Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations.
暂无分享,去创建一个
[1] Maria M. Reif,et al. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization , 2015, Theoretical Chemistry Accounts.
[2] Michael Hofmann,et al. Comparison of scalable fast methods for long-range interactions. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.
[3] David L Mobley,et al. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. , 2013, The Journal of chemical physics.
[4] Daniel Potts,et al. Parallel Three-Dimensional Nonequispaced Fast Fourier Transforms and Their Application to Particle Simulation , 2013, SIAM J. Sci. Comput..
[5] Markus Christen,et al. Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation , 2012, Comput. Phys. Commun..
[6] Wilfred F van Gunsteren,et al. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. , 2011, The journal of physical chemistry. B.
[7] Wilfred F van Gunsteren,et al. On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase. , 2011, Journal of chemical theory and computation.
[8] Holger Dachsel,et al. Corrected article: "An error-controlled fast multipole method" [J. Chem. Phys. 131, 244102 (2009)]. , 2010, The Journal of chemical physics.
[9] C. Holm,et al. P3M algorithm for dipolar interactions. , 2008, The Journal of chemical physics.
[10] Tim N. Heinz,et al. Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations. , 2005, The Journal of chemical physics.
[11] Bernard R Brooks,et al. Isotropic periodic sum: a method for the calculation of long-range interactions. , 2005, The Journal of chemical physics.
[12] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[13] Paul Tavan,et al. A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water , 2003 .
[14] O. Steinhauser,et al. The dielectric self-consistent field method. II. Application to the study of finite range effects , 2001 .
[15] W. V. van Gunsteren,et al. Comparison of different schemes to treat long‐range electrostatic interactions in molecular dynamics simulations of a protein crystal , 2001, Proteins.
[16] A Kusumi,et al. Molecular dynamics generation of nonarbitrary membrane models reveals lipid orientational correlations. , 2000, Biophysical journal.
[17] J. Mccammon,et al. Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation , 2000 .
[18] R. Fox,et al. Classical Electrodynamics, 3rd ed. , 1999 .
[19] Andrew E. Torda,et al. The GROMOS biomolecular simulation program package , 1999 .
[20] M. Berkowitz,et al. Dielectric constant of water at high electric fields: Molecular dynamics study , 1999 .
[21] J. Mccammon,et al. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. , 1999, Biophysical chemistry.
[22] M. Deserno,et al. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998, cond-mat/9807099.
[23] M. Deserno,et al. HOW TO MESH UP EWALD SUMS. II. AN ACCURATE ERROR ESTIMATE FOR THE PARTICLE-PARTICLE-PARTICLE-MESH ALGORITHM , 1998, cond-mat/9807100.
[24] G. Sutmann. Structure formation and dynamics of water in strong external electric fields , 1998 .
[25] Martin Head-Gordon,et al. PERIODIC BOUNDARY CONDITIONS AND THE FAST MULTIPOLE METHOD , 1997 .
[26] B. Luty,et al. Space-time correlated reaction field: A stochastic dynamical approach to the dielectric continuum , 1997 .
[27] L. Greengard,et al. A new version of the Fast Multipole Method for the Laplace equation in three dimensions , 1997, Acta Numerica.
[28] Wilfred F. van Gunsteren,et al. Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions , 1996 .
[29] Wilfred F. van Gunsteren,et al. A generalized reaction field method for molecular dynamics simulations , 1995 .
[30] Martin Head-Gordon,et al. Derivation and efficient implementation of the fast multipole method , 1994 .
[31] Wilfred F. van Gunsteren,et al. A molecular dynamics simulation study of chloroform , 1994 .
[32] B. Wood,et al. MOLECULAR-DYNAMICS STUDY OF THE DIELECTRIC-CONSTANT OF WATER UNDER HIGH-PRESSURE AND TEMPERATURE CONDITIONS , 1994 .
[33] T. Darden,et al. The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods , 1993 .
[34] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[35] Bernard Pettitt,et al. Peptides in ionic solutions: A comparison of the Ewald and switching function techniques , 1991 .
[36] Leslie Greengard,et al. A fast algorithm for particle simulations , 1987 .
[37] Piet Hut,et al. A hierarchical O(N log N) force-calculation algorithm , 1986, Nature.
[38] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[39] Martin Neumann,et al. Dipole moment fluctuation formulas in computer simulations of polar systems , 1983 .
[40] Andrew W. Appel,et al. An Efficient Program for Many-Body Simulation , 1983 .
[41] D. Heyes,et al. Electrostatic potentials and fields in infinite point charge lattices , 1981 .
[42] J. Perram,et al. Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants , 1980, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.
[43] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[44] D. D. Yue,et al. Theory of Electric Polarization , 1974 .
[45] J. A. Barker,et al. Monte Carlo studies of the dielectric properties of water-like models , 1973 .
[46] Z. Birnbaum,et al. One-Sided Confidence Contours for Probability Distribution Functions , 1951 .
[47] W. Rudin. Uniqueness theory of Hermite series , 1951 .
[48] N. Smirnov. Table for Estimating the Goodness of Fit of Empirical Distributions , 1948 .
[49] W. Feller. On the Kolmogorov–Smirnov Limit Theorems for Empirical Distributions , 1948 .
[50] L. Onsager. Electric Moments of Molecules in Liquids , 1936 .
[51] Christian Holm,et al. How to Mesh up Ewald Sums , 2000 .
[52] A. N. Shiryayev,et al. 15. On The Empirical Determination of A Distribution Law , 1992 .
[53] W. M. Haynes. CRC Handbook of Chemistry and Physics , 1990 .
[54] C. Brooks. Computer simulation of liquids , 1989 .
[55] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[56] R. Hockney. The potential calculation and some applications , 1970 .
[57] P. P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .