Bibliography

1
Robert B. Sandberg, Martina Banchelli, Carlo Guardiani, Stefano Menichetti, Gabriella Caminati, and Piero Procacci.
Efficient nonequilibrium method for binding free energy calculations in molecular dynamics simulations.
Journal of Chemical Theory and Computation, 11(2):423-435, 2015.

2
P. Procacci, T. Darden, E. Paci, and M. Marchi.
J. Comput. Chem., 18:1848, 1997.

3
S. J. Wiener, P. A. Kollmann, D. T. Nguyen, and D. A. Case.
J. Comput. Chem., 7:230, 1986.

4
W. D. Cornell, P. Cieplak, C. I. Bavly, I. R. Gould, K. M. Merz Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. Kollmann.
J. Am. Chem. Soc., 117:5179, 1995.

5
B. R. Brooks, R. E. Bruccoeri, B. D. Olafson, D.J. States, S. Swaminanthan, and M. Karplus.
J. Comput. Chem., 4:187, 1983.

6
W.F. van Gunsteren and H. J. C. Berendsen.
Groningen Molecular Simulation (GROMOS) Library Manual.
Biomos, Groningen, 1987.

7
A. D. MacKerrel, J. Wirkeiwicz-Kuczera, and M. Karplus.
J. Am. Chem. Soc, 117:11946, 1995.

8
J. J. Pavelites, P. A. Gao, and A. D. MacKerrel.
Biophysical J., 18:221, 1997.

9
A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick T., Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus.
J. Phys. Chem. B, 102:3586, 1998.

10
J. P. Ryckaert, G. Ciccotti, and H. J. C Berendsen.
J. Comput. Phys., 23:327, 1977.

11
G. Ciccotti and J. P. Ryckaert.
Comp. Phys. Report, 4:345, 1986.

12
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, Walton Street, Oxford OX2 6DP, 1989.

13
P. Procacci, T. Darden, and M. Marchi.
J. Phys. Chem, 100:10464, 1996.

14
W. B. Street, D.J. Tildesley, and G. Saville.
Mol. Phys., 35:639, 1978.

15
O. Teleman and B. Joensonn.
J. Comput. Chem., 7:58, 1986.

16
M. E. Tuckerman, G. J. Martyna, and B. J. Berne.
J. Chem. Phys., 94:6811, 1991.

17
M. E. Tuckerman and B. J. Berne.
J. Chem. Phys., 95:8362, 1991.

18
M. E. Tuckerman, B. J. Berne, and A. Rossi.
J. Chem. Phys., 94:1465, 1990.

19
H. Grubmuller, H. Heller, A. Winemuth, and K. Schulten.
Mol. Simul., 6:121, 1991.

20
M. E. Tuckerman, B.J. Berne, and G.J. Martyna.
J. Chem. Phys., 97:1990, 1992.

21
M. E. Tuckerman, B. J. Berne, and G. J. Martyna.
J. Chem. Phys., 99:2278, 1993.

22
D. D. Humphreys, R. A. Friesner, and B. J. Berne.
J. Phys. Chem., 98:6885, 1994.

23
P. Procacci and B. J. Berne.
J. Chem. Phys., 101:2421, 1994.

24
P. Procacci and M. Marchi.
J. Chem. Phys., 104:3003, 1996.

25
G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein.
Mol. Phys., 87:1117, 1996.

26
P. Procacci and B. J. Berne.
Mol. Phys., 83:255, 1994.

27
M. Marchi and P. Procacci.
J. Chem. Phys., 109:5194, 1998.

28
M. Saito.
J. Chem. Phys., 101:4055, 1994.

29
H. Lee, T. A. Darden, and L. G. Pedersen.
J. Chem. Phys., 102:3830, 1995.

30
J. A. Barker and R. O. Watts.
Mol. Phys., 26:789, 1973.

31
J. A. Barker.
The problem of long-range forces in the computer simulation of condensed matter.
volume 9, page 45. NRCC Workshop Proceedings, 1980.

32
P. Ewald.
Ann. Phys., 64:253, 1921.

33
S.W. deLeeuw, J. W. Perram, and E. R. Smith.
Proc. R. Soc. London A, 373:27, 1980.

34
T. Darden, D. York, and L. Pedersen.
J. Chem. Phys., 98:10089, 1993.

35
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen.
J. Chem. Phys., 101:8577, 1995.

36
R. W. Hockney.
Computer Simulation Using Particles.
McGraw-Hill, New York, 1989.

37
H.G. Petersen, D. Soelvanson, and J. W. Perram.
J. Chem. Phys, 101:8870, 1994.

38
L. Greengard and V. Rokhlin.
J. Comput. Phys., 73:325, 1987.

39
J. Shimada, H. Kaneko, and T. Takada.
J. Comput. Chem., 15:28, 1994.

40
R. Zhou and B. J. Berne.
J. Chem. Phys., 103:9444, 1996.

41
Y. Duan and P. A. Kollman.
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
Science, 282:740-744, 1998.

42
R. H. Swendsen and J. S. Wang.
Phys. Rev. Lett., 57:2607, 1986.

43
C. G. Geyer.
in Computing Science and Statistics, Proceedings of the 23rd Symposium on the Interface, edited by E. M. Keramidis, page 156, 1991.

44
E. Marinari and G. Parisi.
Europhys. Lett., 19:451, 1992.

45
K. Hukushima and K. Nemoto.
J. Phys. Soc. Jpn., 65:1604, 1996.

46
Y. Okamoto.
J. Mol. Graphics Modell., 22:425, 2004.

47
A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov.
J. Chem. Phys., 96:1776, 1992.

48
S. Rauscher, C. Neale, and R. Pomès.
J. Chem. Theory Comput., 5:2640, 2009.

49
S. Park.
Phys. Rev. E, 77:016709, 2008.

50
C. Zhang and J. Ma.
J. Chem. Phys., 129:134112, 2008.

51
J. G. Kirkwood.
J. Chem. Phys., 3:300, 1935.

52
D. A. McQuarrie.
Statistical Mechanics.
HarperCollinsPublishers, New York, USA, 1976.

53
S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg.
J. Comput. Chem., 13:1011, 1992.

54
A. M. Ferrenberg and R. H. Swendsen.
Phys. Rev. Lett., 63:1195, 1989.

55
C. J. Woods, J. W. Essex, and M. A. King.
J. Phys. Chem. B, 107:13703, 2003.

56
R. Chelli.
J. Chem. Theory. Comput., 6:1935, 2010.

57
G. M. Torrie and J. P. Valleau.
Chem. Phys. Lett., 28:578-581, 1974.

58
A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99:12562-12566, 2002.

59
S. Marsili, A. Barducci, R. Chelli, P. Proccaci, and V. Schettino.
J. Phys. Chem. B, 110:14011-14014, 2006.

60
F. Wang and D. P. Landau.
Phys. Rev. Lett., 86:2050-2053, 2001.

61
J. Henin and C. Chipot.
J. Chem. Phys., 121:2904-2914, 2004.

62
A. Laio, A. Rodriguez-Fortea, F. L. Gervasio, M. Ceccarelli, and M. Parrinello.
Assessing the accuracy of metadynamics.
J. Phys. Chem. B, 109:6714-6721, 2005.

63
C. Jarzynski.
Nonequilibrium equality for free energy differences.
Phys. Rev. Lett., 78:2690-2693, 1997.

64
G. E. Crooks.
J. Stat. Phys., 90:1481-1487, 1998.

65
G. Hummer and A. Szabo.
Proc. Natl. Acad. Sci. USA, 98:3658-3661, 2001.

66
M. R. Shirts, E. Bair, G. Hooker, and V. S. Pande.
Phys. Rev. Lett., 91:140601, 2003.

67
D. Chandler.
Introduction to Modern Statistical Mechanics.
Oxford University Press, 1987.

68
J. M. Sanz-Serna.
Acta Numerica, 1:243, 1992.

69
S. K. Grey, D. W. Noid, and B. G. Sumpter.
J. Chem. Phys., 101:4062, 1994.

70
J. J. Biesiadecki and R. D. Skeel.
J. Comp. Physics., 109:318, 1993.

71
P. J. Channel and C. Scovel.
Nonlinearity, 3:231, 1990.

72
H. Goldstein.
Classical Mechanics.
Addison-Wesley, Reading MA, 1980.

73
V. I. Arnold.
Mathematical Methods of Classical Mechanics.
Springer-Verlach, Berlin, 1989.

74
H. F. Trotter.
Proc. Am. Math Soc., 10:545, 1959.

75
H. de Raedt and B. De Raedt.
Phys. Rev. A, 28:3575, 1983.

76
H. Yoshida.
Phys. Letters A, 150:262, 1990.

77
S. J. Toxvaerd.
J. Chem. Phys., 87:6140, 1987.

78
H.C Andersen.
J. Comput. Phys., 52:24, 1983.

79
M. E. Tuckerman and M. Parrinello.
J. Chem. Phys., 101:1302, 1994.

80
S. Nose and M. L. Klein.
Mol. Phys., 50:1055, 1983.

81
G. Herzberg.
Spectra of Diatomic Molecules.
Van Nostrand, New York, 1950.

82
M. Watanabe and M. Karplus.
J. Phys. Chem., 99:5680, 1995.

83
J. K. Kjems an G. Dolling.
Phys. Rev. B, 11:16397, 1975.

84
F. D. Medina and W. B. Daniels.
J. Chem. Phys., 64:150, 1976.

85
G. Cardini and V. Schettino.
Chem. Phys., 146:147, 1990.

86
D. Frenkel and B. Smit.
Understanding Molecular Simulations.
Academic Press, San Diego, 1996.

87
D. C. Rapaport.
The Art of Molecular Dynamics Simulation.
Cambridge University Press, Cambridge (UK), 1995.

88
S. Nosé.
In M. Meyer and V. Pontikis, editors, Computer Simulation in Materials Science, page 21. Kluwer Academic Publishers, 1991.

89
S. Nosé.
Prog. Theor. Phys. Supp., 103:1, 1991.

90
M. Ferrario.
In M.P.Allen and D.J.Tildesley, editors, Computer Simulation in Chemical Physics, page 153. Kluwer Academic Publishers, 1993.

91
G. J. Martyna, D. J. Tobias, and M. L. Klein.
J. Chem. Phys., 101:4177, 1994.

92
H. C. Andersen.
J. Chem. Phys., 72:2384, 1980.

93
M. Parrinello and A. Rahman.
Phys. Rev. Letters, 45:1196, 1980.

94
S. Nose.
Mol. Phys., 52:255, 1984.

95
M. Ferrario and J.-P. Ryckaert.
Mol. Phys., 78:7368, 1985.

96
M. E. Tuckerman, C. J. Mundy, and M. L. Klein.
Phys. Rev. Letters, 78:2042, 1997.

97
S. Melchionna, G. Ciccotti, and B. L. Holian.
Mol. Phys., 78:533, 1993.

98
H.J.C.Berendsen.
Lectures notes unpublished; reported by G. Ciccotti and J.P. Ryckaert, Comp. Physics Report 4 (1986) 345, 1986.

99
E. Paci and M. Marchi.
J. Phys. Chem., 104:3003, 1996.

100
S. Toxvaerd.
Phys. Rev. B., 47:343, 1993.

101
J.-P. Hansen.
Molecular-dynamics simulation of coulomb systems in two and three dimensions.
In Molecular Dynamics Simulation of Statistical-Mechanics Systems, Proceedings of the International School of Physics "Enrico Fermi". North Holland Physics, 1986.

102
H.G. Petersen.
J. Chem. Phys., 103:3668, 1995.

103
S. J. Stuart, R. Zhou, and B. J. Berne.
J. Chem. Phys., 105:1426, 1996.

104
P. Procacci, M. Marchi, and G. J. Martyna.
J. Chem. Phys., 108:8799, 1998.

105
A. Rahman and F. H. Stillinger.
J. Chem. Phys., 55:3336, 1971.

106
P. Liu, B. Kim., R. A. Friesner, and B. J. Berne.
Proc. Acad. Sci., 102:13749-13754, 2005.

107
M. R. Shirts and J. D. Chodera.
J. Chem. Phys., 129:124105, 2008.

108
U. H. E. Hansmann and Y. Okamoto.
J. Comput. Chem., 18:920, 1997.

109
A. Irbäck and F. Potthast.
J. Chem. Phys., 103:10298, 1995.

110
A. Mitsutake and Y. Okamoto.
Chem. Phys. Lett., 332:131, 2000.

111
S. Park and V. S. Pande.
Phys. Rev. E, 76:016703, 2007.

112
X. Huang, G. R. Bowman, and V. S. Pande.
J. Chem. Phys., 128:205106, 2008.

113
C. Zhang and J. Ma.
Phys. Rev. E, 76:036708, 2007.

114
R. Denschlag, M. Lingenheil, P. Tavan, and G. Mathias.
J. Chem. Theory Comput., 5:2847, 2009.

115
S. Park, D. L. Ensign, and V. S. Pande.
Phys. Rev. E, 74:066703, 2006.

116
R. Chelli, S. Marsili, A. Barducci, and P. Procacci.
Phys. Rev. E, 75:050101, 2007.

117
R. Chelli.
J. Chem. Phys., 130:054102, 2009.

118
C. H. Bennett.
J. Comp. Phys., 22:245, 1976.

119
R. W. Zwanzig.
J. Chem. Phys., 22:1420, 1954.

120
A. Mitsutake and Y. Okamoto.
J. Chem. Phys., 130:214105, 2009.

121
W. G. Hoover.
Phys. Rev. A, 31:1695, 1985.

122
W. G. Hoover.
Phys. Rev. A, 34:2499, 1986.

123
G.L. Martyna, M.L. Klein, and M. E. Tuckerman.
J. Chem. Phys., 97:2635, 1992.

124
Y. Sugita and Y. Okamoto.
Chem. Phys. Lett., 314:141, 1999.

125
D. D. Minh and A. B. Adib.
Phys. Rev. Lett., 100:180602, 2008.

126
P. Nicolini, P. Procacci, and R. Chelli.
J. Phys. Chem. B, 114:9546, 2010.

127
S. R. Williams, D. J. Searles, and D. J. Evans.
Phys. Rev. Lett., 100:250601, 2008.

128
J. Gore, F. Ritort, and C. Bustamante.
Proc. Natl. Acad. Sci. USA, 100:12564, 2003.

129
G. Cowan.
Statistical data analysis.
Oxford University Press, 1998.

130
M. Mezei.
J. Comput. Phys., 68:237, 1987.

131
G. H. Paine and H. A. Scheraga.
Biopolymers, 24:1391, 1985.

132
T. Huber, A. E. Torda, and W. F. van Gunsteren.
J. Comput.-Aided Mol. Des., 8:695, 1994.

133
S. Marsili, A. Barducci, R. Chelli, P. Procacci, and V. Schettino.
J. Phys. Chem. B, 110:14011, 2006.

134
M. Watanabe and W. P. Reinhardt.
Phys. Rev. Lett, 65:3301, 1990.

135
N. G. Van Kampen.
Stochastic Processes in Physics and Chemistry.
North-Holland, 1992.

136
M. Iannuzzi, A. Laio, and M. Parrinello.
Phys. Rev. Lett., 90:238302, 2003.

137
V. Babin, C. Roland, T. A. Darden, and C. Sagui.
J. Chem. Phys., 125:204909, 2006.

138
L. B. Lucy.
Astronom. J., 82:1013, 1977.

139
W. G. Hoover. and C. G. Hoover.
Phys. Rev. E, 73:016702, 2006.

140
D. J. Earl and M. W. Deem.
J. Phys. Chem. B, 109:6701, 2005.

141
C. Zhou and R. N. Bhatt.
Phys. Rev. E, 72:0205701(R), 2005.

142
R. E. Belardinelli and V. D. Pereira.
Phys. Rev. E, 75:046701, 2007.

143
A. Barducci, G. Bussi, and M. Parrinello.
Phys. Rev. Lett., 100:020603, 2008.

144
P. Raiteri, F. L. Gervasio, C. Micheletti, and M. Parrinello.
J. Phys. Chem. B, 110:3533, 2006.

145
B. Isralewitz, M. Gao, and K. Schulten.
Curr. Op. Struct. Biol., 11:224-230, 2001.

146
D. J. Evans and D. J. Searls.
Phys. Rev. E, 50:1645-1648, 1994.

147
M. Sprik and G. Ciccotti.
J. Chem. Phys., 109:7737-7744, 1998.

148
S. Park and K. Schulten.
J. Chem. Phys., 120:5946-5961, 2004.

149
R. H. Wood and W. C. F. Muehlbauer.
J. Phys. Chem., 95:6670-6675, 1991.

150
R. Chelli and P. Procacci.
Phys. Chem. Chem. Phys., 11:1152-1158, 2009.

151
M.R. Shirts and V.S. Pande.
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
J. Chem. Phys., page 134508, 2005.

152
M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande.
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins.
J. Chem. Phys., 119:5740-5761, 2003.

153
In the formulation of Eq. 9.1, we have implicitly assumed the so-called "tin-foil" boundary conditions: the Ewald sphere is immersed in a perfectly conducting medium and hence the dipole term on the surface of the Ewald sphere is zero [S.W. deLeeuw, J. W. Perram, and E. R. Smith. Proc. R. Soc. London A, 373:27, 1980].

154
See for example the GROMACS manual and the tutorial for alchemical calculations: Hands-on tutorial Solvation free energy of ethanol available at http://www.gromacs.org. For NAMD, See the tutorial: In silico alchemy: A tutorial for alchemical free-energy perturbation calculations with NAMD available at http://www.ks.uiuc.edu.

155
P. Procacci, S. Marsili, A. Barducci, G. F. Signorini, and R. Chelli.
J. Chem. Phys., 125:164101, 2006.

156
Lingle Wang, Yujie Wu, Yuqing Deng, Byungchan Kim, Levi Pierce, Goran Krilov, Dmitry Lupyan, Shaughnessy Robinson, Markus K. Dahlgren, Jeremy Greenwood, Donna L. Romero, Craig Masse, Jennifer L. Knight, Thomas Steinbrecher, Thijs Beuming, Wolfgang Damm, Ed Harder, Woody Sherman, Mark Brewer, Ron Wester, Mark Murcko, Leah Frye, Ramy Farid, Teng Lin, David L. Mobley, William L. Jorgensen, Bruce J. Berne, Richard A. Friesner, and Robert Abel.
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
Journal of the American Chemical Society, 137(7):2695-2703, 2015.

157
Piero Procacci.
Unbiased free energy estimates in fast nonequilibrium transformations using gaussian mixtures.
The Journal of Chemical Physics, 142(15):154117, 2015.

158
C. Brot B. Quentrec.
J. Comp. Phys, 13:430, 1975.

159
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, Walton Street, Oxford OX2 6DP, 1989.

160
R. M. Levy E. Gallicchio.
Agbnp: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
J. Comput. Chem., 25:479-499, 2004.

161
Matteo Frigo and Steven G. Johnson.
The design and implementation of FFTW3.
Proceedings of the IEEE, 93(2):216-231, 2005.
Special issue on ``Program Generation, Optimization, and Platform Adaptation''.


procacci 2021-12-29