Short-Range Molecular Dynamics

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter‐atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be dicult to parallelize eciently

[1]  Peter Schuster,et al.  Parallel molecular dynamics of biomolecules , 1992, Parallel Computing.

[2]  Takao Yamazaki,et al.  A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines , 1993 .

[3]  Taylor,et al.  Adhesion between atomically flat metallic surfaces. , 1991, Physical review. B, Condensed matter.

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

[5]  Jill P. Mesirov,et al.  Parallel approaches to short range molecular dynamics simulations , 1991, Proceedings of the 1991 ACM/IEEE Conference on Supercomputing (Supercomputing '91).

[6]  M. Baskes,et al.  Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals , 1984 .

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

[8]  Piet Hut,et al.  A hierarchical O(N log N) force-calculation algorithm , 1986, Nature.

[9]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics: II. Design considerations for distributed processing , 1991 .

[10]  Rolf Riesen,et al.  SUNMOS for the Intel Paragon - a brief user`s guide , 1994 .

[11]  R. A. van de Geijn,et al.  Efficient Global Combine Operations , 1991 .

[12]  James Andrew McCammon,et al.  Parallel Molecular Dynamics , 1991, PPSC.

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

[14]  J. G. Lewis,et al.  Distributed memory matrix-vector multiplication and conjugate gradient algorithms , 1993, Supercomputing '93.

[15]  Murray S. Daw,et al.  Atomic-Scale Simulation in Materials Science , 1988 .

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

[17]  Helmut Grubmüller,et al.  Molecular dynamics simulation on a parallel computer. , 1990 .

[18]  Jill P. Mesirov,et al.  Hypercube Algorithms for Direct N-Body Solvers for Different Granularities , 1993, SIAM J. Sci. Comput..

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

[20]  S. J. Plimpton,et al.  Molecular Dynamics Simulations of Short-Range Force Systems on 1024-Node Hypercubes , 1990, Proceedings of the Fifth Distributed Memory Computing Conference, 1990..

[21]  D. J. Tildesley,et al.  Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm , 1991 .

[22]  F. Abraham,et al.  Computational statistical mechanics methodology, applications and supercomputing , 1986 .

[23]  J. Watts,et al.  Interprocessor collective communication library (InterCom) , 1994, Proceedings of IEEE Scalable High Performance Computing Conference.

[24]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[25]  Steven J. Plimpton,et al.  Parallel Molecular Dynamics With the Embedded Atom Method , 1992 .

[26]  Berend Smit,et al.  Efficient Parallel Implementation of Molecular Dynamics on a Toroidal Network. Part I. Parallelizing Strategy , 1993 .

[27]  William Smith,et al.  Molecular dynamics on hypercube parallel computers , 1991 .

[28]  David M. Beazley,et al.  A high performance communications and memory caching scheme for molecular dynamics on the CM-5 , 1994, Proceedings of 8th International Parallel Processing Symposium.

[29]  Bruce Hendrickson,et al.  The Torus-Wrap Mapping for Dense Matrix Calculations on Massively Parallel Computers , 1994, SIAM J. Sci. Comput..

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

[31]  Jill P. Mesirov,et al.  An optimal hypercube direct N-body solver on the Connection Machine , 1990, Proceedings SUPERCOMPUTING '90.

[32]  Bruce Hendrickson,et al.  An Improved Spectral Graph Partitioning Algorithm for Mapping Parallel Computations , 1995, SIAM J. Sci. Comput..

[33]  Wolfgang J. Paul,et al.  A special purpose parallel computer for molecular dynamics: motivation, design, implementation, and application , 1987 .

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

[35]  G. C. Fox,et al.  Solving Problems on Concurrent Processors , 1988 .

[36]  Roscoe Giles,et al.  A parallel scalable approach to short-range molecular dynamics on the CM-5 , 1992, Proceedings Scalable High Performance Computing Conference SHPCC-92..

[37]  George H. Gilmer,et al.  A special purpose computer for molecular dynamics calculations , 1990 .

[38]  Steven J. Plimpton,et al.  A new parallel method for molecular dynamics simulation of macromolecular systems , 1994, J. Comput. Chem..

[39]  Sumnesh Gupta,et al.  Computing aspects of molecular dynamics simulation , 1992 .

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

[41]  David Fincham,et al.  Parallel Computers and Molecular Simulation , 1987 .

[42]  G. S. Pawley,et al.  Molecular dynamics of clusters of particles interacting with pairwise forces using a massively parallel computer , 1988 .

[43]  Rob H. Bisseling,et al.  Parallel LU Decomposition on a Transputer Network , 1988, Shell Conference.

[44]  Steven J. Plimpton,et al.  Parallel Many-Body Simulations without All-to-All Communication , 1995, J. Parallel Distributed Comput..

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

[46]  Soumya S. Patnaik,et al.  Molecular Dynamics Simulation Of A Cyclic Siloxane Based Liquid Crystalline Material , 1993 .

[47]  Klaus Schulten,et al.  Molecular dynamics simulation on the connection machine , 1991 .

[48]  Steven J. Plimpton,et al.  Scalable parallel molecular dynamics on MIMD supercomputers , 1992, Proceedings Scalable High Performance Computing Conference SHPCC-92..

[49]  Bruce M. Boghosian,et al.  Computational physics on the Connection Machine , 1989 .

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

[51]  Rajiv K. Kalia,et al.  Parallel multiple-time-step molecular dynamics with three-body interaction , 1993 .