TCB Publications - Abstract

Helmut Heller and Klaus Schulten. Parallel distributed computing for molecular dynamics: Simulation of large heterogeneous systems on a systolic ring of transputers. Chemical Design Automation News, 7:11-22, 1992.

HELL92B For the purpose of molecular dynamics simulations we have built a parallel computer based on a systolic double ring architecture, with Transputers as a computational units, 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 data stored in the external RAM. Our program, EGO, designed for simulation of very large molecules (up to 50,000 atoms), is compatible with the programs CHARMM and X-PLOR. EGO increases its computational throughput nearly linearly with the number of computational modes. Results of simulations on the Transputer system of a lipid bilayer are presented.

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