Spectral accuracy in fast Ewald-based methods for particle simulations
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[1] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[2] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[3] P. Koehl. Electrostatics calculations: latest methodological advances. , 2006, Current opinion in structural biology.
[4] L. Trefethen. Spectral Methods in MATLAB , 2000 .
[5] Robert D. Skeel,et al. Multiple grid methods for classical molecular dynamics , 2002, J. Comput. Chem..
[6] Gaston H. Gonnet,et al. On the LambertW function , 1996, Adv. Comput. Math..
[7] Steven G. Johnson,et al. The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.
[8] J. Strain. Fast potential theory. II: Layer potentials and discrete sums , 1992 .
[9] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[10] Franz Franchetti,et al. How to Write Fast Numerical Code: A Small Introduction , 2007, GTTSE.
[11] Vladimir Rokhlin,et al. Fast Fourier Transforms for Nonequispaced Data , 1993, SIAM J. Sci. Comput..
[12] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[13] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[14] R. Dror,et al. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. , 2005, The Journal of chemical physics.
[15] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[16] Anna-Karin Tornberg,et al. Spectrally accurate fast summation for periodic Stokes potentials , 2010, J. Comput. Phys..
[17] P. P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .
[18] 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.
[19] Eric F Darve,et al. A smooth particle-mesh Ewald algorithm for Stokes suspension simulations: The sedimentation of fibers , 2005 .
[20] Leslie Greengard,et al. Accelerating the Nonuniform Fast Fourier Transform , 2004, SIAM Rev..
[21] J. Banavar,et al. Computer Simulation of Liquids , 1988 .
[22] J. Perram,et al. Cutoff Errors in the Ewald Summation Formulae for Point Charge Systems , 1992 .
[23] Hiroki Takemoto,et al. Direct Sum of Coulomb Potential without Ambiguities of Conditionally Convergent Series , 2003 .
[24] Guido Germano,et al. Efficiency of linked cell algorithms , 2010, Comput. Phys. Commun..
[25] R. Kress. Numerical Analysis , 1998 .
[26] John Strain,et al. A geometric nonuniform fast Fourier transform , 2009, J. Comput. Phys..
[27] Christian Holm,et al. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .
[28] Ilpo Vattulainen,et al. Long-range interactions and parallel scalability in molecular simulations , 2007, Comput. Phys. Commun..
[29] David S Cerutti,et al. Multi-Level Ewald: A hybrid multigrid / Fast Fourier Transform approach to the electrostatic particle-mesh problem. , 2010, Journal of chemical theory and computation.
[30] Thierry Matthey,et al. MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms , 2005, J. Comput. Chem..
[31] R W Hockney,et al. Computer Simulation Using Particles , 1966 .
[32] C. Sagui,et al. Multigrid methods for classical molecular dynamics simulations of biomolecules , 2001 .
[33] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[34] Terry P Lybrand,et al. Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility. , 2009, Journal of chemical theory and computation.
[35] I. Tsukerman. Efficient computation of long-range electromagnetic interactions without Fourier transforms , 2004, IEEE Transactions on Magnetics.