ARGOS, a vectorized general molecular dynamics program

T. P. Straatsma, J. A. McCammon

Research output: Contribution to journalArticlepeer-review

63 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)943-951
Number of pages9
JournalJournal of Computational Chemistry
Volume11
Issue number8
DOIs
StatePublished - Sep 1990
Externally publishedYes

Fingerprint

Dive into the research topics of 'ARGOS, a vectorized general molecular dynamics program'. Together they form a unique fingerprint.

Cite this