‹ Abrams Group

References

[1]
D. Frenkel and B. Smit. Understanding Molecular Simulation: From Algorithms to Applications. Academic Press, San Diego, 2 edition, 2002.
[2]
M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Oxford University Press, New York, 1987.
[3]
D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, Cambridge, 1995.
[4]
Andrew R. Leach. Molecular Modelling: Principles and Applications. Prentice-Hall, 2001.
[5]
D. Chandler. An Introduction to Modern Statistical Mechanics. Oxford University Press, New York, 1987.
[6]
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. N. Teller, and E. Teller. Equation of state calculations by fast computing methods. J. Chem. Phys., 21:1087–1092, 1953.
[7]
Loup Verlet. Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Physical Review, 159(1):98–103, 1967.
[8]
W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Applications to small water clusters. J. Chem. Phys., 76(1):637–649, 1982.
[9]
M. Tuckerman, B. J. Berne, and G. J. Martyna. Reversible multiple time scale molecular dynamics. J. Chem. Phys., 97(3):1990–2001, 1992.
[10]
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81(8):3684–90, 1984.
[11]
H. C. Andersen. Molecular dynamics at constant pressure and/or temperature. J. Chem. Phys., 72:2384–2393, 1980.
[12]
G. S. Grest and K. Kremer. Molecular-dynamics simulation for polymers in the presence of a heat bath. Phys. Rev. A, 33(5):3628–3631, 1986.
[13]
P. Nikunen, M. Karttunen, and I. Vattulainen. How would you integrate the equations of motion in dissipative particle dynamics simulations? Comput. Phys. Comm., 153(3):407–423, 2003.
[14]
T. Soddemann, B. Dünweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68(4):046702, 2003.
[15]
I. G. Tironi and W. F. van Gunsteren. A molecular-dynamics simulation study of chloroform. Mol. Phys., 83(2):381–403, 1994.
[16]
F. H. Stillinger and T. A. Weber. Computer simulation of local order in condensed phases of silicon. Phys. Rev. B, 31(8):5262–71, 1985.
[17]
C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler. Transition path sampling and the calculation of rate constants. J. Chem. Phys, 108(5):1964–1977, 1998.
[18]
C. Dellago, P. G. Bolhuis, and D. Chandler. On the calculation of reaction rate constants in the transition path ensemble. J. Chem. Phys., 110(14):6617–6625, 1999.
[19]
P. G. Bolhuis. Transition-path sampling of \(\beta \)-hairpin folding. Proc. Nat. Acad. Sci., 100(21):12129–12134, 2003.
[20]
P. Ewald. Ann. Phys. (Leipzig), 64:253, 1921.
[21]
M. Deserno. Counterion condensation for rigid linear polyelectrolytes. PhD thesis, Johannes Gutenberg-Universität, Mainz, Germany, 2000.
[22]
F. Wang and D. P. Landau. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett., 86(10):2050–2053, 2001.
[23]
F. Wang and D. P. Landau. Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram. Phys. Rev. E, 64:056101, 2001.
[24]
M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos. An improved Monte-Carlo for direct calculation of the density of states. J. Chem. Phys., 119(18):9406–9411, 2003.
[25]
N. Rathore, T. A. Knotts IV, and J. J. de Pablo. Configurational temperature density of states simulations of proteins. Biophys. J., 85:3963–3968, 2003.
[26]
M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos. Generalization of the wang-landau method for off-lattice simulations. Phys. Rev. E, 66:056703, 2002.
[27]
F. Y. Wu. The potts model. Rev. Mod. Phys., 54:235–268, 1982.
[28]
H. B. Dwight. Tables of Integrals and Other Mathematical Data. MacMillan, 1961.