Optimizing the Accuracy and Efficiency of Fast Hierarchical Multipole Expansions for MD Simulations.
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Paul Tavan | Philipp Tröster | Magnus Schwörer | Konstantin Lorenzen | P. Tavan | M. Schwörer | Simon Mates | K. Lorenzen | Philipp Tröster | S. Mates
[1] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[2] J. Kirkwood,et al. Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .
[3] Piet Hut,et al. A hierarchical O(N log N) force-calculation algorithm , 1986, Nature.
[4] 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..
[5] Andrew W. Appel,et al. An Efficient Program for Many-Body Simulation , 1983 .
[6] W. V. van Gunsteren,et al. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations , 2001 .
[7] Michael S. Warren,et al. A portable parallel particle program , 1995 .
[8] P. Tavan,et al. Relaxation time prediction for a light switchable peptide by molecular dynamics. , 2010, Physical chemistry chemical physics : PCCP.
[9] Tetsu Narumi,et al. A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics. , 2011, The Journal of chemical physics.
[10] Martin Head-Gordon,et al. PERIODIC BOUNDARY CONDITIONS AND THE FAST MULTIPOLE METHOD , 1997 .
[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] B. Berne,et al. Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators , 1997 .
[13] W. Goddard,et al. The reduced cell multipole method for Coulomb interactions in periodic systems with million-atom unit cells , 1992 .
[14] T. Amisaki. Precise and efficient Ewald summation for periodic fast multipole method , 2000 .
[15] P. Tavan,et al. Molecular Dynamics Simulations of Proteins and Peptides: Problems, Achievements, and Perspectives , 2008 .
[16] Paul Tavan,et al. A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields , 1999 .
[17] J. Mccammon,et al. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. , 1999, Biophysical chemistry.
[18] He Huang,et al. Accelerated Cartesian expansions - A fast method for computing of potentials of the form R-ν for all real ν , 2007, J. Comput. Phys..
[19] 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 .
[20] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[21] P. Kollman,et al. An approach to computing electrostatic charges for molecules , 1984 .
[22] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[23] W. Goddard,et al. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .
[24] Wilfred F. van Gunsteren,et al. Lattice‐sum methods for calculating electrostatic interactions in molecular simulations , 1995 .
[25] Walter Dehnen,et al. A Hierarchical O(N) Force Calculation Algorithm , 2002 .
[26] P. Tavan,et al. A structure adapted multipole method for electrostatic interactions in protein dynamics , 1994 .
[27] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[28] Alessandro Laio,et al. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations , 2002 .
[29] L. Verlet. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .
[30] Wilfred F van Gunsteren,et al. Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.
[31] P. Hünenberger,et al. Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water , 1998 .
[32] Jiro Shimada,et al. Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations , 1994, J. Comput. Chem..
[33] Wilfred F. van Gunsteren,et al. A generalized reaction field method for molecular dynamics simulations , 1995 .
[34] Thomas Martinetz,et al. 'Neural-gas' network for vector quantization and its application to time-series prediction , 1993, IEEE Trans. Neural Networks.
[35] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[36] P. Tavan,et al. Highly polar environments catalyze the unfolding of PrPC helix 1 , 2010, European Biophysics Journal.
[37] B. U. Felderhof,et al. Reduced description of electric multipole potential in Cartesian coordinates , 1992 .
[38] Leslie Greengard,et al. A fast algorithm for particle simulations , 1987 .
[39] Helmut Grubmüller,et al. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. , 1997 .
[40] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[41] Christoph Niedermeier,et al. Fast Version of the Structure Adapted Multipole Method–Efficient Calculation of Electrostatic Forces in Protein Dynamics , 1996 .