Estimation of Free Energy Systematic Errors in Molecular Simulations of Globular Proteins Surrounded by Finite Water Clusters. One Center Multipole Expansion of Reaction Field Differences

References

• Beveridge , D. L. and DiCapua , F. M. 1989 . Free energy via molecular simulation: Applications to chemical and biomolecular systems. . Ann. Rev. Biophys. Chem. , 18 : 431 – 492 .
   PubMedGoogle Scholar
• Brooks , C. L. III , Karplus , M. and Pettitt , B. M. 1988 . “ Proteins: A Theoretical Perspective of Dynamics ” . In Structure, and Thermodynamics , 36 – 38 . John Wiley & Sons Inc .
   Google Scholar
• Neumann , M. 1986 . Dielectric relaxation in water. Computer simulations with TIP4P potential . J. Chem. Phys. , 85 : 1567 – 1580 .
   Web of Science ®Google Scholar
• Gray , G. G. , Sainger , S. , Joslin , G. G. , Cummings , P. T. and Goldman , S. 1986 . Computer simulation of dipolar fluids. Dependence of the dielectric constant on system size: A comparative study of Ewald sum & reaction field approaches . J. Chem. Phys , 85 : 1502 – 04 .
   Web of Science ®Google Scholar
• Beveridge , D. L. and Schnuelle , G. W. 1975 . A statistical thermodynamic supermolecule continuum study of ion hydration. I. Site method. . J. Phys. Chem , 79 : 2566 – 2573 .
   Google Scholar
• Straatsma , T. P. and Berendsen , H. J.C. 1988 . Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics . J. Chem. Phys. , 89 : 5876 – 5886 .
   Web of Science ®Google Scholar
• Maroncelli , M. and Fleming , G. 1988 . Computer simulations of the dynamics of aqueous solvation . J. Chem. Phys. , 89 : 5044 – 5069 .
   Web of Science ®Google Scholar
• Gordon , H. and Goldman , S. 1989 . The dielectric constant of the TIP4P and SPC point charge models for water at ordinary and high temperatures . Molecular Simulation , 2 : 177 – 187 .
   Web of Science ®Google Scholar
• Strauch , H. J. and Cummings , P. T. 1989 . Computer simulation of the dielectric properties of liquid water . Molecular Simulation , 2 : 89 – 104 .
   Web of Science ®Google Scholar
• Steinhauser , O. 1983 . On dielectric theory and computer simulation of water . Chemical Physics , 79 : 465 – 482 .
   Web of Science ®Google Scholar
• Kirkwood , J. G. 1939 . The dielectric polarization of polar liquids . J. Chem. Phys. , 7 : 911
   Web of Science ®Google Scholar
• Beveridge , D. L. and Schnuelle , G. W. 1975 . Free energy of a charge distribution in concentric dielectric continua . J. Phys. Chem , 79 : 2062 – 2065 .
   Google Scholar
• Gilson , M. K. and Honig , B. H. 1986 . The dielectric constant of folded protine . Biopolymers , 25 : 2097 – 2119 .
   PubMed Web of Science ®Google Scholar
• Nakamura , H. , Sakamoto , T. and Wada , A. 1988 . Theoretical study of dielectric constant of protein . Protein Engineering , 2 : 177 – 183 .
   PubMedGoogle Scholar
• Bottcher , C. J.F. 1973 . 141 – 146 . Amsterdam London New York : Theory of electric polarization Elsevier Scientific Publishing Company .
   Google Scholar
• 81 – 84 . ref. [15]
   Google Scholar