Structure and dynamics of liquid water with different long‐range interaction truncation and temperature control methods in molecular dynamics simulations
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[1] R. Levy,et al. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. , 1998, Annual review of physical chemistry.
[2] L. Nilsson,et al. On the truncation of long-range electrostatic interactions in DNA. , 2000, Biophysical journal.
[3] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[4] H. Schreiber,et al. Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work , 1992 .
[5] Shuichi Nosé,et al. Constant-temperature molecular dynamics , 1990 .
[6] Bernard R. Brooks,et al. New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..
[7] Stefan Boresch,et al. Rationalizing the effects of modified electrostatic interactions in computer simulations: The dielectric self-consistent field method , 1999 .
[8] S. Harvey,et al. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition , 1998, J. Comput. Chem..
[9] Alan K. Soper,et al. A new determination of the structure of water at 25°C , 1986 .
[10] O. Steinhauser,et al. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. , 1992, Biochemistry.
[11] Olle Teleman. An Efficient Way to Conserve the Total Energy in Molecular Dynamics Simulations; Boundary Effects on Energy Conservation and Dynamic Properties , 1988 .
[12] Terry R. Stouch,et al. Effects of Switching Functions on the Behavior of Liquid Water in Molecular Dynamics Simulations , 1994 .
[13] Eric Jakobsson,et al. Collective motion artifacts arising in long‐duration molecular dynamics simulations , 2000 .
[14] Stefan Boresch,et al. RATIONALIZATION OF THE DIELECTRIC PROPERTIES OF COMMON THREE-SITE WATER MODELS IN TERMS OF THEIR FORCE FIELD PARAMETERS , 1998 .
[15] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[16] Terry S. Cohen,et al. Effects of long-range interactions on the dynamics of ions in aqueous solution , 1994 .
[17] O. Steinhauser,et al. Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method. , 1992, Journal of molecular biology.
[18] M. Karplus,et al. Simulation of activation free energies in molecular systems , 1996 .
[19] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[20] J. Mccammon,et al. Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation , 2000 .
[21] K. Tasaki,et al. Observations concerning the treatment of long‐range interactions in molecular dynamics simulations , 1993, J. Comput. Chem..
[22] Michael Levitt,et al. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution , 1997 .
[23] T. Darden,et al. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. , 1999, Annual review of biophysics and biomolecular structure.
[24] P. P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .
[25] H. Berendsen,et al. A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field , 1998 .
[26] H. Berendsen,et al. COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .
[27] L. Nilsson,et al. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .
[28] R. Mills,et al. Self-diffusion in normal and heavy water in the range 1-45.deg. , 1973 .
[29] S. Nosé. A molecular dynamics method for simulations in the canonical ensemble , 1984 .
[30] A Elofsson,et al. Study of the electrostatics treatment in molecular dynamics simulations , 1999, Proteins.
[31] Shoshana J. Wodak,et al. Computer simulations of liquid water: treatment of long-range interactions , 1990 .
[32] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[33] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[34] William S. Price,et al. Self-Diffusion of Supercooled Water to 238 K Using PGSE NMR Diffusion Measurements , 1999 .
[35] Ulrich Essmann,et al. Effect of the treatment of long‐range forces on the dynamics of ions in aqueous solutions , 1995 .
[36] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[37] R. Ornstein,et al. Molecular dynamics simulations of a protein-protein dimer: particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model. , 1999, Journal of biomolecular structure & dynamics.
[38] Wilfred F. van Gunsteren,et al. Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions , 1996 .
[39] B. Brooks,et al. Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water , 1996 .
[40] Alan K. Soper,et al. Site–site pair correlation functions of water from 25 to 400 °C: Revised analysis of new and old diffraction data , 1997 .
[41] Gerhard Hummer,et al. Molecular Theories and Simulation of Ions and Polar Molecules in Water , 1998 .
[42] B. Montgomery Pettitt,et al. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids , 1985 .
[43] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[44] P Mark,et al. 298KでのTIP3P,SPC及びSPC/E水モデルの構造及び動力学 , 2001 .