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Abstract:
For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer
with a systolic loop architecture, based on Transputers as computational units, and have programmed it
in Occam 11. The computational nodes of the computer are linked together in a systolic ring. The program
based on this .topology for large biopolymers increases its computational throughput nearly linearly with
the number of computational nodes. The program developed is closely related to the simulation programs
CHARMM and XPLOR, the input files required (force field, protein structure file, coordinates) and output
files generated (sets of atomic coordinates representing dynamic trajectories and energies) are compatible
with the corresponding files of these programs. Benchmark results of simulations of biopolymers comprising
66, 568, 3 634, 5 797 and 12 637 atoms are compared with XPLOR simulations on conventional
computers (Cray, Convex, Vax). These results demonstrate that the software and hardware developed
provide extremely cost effective biopolymer simulations. We present also a simulation (equilibrium of
X-ray structure) of the complete photosynthetic reaction center of Rhodopseudomonus viridis (12 637
atoms). The simulation accounts for the Coulomb forces exactly, i.e. no cut-off had been assumed.
