180
H. Sun et al.
74. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly
efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
75. Smit B, Frenkel D (1996) Understanding molecular simulation: from algorithms to applications
76. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle
mesh Ewald method. J Chem Phys 103(19):8577–8593
77. Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE
algorithm for rigid water models. J Comput Chem 13:952–962
78. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for
molecular simulations. J Comput Chem 18(12):1463–1472
79. Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J
Chem Phys 126:014101
80. Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular
dynamics method. J Appl Phys 52(12):7182–7190
81. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys
117:1–19
82. Hockney RW, Eastwood JW (1989) Computer simulation using particles. Taylor & Francis
83. Nosé S (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol
Phys 52:255–268
84. Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev a
31:1695–1697
85. Yeh I-C, Berkowitz ML (1999) Ewald summation for systems with slab geometry. J Chem
Phys 111(7):3155–3162
86. Rowlinson JS, Widom B (2013) Molecular theory of capillarity. Courier Corporation
87. Bennett C (1976) Efficient estimation of free energy differences from Monte Carlo data. J
Comput Phys 22:245–268
88. Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple
equilibrium states. J Chem Phys 129:124105
89. Beutler TC, Mark AE, van Schaik RC, Gerber PR, van Gunsteren WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations.
Chem Phys Lett 222:529–539
H. Sun et al.
74. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly
efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
75. Smit B, Frenkel D (1996) Understanding molecular simulation: from algorithms to applications
76. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle
mesh Ewald method. J Chem Phys 103(19):8577–8593
77. Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE
algorithm for rigid water models. J Comput Chem 13:952–962
78. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for
molecular simulations. J Comput Chem 18(12):1463–1472
79. Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J
Chem Phys 126:014101
80. Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular
dynamics method. J Appl Phys 52(12):7182–7190
81. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys
117:1–19
82. Hockney RW, Eastwood JW (1989) Computer simulation using particles. Taylor & Francis
83. Nosé S (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol
Phys 52:255–268
84. Hoover WG (1985) Canonical dynamics: equilibrium phase-space distributions. Phys Rev a
31:1695–1697
85. Yeh I-C, Berkowitz ML (1999) Ewald summation for systems with slab geometry. J Chem
Phys 111(7):3155–3162
86. Rowlinson JS, Widom B (2013) Molecular theory of capillarity. Courier Corporation
87. Bennett C (1976) Efficient estimation of free energy differences from Monte Carlo data. J
Comput Phys 22:245–268
88. Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple
equilibrium states. J Chem Phys 129:124105
89. Beutler TC, Mark AE, van Schaik RC, Gerber PR, van Gunsteren WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations.
Chem Phys Lett 222:529–539