Computing aspects of molecular dynamics simulation

Abstract Molecular dynamics simulation has substantial computing requirements. In this paper, we review these computing requirements for simulations involving fluids of spheres as well as nonspherical molecules and the determination of properties. Current trends to simulate systems of increased complexity and magnitude have resulted in increased computing requirements, thus, the need for algorithmic improvements as well as more powerful computing hardware including pipeline and parallel processing computers. In this regard, we review the existing and possible developments in a systematic manner with an emphasis on the evaluation of forces. We discuss the pipeline processing methods for molecular dynamics using the inner loop, the streched single loop, and the hybrid pipelining strategies. We also discuss the coarse-grain and fine-grain strategies for distributing the load on different processors for parallel molecular dynamics simulation. Limitations of and trends in molecular dynamics simulations are also discussed.

[1]  Stefan Brode,et al.  An optimized MD program for the vector computer cyber 205 , 1986 .

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

[3]  C. Hoheisel,et al.  Comparison of the Singer method and the constraints method for molecular dynamics with linear molecules on the VECTOR computer Cyber 205 , 1987 .

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

[5]  Hoover,et al.  Time-reversible equilibrium and nonequilibrium isothermal-isobaric simulations with centered-difference Stoermer algorithms. , 1990, Physical review. A, Atomic, molecular, and optical physics.

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

[7]  Isaiah Shavitt,et al.  Supercomputers in Chemistry , 1981 .

[8]  Stefan Brode,et al.  A new rigid motion algorithm for MD simulations , 1986 .

[9]  Kai Hwang,et al.  Computer architecture and parallel processing , 1984, McGraw-Hill Series in computer organization and architecture.

[10]  Peter Lykos,et al.  Computer Modeling of Matter , 1978 .

[11]  I. R. Mcdonald,et al.  Theory of simple liquids , 1998 .

[12]  L. Verlet,et al.  Molecular dynamics calculations of transport coefficients , 1987 .

[13]  J. Haile,et al.  A multiple time-step method for molecular dynamics simulations of fluids of chain molecules , 1984 .

[14]  Sarah L. Price,et al.  SOME NEW IDEAS IN THE THEORY OF INTERMOLECULAR FORCES - ANISOTROPIC ATOM ATOM POTENTIALS , 1988 .

[15]  David Beeman,et al.  Some Multistep Methods for Use in Molecular Dynamics Calculations , 1976 .

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

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

[18]  W. B. Sediawan,et al.  Computer modeling of naphthalene , 1989 .

[19]  Neil S. Ostlund,et al.  A Machine Architecture for Molecular Dynamics: The Systolic Loop a , 1985 .

[20]  H. G. Petersen,et al.  Molecular dynamics on transputer arrays. I: Algorithm design, programming issues, timing experiments and scaling projections , 1989 .

[21]  J. M. Haile,et al.  Molecular-based study of fluids , 1983 .

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

[23]  D. J. Tildesley,et al.  Equation of state for the Lennard-Jones fluid , 1979 .

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

[25]  Hoover,et al.  Fragmentation of suddenly heated liquids. , 1985, Physical review. A, General physics.

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

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

[28]  C. W. Gear,et al.  Numerical initial value problem~ in ordinary differential eqttations , 1971 .

[29]  D. J. Tildesley,et al.  Computer simulation of molecular liquid mixtures. I. A diatomic Lennard‐Jones model mixture for CO2/C2H6 , 1986 .

[30]  S. Gupta,et al.  Vectorization of molecular dynamics simulation for fluids of nonspherical molecules , 1988 .

[31]  C. Hoheisel,et al.  Liquid CH4, liquid CF4 and the partially miscible liquid mixture CH4/CF4 , 1986 .

[32]  William Celmaster,et al.  The BBN Butterfly used to simulate a molecular liquid , 1989, Parallel Comput..

[33]  W. G. Hoover.  molecular dynamics , 1986, Catalysis from A to Z.

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

[35]  Michael J. Quinn,et al.  Designing Efficient Algorithms for Parallel Computers , 1987 .

[36]  David Fincham,et al.  Molecular dynamics simulation using the cray-1 vector processing computer , 1981 .

[37]  G. S. Pawley,et al.  The implementation of lattice calculations on the DAP , 1982 .

[38]  Keith E. Gubbins,et al.  Theory of molecular fluids , 1984 .

[39]  D. Fincham,et al.  Recent advances in molecular-dynamics computer simulation , 1985 .

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

[41]  D. J. Adams,et al.  Taming the Edwald sum in the computer simulation of charged systems , 1987 .

[42]  Francis Sullivan,et al.  Molecular dynamics on vector computers , 1985 .

[43]  H. A. Luther,et al.  Applied numerical methods , 1969 .

[44]  H. G. Petersen,et al.  An algorithm for the simulation of condensed matter which grows as the 3/2 power of the number of particles , 1988 .

[45]  R. Vogelsang,et al.  Vectorization of molecular dynamics Fortran programs using the cyber 205 vector processing computer , 1983 .

[46]  David Fincham,et al.  Systolic loop methods for molecular dynamics simulation using multiple transputers , 1989 .

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

[48]  Christopher Lazou.  Supercomputers and their use , 1986 .