Implementation of a macromolecular mechanics program on a cyber 205 supercomputer

We describe the steps involved in the conversion and vectorization of a macromolecular mechanics program on a CYBER 205 supercomputer. Several programming problems that we have encountered in optimizing a molecular mechanics program for a CYBER 205 are discussed including: the effect of vector length on speed, design of alternative algorithms, the migration of bottlenecks and rate differences obtained for logical vs arithmetic operations. The vectorized code for particular subroutines runs more than 200 times faster on the CYBER 205 as compared with a VAX 11/780. Using an enzyme-inhibitor complex, Rhizopus Chinensis carboxyl protease-pepstatin, containing 2,844 atoms as a model for this type of calculation, we have obtained an overall increase in speed of between 80-120 over a VAX 11/780 equipped with floating point accelerator for the evaluation of the conformational energy and forces on the atoms.