Klaus Boehncke, Helmut Heller, Helmut Grubmüller, and Klaus Schulten.
Molecular dynamics simulations on a systolic ring of transputers.
In Alan S. Wagner, editor, NATUG 3: Transputer Research and
Applications 3, pp. 83-94, Amsterdam, 1990. North American Transputer Users
Group, IOS Press.
BOEH90
For the purpose of molecular dynamics simulations, a parallel computer based on a systolic ring architecture, with Transputers as computational units, has been built and programmed in OCCAM II. The design is very compact and achieves high reliability even on continuous duty cycles of several months. A parity check logic ensures the correctness of the data stored in the external RAM. Our program for simulation of very large molecules (up to 32000 atoms) is compatible with the programs CHARMM and X-PLOR. It increases its computational throughput nearly linearly with the number of computational nodes. Exploiting the MIMD structure of our Transputer network, we have added to our program the capability to compute explicit hydrogen bonds. One node is now entirely devoted to this task. Benchmarks comparing simulations of several molecules - ranging from 66 to 12637 atoms - on the Transputer system with those on conventional machines are provided. The results demonstrate that the software and hardware developed provide an extremely cost-effective means for simulations of molecules. We have simulated the photosynthetic reaction center, a protein complex of 12637 atoms, as well as drug-DNA complexes, on our computer.
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