A Fast Adaptive Multipole Algorithm for Calculating Screened Coulomb (Yukawa) Interactions

The screened Coulomb (Yukawa or Debye?Huckel) potential, ?=exp(??r)/r, whereris the separation distance and ? is the Debye?Huckel screening parameter, gives a good description of the electrostatic interactions in a variety of biologically and physically important charged systems. It is well known that the direct calculation of the energy and forces due to a collection ofNcharged particles involves the pairwise summation of all charged particle interactions and exhibits anO(N2) computational complexity which severely restricts maximum problem size. This has prompted the development of fast summation algorithms that allow the electrostatic energy and forces to be obtained in onlyO(NlogN) operations. To date, however, practically all such implementations have been limited exclusively to pure Coulombic potentials (?=0), and the central contribution of the present method is to extend this capability to the entire range of the inverse Debye length, ??0. The basic formulation and computational implementation of the spherical modified Bessel function-based multipole expansions appropriate for the screened Coulomb kernel are first presented. Next, a simple model system consisting of a single source charged particle is studied to show that the maximum electrostatic energy error incurred by anM-order multipole expansion for the Yukawa potential is bounded above by the error of the equivalent multipole expansion for the Coulombic potential. Finally, timing and accuracy studies are presented for a variety of charged systems including polyelectrolyte chains, random distributions of charges inside a cube, and face-centered-cubic lattice charge configurations containing up to 103,823 charges.

[1]  The electrostatic persistence length calculated from Monte Carlo, variational and perturbation methods , 1997, cond-mat/9612234.

[2]  L. Greengard,et al.  Regular Article: A Fast Adaptive Multipole Algorithm in Three Dimensions , 1999 .

[3]  A. Varnek,et al.  A fast and Space‐efficient boundary element method for computing electrostatic and hydration effects in large molecules , 1996 .

[4]  R. Wade,et al.  Importance of explicit salt ions for protein stability in molecular dynamics simulation. , 1998, Biophysical journal.

[5]  Wilfred F. van Gunsteren,et al.  A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems , 1994 .

[6]  Leslie Greengard,et al.  On the evaluation of electrostatic interactions in molecular modeling , 1988 .

[7]  Jussi Rahola,et al.  Diagonal forms of the translation operators in the fast multipole algorithm for scattering problems , 1995 .

[8]  K Schulten,et al.  How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry. , 1997, Biophysical journal.

[9]  W. Reed,et al.  Monte Carlo study of light scattering by linear polyelectrolytes , 1992 .

[10]  K. Schulten,et al.  Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics , 1997 .

[11]  Robbins,et al.  Phase diagram of Yukawa systems: Model for charge-stabilized colloids. , 1986, Physical review letters.

[12]  Jim Glosli,et al.  Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems , 1996 .

[13]  M. Muthukumar,et al.  Tuning the Density Profile of Dendritic Polyelectrolytes , 1998 .

[14]  K Rippe,et al.  Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. , 1998, Biophysical journal.

[15]  Martin Head-Gordon,et al.  Derivation and efficient implementation of the fast multipole method , 1994 .

[16]  Tamar Schlick,et al.  Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA , 1992, Science.

[17]  V. Rokhlin,et al.  Rapid Evaluation of Potential Fields in Three Dimensions , 1988 .

[18]  C. Peterson,et al.  A Monte Carlo study of titrating polyelectrolytes , 1996 .

[19]  H. Berendsen,et al.  The electric potential of a macromolecule in a solvent: A fundamental approach , 1991 .

[20]  D. Beveridge,et al.  Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. , 1998, Journal of molecular biology.

[21]  Christian Holm,et al.  How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .

[22]  Sharon Brunett,et al.  Molecular dynamics for very large systems on massively parallel computers: The MPSim program , 1997 .

[23]  Enrico O. Purisima,et al.  Fast summation boundary element method for calculating solvation free energies of macromolecules , 1998 .

[24]  Jiro Shimada,et al.  Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations , 1994, J. Comput. Chem..

[25]  W. Olson,et al.  Electrostatic effects in short superhelical DNA. , 1994, Biophysical chemistry.

[26]  S. Sriharan,et al.  The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems , 1995, J. Comput. Chem..

[27]  B. Jönsson,et al.  On the mean spherical approximation (MSA) for colloidal systems: A comparison with results from Monte Carlo simulations , 1983 .

[28]  V. Vlachy,et al.  Structure and thermodynamics of the screened Coulomb liquid , 1988 .

[29]  S. Carnie,et al.  Computer simulations of polyelectrolyte chains in salt solution , 1990 .

[30]  N. Cozzarelli,et al.  Modeling of long‐range electrostatic interactions in DNA , 1995, Biopolymers.

[31]  Marcia O. Fenley,et al.  Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA , 1996, J. Comput. Chem..

[32]  Henrik Gordon Petersen,et al.  The very fast multipole method , 1994 .

[33]  Wilfred F. van Gunsteren,et al.  Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions , 1996 .

[34]  S Subramaniam,et al.  Computation of molecular electrostatics with boundary element methods. , 1997, Biophysical journal.

[35]  L. Greengard The Rapid Evaluation of Potential Fields in Particle Systems , 1988 .

[36]  W. Goddard,et al.  Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .

[37]  Steven Raymond Lustig,et al.  The Fast Multipole Method in Canonical Ensemble Dynamics on Massively Parallel Computers , 1992 .

[38]  B. J. Yoon,et al.  A boundary element method for molecular electrostatics with electrolyte effects , 1990 .

[39]  R. Farouki,et al.  Phase diagram of Yukawa systems near the one-component-plasma limit revisited , 1996 .

[40]  Abhinandan Jain,et al.  Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton‐Euler inverse mass operator method for internal coordinate dynamics , 1994, Proteins.

[41]  Orlandini,et al.  Knotting and supercoiling in circular DNA: A model incorporating the effect of added salt. , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[42]  Leslie Greengard,et al.  A fast algorithm for particle simulations , 1987 .

[43]  P. Kollman,et al.  Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins , 1995 .

[44]  J. Michael Schurr,et al.  Comparison of hard‐cylinder and screened coulomb interactions in the modeling of supercoiled DNAs , 1997, Biopolymers.

[45]  Vladimir Rokhlin,et al.  An Improved Fast Multipole Algorithm for Potential Fields , 1998, SIAM J. Sci. Comput..

[46]  J. W. Causey,et al.  Accelerated molecular dynamics simulation with the parallel fast multipole algorithm , 1992 .

[47]  Martin Head-Gordon,et al.  PERIODIC BOUNDARY CONDITIONS AND THE FAST MULTIPOLE METHOD , 1997 .

[48]  John A. Board,et al.  Fast Fourier Transform Accelerated Fast Multipole Algorithm , 1996, SIAM J. Sci. Comput..

[49]  L. Greengard,et al.  A new version of the Fast Multipole Method for the Laplace equation in three dimensions , 1997, Acta Numerica.

[50]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[51]  R. Farouki,et al.  Thermodynamics of strongly‐coupled Yukawa systems near the one‐component‐plasma limit. II. Molecular dynamics simulations , 1994 .

[52]  K. Schmidt,et al.  Implementing the fast multipole method in three dimensions , 1991 .

[53]  T Schlick,et al.  The influence of salt on the structure and energetics of supercoiled DNA. , 1994, Biophysical journal.

[54]  H. Totsuji,et al.  Structure of Confined Yukawa System (Dusty Plasma) , 1997 .

[55]  B. Berne,et al.  Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators , 1997 .

[56]  R. Ornstein,et al.  Inherent DNA curvature and flexibility correlate with TATA box functionality. , 1998, Biopolymers.

[57]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[58]  Michael A. Epton,et al.  Multipole Translation Theory for the Three-Dimensional Laplace and Helmholtz Equations , 1995, SIAM J. Sci. Comput..

[59]  J. Prausnitz,et al.  Monte Carlo simulations of hydrophobic polyelectrolytes. Evidence for a structural transition in response to increasing chain ionization , 1990 .

[60]  V. Rokhlin Diagonal Forms of Translation Operators for the Helmholtz Equation in Three Dimensions , 1993 .

[61]  J. Board,et al.  Ewald summation techniques in perspective: a survey , 1996 .