A. B. M. Linnsen, and H. J. C. Berendsen.
Essential dynamics of proteins.
PROTEINS: Struc., Func., and Genetics, 17:412-425, 1993.

4

H. C. Andersen.
Molecular dynamics simulations at constant pressure and/or temperature.
J. Chem. Phys., 72:2384-2393, 1980.

5

S. F. Ashby, T. A. Manteuffel, and P. E. Saylor.
A taxonomy for conjugate gradient methods.
SIAM Journal on Numerical Analysis, 27(6):1542-1568, 1990.

6

P. F. Batcho and T. Schlick.
New splitting formulations for lattice summations.
J. Chem. Phys., 2001.

7

D. M. Beazley and P. S. Lomdahl.
Message-passing multi-cell molecular dynamics on the connection machine 5.
Parallel Computing, 20:173-195, 1994.

8

D. M. Beazley and P. S. Lomdahl.
Lightweight computational steering of very large scale molecular dynamics simulations.
In Proceedings of Supercomputing '96, 1996.

9

H. J. C. Berendsen.
Molecular dynamics simulations: The limits and beyond.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pages 3-36. Springer-Verlag, Nov. 1998.

10

T. C. Bishop, D. Kosztin, and K. Schulten.
How hormone receptor-DNA binding affects nucleosomal DNA: The role of symmetry.
Biophys. J., 72:2056-2067, May 1997.

11

A. Brass, B. J. Pendleton, Y. Chen, and B. Robson.
Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics.
Biopolymers, 33:1307-1315, 1993.

12

B. R. Brooks and M. Hodoscek.
Parallelization of CHARMm for MIMD machines.
CDA, 7:16-22, Dec. 1992.

13

C. L. Brooks III, M. Karplus, and B. M. Pettitt.
volume LXXI of Advances in Chemical Physics.
John Wiley & Sons, New York, 1988.

14

C. L. Brooks III, M. Karplus, and B. M. Pettitt.
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics.
John Wiley and Sons, 1988.

15

D. Brown, H. Minoux, and B. Maigret.
A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity.
Computer Physics Communications, 103:170-186, 1997.

16

A. T. Brünger.
X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR.
Yale University Press, New Haven and London, 1992.

17

A. M. Brzozowski, A. C. W. Pike, Z. Dauter, R. E. Hubbard, T. Bonn, O. Engstrom, L. Ohman, G. L. Greene, J. Ake Gustafsson, and M. Carlquist.
Molecular basis of agonism and antagonism in the oestrogen receptor.
Nature, 389:753-758, October 1997.

18

J. Cao and B. J. Berne.
Monte Carlo methods for accelerating barrier crossing: Anti-force-bias and variable step algorithms.
J. Chem. Phys., 92:1980, 1990.

19

Z. M. Chen, T. Cagin, and W. A. Goddard.
Fast Ewald sums for general van der Waals potentials.
J. Comp. Chem., 18:1365-1370, 1997.

20

C. T. Choma and P. T. T. Wong.
The structure of anhydrous and hydrated dimyristoylphosphatidyl glycerol: a pressure tuning infrared spectroscopic study.
Chem. Phys. Lipids, 61:131-137, 1992.

21

S. Chung, T. W. Allen, M. Holes, and S. Kuyucak.
Permeation of ions across the potassium channel: Brownian dynamics studies.
Biophysical Journal, 77:2517-2533, 1999.

22

M. E. Clamp, P. G. Baker, C. J. Stirling, and A. Brass.
Hybrid Monte Carlo: An efficient algorithm for condensed matter simulation.
J. Comput. Chem., 15(8):838-846, 1994.

23

T. W. Clark, R. v. Hanxleden, J. A. McCammon, and L. R. Scott.
Parallelizing molecular dynamics using spatial decomposition.
In Proceedings of the Scalable High-Performance Computing Conference, pages 95-102, Los Alamitos, Calif., 1994. IEEE Computer Society Press.

24

D. M. Cortes, L. G. Cuello, and E. Perozo.
Molecular architecture of full-length KcsA.
J. Gen Physiology, 117:165-180, 2001.

25

T. Darden, D. York, and L. Pedersen.
Particle mesh Ewald. An N$\cdot$log(N) method for Ewald sums in large systems.
J. Chem. Phys., 98:10089-10092, 1993.

26

K. A. Dill and H. S. Chan.
From levinthal to pathways to funnels.
Nature Struct. Biol., 4:10-19, 1997.

27

D. A. Doyle, J. M. Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbis, S. L. Cohen, B. T. Chait, and R. MacKinnon.
The structure of the potassium channel: Molecular basis of ${K}^+$ conduction and selectivity.
Science, 280:69-77, 1998.

28

Y. Duan and P. Kollman.
Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution.
Science, 282:740-744, 1998.

29

H. Dufner, S. M. Kast, J. Brickmann, and M. Schlenkrich.
Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids: A quantitative study.
J. Comp. Chem., 18:660-676, 1997.

30

P. Ewald.
Die berechnung optischer und elektrostatischer gitterpotentiale.
Ann. Phys., 64:253-287, 1921.

31

A. Fischer, F. Cordes, and C. Schütte.
Hybrid Monte Carlo with adaptive temperature in a mixed-canonical ensemble: Efficient conformational analysis of rna.
Technical Report SC 97-67, Konrad-Zuse-Zentrum für Informationstechnik Berlin, Dec. 1997.
Available via http://www.zib.de/bib/pub/pw/.

32

T. Forester and W. Smith.
On multiple time-step algorithms and the Ewald sum.
Mol. Sim., 13(3):195-204, 1994.

33

B. M. Forrest and U. W. Suter.
Hybrid Monte Carlo simulations of dense polymer systems.
J. Chem. Phys., 101, 1994.

34

D. Frenkel and B. Smit.
Understanding Molecular Simulation: From Algorithms to Applications.
Academic Press, 1996.

35

B. García-Archilla, J. M. Sanz-Serna, and R. D. Skeel.
Long-time-step methods for oscillatory differential equations.
SIAM J. Sci. Comput., 20(3):930-963, Oct. 20, 1998.

36

D. G. Gromov and J. J. de Pablo.
Structure of binary polymer blends - multiple time step hybrid Monte Carlo simulations and self-consistent integral-equation theory.
J. Chem. Phys., 103(18):8247-8256, November 1995.

37

A. Grzybowski, E. Gwozdz, and A. Brodka.
Ewald summation of electrostatic interactions in molecular dynamics of a three-dimensional system with periodicity in two directions.
Phys. Rev., 61:6706-6712, 2000.

38

J. M. Haile.
Molecular Dynamics Simulation.
John Wiley and Sons, 1992.

39

U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger.
Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble.
Chem. Phys. Lett., 259:321-330, September 1996.

40

K. Hoogsteen.
The crystal and molecular structure of a hydrogen-bonded complex between 1-methyl thymin and 9-methyl adenine.
Acta Cryst., 16:907-916, 1963.

41

W. F. Humphrey, A. Dalke, and K. Schulten.
VMD - Visual Molecular Dynamics.
J. Mol. Graphics, 14:33-38, 1996.

42

Y.-S. Hwang, R. Das, J. H. Saltz, M. Hodošcek, and B. R. Brooks.
Parallelizing molecular dynamics programs for distributed-memory machines.
IEEE Computational Science & Engineering, 2(2):18-29, Summer 1995.

43

A. Irbäck.
Hybrid Monte Carlo simulation of polymer chains.
J. Chem. Phys., 101(2):1661-1667, July 1994.

44

J. A. Izaguirre.
Longer Time Steps for Molecular Dynamics.
PhD thesis, University of Illinois at Urbana-Champaign, 1999.
Also UIUC Technical Report UIUCDCS-R-99-2107. Available online via http://www.cs.uiuc.edu/research/tech-reports.html.

45

J. A. Izaguirre.
http://www.cse.nd.edu/academics/cse598e/www, 2000.
Home page for course "Computational Methods in Biomolecular Modeling".

46

J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, and R. D. Skeel.
Langevin stabilization of molecular dynamics.
J. Chem. Phys., 114(5):2090-2098, Feb. 1, 2001.

47

J. A. Izaguirre, Q. Ma, T. Matthey, J. Willcock, T. Slabach, B. Moore, and G. Viamontes.
Overcoming instabilities in verlet-i/r-RESPA with the mollified impulse method.
In T. Schlick, editor, Proceedings of International Workshop on Methods for Macromolecular Modeling, New York, 2001. Springer Verlag.
Available from http://www.nd.edu/~izaguirr/papers/newM3paper.pdf.

48

J. A. Izaguirre, T. Matthey, J. Willcock, Q. Ma, B. Moore, T. Slabach, and G. Viamontes.
A tutorial on the prototyping of multiple time stepping integrators for molecular dynamics.
Available from http://www.cse.nd.edu/~lcls/Protomol.html, 2001.

49

J. A. Izaguirre, S. Reich, and R. D. Skeel.
Longer time steps for molecular dynamics.
J. Chem. Phys., 110(19):9853-9864, May 15, 1999.

50

J. A. Izaguirre, J. Willcock, T. Matthey, T. B. Slabach, T. Steinbach, S. Stender, G. F. Viamontes, and J. Mohnke.
ProtoMol: An object oriented framework for molecular dynamics.
Available online via http://www.cse.nd.edu/~lcls/Protomol.html, 2000.

51

J. A. Izaguirre, J. J. Willcock, T. S. Slabach, and G. V. Viamontes.
Object oriented program for molecular dynamics.
In Proc. Midwest Numerical Analysis Day, 2000.

52

W. Kabsch and C. Sander.
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers, 22:2577-637, 1983.

53

L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten.
NAMD2: Greater scalability for parallel molecular dynamics.
J. Comp. Phys., 151:283-312, 1999.

54

M. Karplus.
Molecular dynamics: Applications to proteins.
In J.-L. Rivail, editor, Modelling of Molecular Structures and Properties, volume 71 of Studies in Physical and Theoretical Chemistry, pages 427-461, Amsterdam, 1990. Elsevier Science Publishers.
Proceedings of an International Meeting.

55

M. Kawata and M. Mikami.
Acceleration of the canonical molecular dynamics simulation by the particle mesh Ewald method combined with the multiple time-step integrator algorithm.
Chem. Phys. Lett., 313:261-266, 1999.

56

A. D. Kennedy.
The theory of hybrid stochastic algorithms.
In P. H. Damgaard, H. Hüffel, and A. Rosenblum, editors, Probabilistic Methods in quantum field theory and quantum gravity, volume 224 of NATO ASI Series, page 209, New York, 1989. Plenum Press.

57

D. Kosztin, T. C. Bishop, and K. Schulten.
Binding of the estrogen receptor to DNA: The role of waters.
Biophys. J., 73:557-570, 1997.

58

S. Kuwajima and A. Warshel.
The extended Ewald method - A general treatment of long-range lectrostatic interactions in microscopic simulations.
J. Chem. Phys., 89:3751-3759, 1988.

59

A. R. Leach.
Molecular Modelling, Principles and Applications.
Addison Wesley Longman Limited, Essex, 1996.

60

Q. Ma, R. D. Skeel, and J. A. Izaguirre.
Verlet-I/r-RESPA is nonlinearly unstable!
In preparation, 2001.

61

J. I. MacGregor and V. C. Jordan.
Basic guide to the mechanisms of antiestrogen action.
Pharmacological Reviews, 50(2):151-196, June 1998.

62

A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus.
All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field.
J. Phys. Chem. B, 102:3586-3616, 1998.

63

A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus.
Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations.
FASEB J., page 6:A143, 1992.

64

T. Matthey and J. P. Hansen.
Evaluation of MPI's one-sided communication mechanism for short-range molecular dynamics on the Origin2000.
In PARA2000 and Workshop on Applied Parallel Computing, 2000.

65

T. Matthey and J. A. Izaguirre.
ProtoMol: A molecular dynamics framework with incremental parallelization.
In Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01), Proceedings in Applied Mathematics, Philadelphia, March 2001. Society for Industrial and Applied Mathematics.

66

J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.

67

I. K. McDonald and J. M. Thornton.
Satisfying hydrogen bonding potential in proteins.
J. Mol. Biol., 238:777-793, 1994.

68

B. Mehlig, D. W. Heermann, and B. M. Forrest.
Hybrid Monte Carlo method for condensed-matter systems.
Phys. Rev. B, 45(2):679-685, Jan. 1, 1992.

69

R. M. Neal.
Probabilistic inference using Markov chain Monte Carlo methods.
Technical Report CRG-TR-93-1, university of Toronto, 1993.

70

T. M. Nymand and P. Linse.
Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities.
J. Chem. Phys., 112:6152-6160, 2000.

71

R. Olender and R. Elber.
Calculation of classical trajectories with a very large time step: Formalism and numerical examples.
J. Chem. Phys., 105(20):9299-9315, 1996.

72

B. C. Oostenbrink, J. W. Pitera, M. M. H. van Lipzig, J. H. N. Meerman, and W. F. van Gunsteren.
Simulation of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens.
J. Med. Chem., 43:4594-4605, 2000.

73

E. Perozo, D. M. Cortes, and L. G. Cuello.
Structural rearrangements underlying ${K}^+$ channel activation gating.
Science, 285:73-78, 1999.

74

C. S. Peskin and T. Schlick.
Molecular dynamics by the backward Euler method.
Comm. Pure and Appl. Math., 42:1001-1031, 1989.

75

G. C. Pimentel and A. L. McClellan.
The Hydrogen Bond.
W. H. Freeman and Co., San Francisco and London, 1960.

76

P. Procacci, M. Marchi, and G. J. Martyna.
Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems.
J. Chem. Phys., 108(21):8799-8803, Jun 1998.

77

C. J. Roberts and P. G. Debenedetti.
Structure and dynamics in concentrated, amorphous carbohydrate-water systems by molecular dynamics simulation.
J. Phys. Chem. B, 103:7308-7318, 1999.

78

J. Sanz-Serna and M. Calvo.
Numerical Hamiltonian Problems.
Chapman and Hall, London, 1994.

79

T. Schlick, M. Mandziuk, R. D. Skeel, and K. Srinivas.
Nonlinear resonance artifacts in molecular dynamics simulations.
J. Comput. Phys., 139:1-29, 1998.

80

K. E. Schmidt and M. A. Lee.
Multipole Ewald sums for the fast multipole method.
J. Stat. Phys., 89:411-424, 1997.

81

R. D. Skeel.
Macromolecular dynamics on a shared-memory multiprocessor.
J. Comp. Chem., 12(2):175-179, January 1991.

82

R. D. Skeel and D. J. Hardy.
Practical construction of modified Hamiltonians.
2001.

83

R. D. Skeel and J. Izaguirre.
The five femtosecond time step barrier.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pages 303-318. Springer-Verlag, Berlin Heidelberg New York, Nov. 1998.

84

D. M. Small.
The Physical Chemistry of Lipids.
Number 4 in Handbook of Lipid Research. Plenum Publishing Corp., New York, 1986.

85

P. E. Smith and B. M. Pettitt.
Efficient Ewald electrostatic calculations for large systems.
CPC, 91(1):339-344, September 1995.

86

D. Solvason, J. Kolafa, H. G. Petersen, and J. W. Perram.
A rigorous comparison of the Ewald method and the fast multipole method in 2 dimensions.
Comp. Phys. Comm., 87:307-318, 1995.

87

J. Stone, J. Gullingsrud, and K. Schulten.
A system for interactive molecular dynamics.
In 2001 Symposium on Interactive 3D Graphics. ACM, 2001.
In Press.

88

T. C. Terwilliger and D. Eisenberg.
The structure of melittin.
J. Biol. Chem., 257:6010, 1982.

89

D. Thirumalai, R. D. Mountain, and T. R. Kirkpatrick.
Ergodic behavior in supercooled liquids and in glasses.
Phys. Rev. A, 39:3563, 1989.

90

T. M. Truskett, P. G. Debenedetti, S. Sastry, and S. Torquato.
A single-bond approach to orientation-dependent interactions and its implications for liquid water.
J. Chem. Phys., 111(6), 8 August 1999.

91

M. Tuckerman, B. J. Berne, and G. J. Martyna.
Reversible multiple time scale molecular dynamics.
J. Chem. Phys, 97(3):1990-2001, 1992.

92

M. E. Tuckerman, D. Yarne, S. O. Samuelson, A. L. Hughes, and G. J. Martyna.
Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers.
CPC, 128:333-376, 2000.

93

J. C. Uitdehaag, B. A. V. der Veen, L. Dijkhuizen, R. Elber, and B. W. Dijkstra.
Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase.
Proteins, 43(3):327-335, May 2001.

94

W. F. van Gunsteren and M. Karplus.
Effect of constraints on the dynamics of macromolecules.
Macromolecules, 15:1528-1544, 1982.

95

J. Vincent and K. M. Merz.
A highly portable parallel implementation of Amber using the message passing interface standard.
J. Comp. Chem., 11:1420-1427, 1995.

96

R. C. Whaley, A. Petitet, and J. J. Dongarra.
Automated empirical optimizations of software and the atlas project.
Technical report, University of Tennessee, Knoxville, TN, Department of Computer Science, Univ. of TN, Knoxville, TN 37996, April 2000.

97

M. R. Yudt and S. Koide.
Preventing estrogen receptor action with dimer-interface peptides.
Steroids, 66:549-558, 2001.

98

G. Zhang and T. Schlick.
Implicit discretization schemes for Langevin dynamics.
Mol. Phys., 84:1077-1098, 1995.

99

M. Zhang and R. D. Skeel.
Cheap implicit symplectic integrators.
Appl. Num. Math., 25:297-302, 1997.

100

F. Zhou and K. Schulten.
long-range force molecular dynamics study on electrostatic and other properties of a membrance-water interface.
Technical Report UIUC-BI-TB-94-01, university of illinois at urbana-champaign, 1994.

101

H. Zhou, S. T. Wlodek, and J. A. McCammon.
Conformation gating as a mechanism for enzyme specificity.
Proc. Natl. Acad. Sci. USA, 95:9280-9283, August 1998.
Biophysics.

102

R. H. Zhou and B. J. Berne.
Smart walking--a new method for Boltzmann sampling of protein conformations.
J. Chem. Phys., 107(21):9185-9196, Dec. 1, 1997.