A fast pairlist‐construction algorithm for molecular simulations under periodic boundary conditions

A new grid‐cell algorithm is presented that permits the fast construction of cutoff‐based nonbonded pairlists in molecular simulations under periodic boundary conditions based on an arbitrary box shape. The key features of the method are (1) the use of a one‐dimensional mask array (to determine which grid cells contain interacting atoms) that incorporates the effect of periodicity, and (2) the grouping of adjacent interacting cells of the mask array into stripes, which permits the handling of empty cells with a very low computational overhead. Testing of the algorithm on water systems of different sizes (containing about 2000 to 11,000 molecules) shows that the method (1) is about an order of magnitude more efficient compared to a standard (double‐loop) algorithm, (2) achieves quasi‐linear scaling in the number of atoms, (3) is weakly sensitive in terms of efficiency to the chosen number of grid cells, and (4) can be easily parallelized. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1474–1486, 2004

[1]  Martin Schoen,et al.  Structure of a simple molecular dynamics FORTRAN program optimized for CRAY vector processing computers , 1989 .

[2]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[3]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics I. Design considerations for vector processing , 1991 .

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

[5]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[6]  Florian Müller-Plathe,et al.  Parallelising a molecular dynamics algorithm on a multi-processor workstation , 1990 .

[7]  B. Quentrec,et al.  New method for searching for neighbors in molecular dynamics computations , 1973 .

[8]  P. P. Ewald.  Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[9]  William D. Mattson,et al.  Near-neighbor calculations using a modified cell-linked list method , 1999 .

[10]  Roger W. Hockney,et al.  P3M3DP-the three-dimensional periodic particle-particle/particle-mesh program , 1984 .

[11]  P. Schofield,et al.  Computer simulation studies of the liquid state , 1973 .

[12]  Nobuyasu Ito,et al.  VECTORIZED AND PARALLELIZED ALGORITHMS FOR MULTI-MILLION PARTICLE MD-SIMULATION , 1993 .

[13]  D. C. Rapaport,et al.  Large-scale molecular dynamics simulation using vector and parallel computers , 1988 .

[14]  M. Pütz,et al.  Optimization techniques for parallel molecular dynamics using domain decomposition , 1998 .

[15]  C. Brooks.  Computer simulation of liquids , 1989 .

[16]  Ron Elber,et al.  Calculations of a list of neighbors in Molecular Dynamics simulations , 1989 .

[17]  Pablo G. Debenedetti,et al.  An automated Verlet neighbor list algorithm with a multiple time-step approach for the simulation of large systems , 1992 .

[18]  R. W. Hockney,et al.  A 10000 particle molecular dynamics model with long range forces , 1973 .

[19]  Kurt Kremer,et al.  A fast grid search algorithm for molecular dynamics simulations with short-range interactions , 1994 .

[20]  H. Berendsen,et al.  COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .

[21]  D. Tildesley,et al.  Multiple time-step methods in molecular dynamics , 1978 .

[22]  Pablo G. Debenedetti,et al.  On the use of the Verlet neighbor list in molecular dynamics , 1990 .

[23]  Juan J. Morales,et al.  A technique for improving the link-cell method , 1990 .

[24]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[25]  Kurt Kremer,et al.  Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles , 1989 .

[26]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[27]  Bernard R. Brooks,et al.  An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs , 2003, J. Comput. Chem..

[28]  Pablo G. Debenedetti,et al.  On the performance of an automated Verlet neighbor list algorithm for large systems on a vector processor , 1991 .

[29]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[30]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[31]  Philippe H. Hünenberger,et al.  Lattice-sum methods for computing electrostatic interactions in molecular simulations , 1999 .

[32]  R. Hockney,et al.  Quiet high resolution computer models of a plasma , 1974 .

[33]  H. Bekker,et al.  Unification of box shapes in molecular simulations , 1997 .

[34]  Anton Arnold,et al.  An efficient method of bookkeeping next neighbours in molecular dynamics simulations , 1990 .

[35]  Gerhard Hummer,et al.  Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics and Aqueous Solutions, Santa Fe, New Mexico, U. S. A., 23-25 June 1999 , 1999 .

[36]  T. Halgren,et al.  Polarizable force fields. , 2001, Current opinion in structural biology.

[37]  Philippe H. Hünenberger,et al.  Optimal charge-shaping functions for the particle–particle—particle–mesh (P3M) method for computing electrostatic interactions in molecular simulations , 2000 .

[38]  J. L. Finney.  Long-range forces in molecular dynamics calculations on water , 1978 .

[39]  Alan E. Mark,et al.  The GROMOS96 Manual and User Guide , 1996 .

[40]  H. Berendsen,et al.  AN EFFICIENT, BOX SHAPE INDEPENDENT NONBONDED FORCE AND VIRIAL ALGORITHM FOR MOLECULAR-DYNAMICS , 1995 .

[41]  Juan J. Morales,et al.  Comparison of link-cell and neighbourhood tables on a range of computers , 1992 .

[42]  H. Berendsen,et al.  A LEAP-FROG ALGORITHM FOR STOCHASTIC DYNAMICS , 1988 .

[43]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

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

[45]  D. Adams,et al.  Computer simulation of ionic systems: The distorting effects of the boundary conditions , 1979 .