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ARGOS, a vectorized general molecular dynamics program

✍ Scribed by T. P. Straatsma; J. A. McCammon

Publisher
John Wiley and Sons
Year
1990
Tongue
English
Weight
732 KB
Volume
11
Category
Article
ISSN
0192-8651

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✦ Synopsis

The organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX-2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX-2/400 than on the VAX 8650.

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