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ARGOS, a vectorized general molecular dynamics program
Author(s) -
Straatsma T. P.,
McCammon J. A.
Publication year - 1990
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540110806
Subject(s) - vectorization (mathematics) , speedup , molecular dynamics , computer science , parallel computing , computation , code (set theory) , computational science , supercomputer , algorithm , computational chemistry , chemistry , programming language , set (abstract data type)
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.