Concurrent Molecular Dynamics Simulation of ST2 Water on a Transputer Array

Abstract A concurrent implementation of a Molecular Dynamics program for ST2 water molecules is presented, which exploits the great potentialities of the Transputer arrays for statistical mechanical calculations. High load-balance efficiency is obtained using a new task decomposition algorithm which evenly distributes particles and interaction calculations among the processors. This approach can also help to solve efficiently the more general problem of task distribution in parallel computing of symmetric pairwise system properties.

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

[2]  Anders Wallqvist,et al.  Exploiting Physical Parallelism Using Supercomputers: Two Examples from Chemical Physics , 1987, Computer.

[3]  David May,et al.  A Tutorial Introduction To Occam Programming , 1987 .

[4]  Othmar Steinhauser,et al.  Reaction field simulation of water , 1982 .

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

[6]  Anthony J. G. Hey,et al.  Simulation of statistical mechanical systems on transputer arrays , 1986 .

[7]  E. Clementi,et al.  A parallel molecular dynamics strategy , 1985 .

[8]  Corporate Inmos Limited.  Transputer Reference Manual , 1988 .

[9]  M. Migliore,et al.  Molecular Dynamics Study of a KCl Aqueous Solution: Dynamical Results , 1987 .

[10]  Sandro L. Fornili,et al.  Solute-induced Water Structure: Computer Simulation on a Model System , 1988 .

[11]  Sandro L. Fornili,et al.  Hydration of the hydroxide ion: Ab initio calculations and monte carlo simulation , 1988 .

[12]  C. R. Jesshope.  Computational physics and the need for parallelism , 1986 .

[13]  Seymour H. Koenig,et al.  The Dynamics of Water-Protein Interactions: Results from Measurements of Nuclear Magnetic Relaxation Dispersion , 1980 .

[14]  Sandro L. Fornili,et al.  Hydration of the hydronium ion , 1986 .

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

[16]  Geoffrey C. Fox,et al.  Algorithms for concurrent processors , 1984 .

[17]  Daniel P. Vercauteren,et al.  MONTE CARLO SIMULATION OF WATER INTERACTION WITH GRAMICIDIN A TRANSMEMBRANE CHANNEL : HYDROGEN BOND ANALYSIS , 1984 .