Large scale simulation of parallel molecular dynamics
PE Bernard and T Gautier and D Trystram, IPPS/SPDP 1999: 13TH INTERNATIONAL PARALLEL PROCESSING SYMPOSIUM & 10TH SYMPOSIUM ON PARALLEL AND DISTRIBUTED PROCESSING, PROCEEDINGS, 638-644 (1999).
This paper aims to describe the implementation of TAKAKAW, an efficient parallel application for the simulation of molecular dynamics designed to handle large proteins in biology: The implementation is based on the multi-heading parallel programming environment, called ATHAPASCAN(1) which allows to implement and evaluate easily several load-balancing strategies. Some experiments run on one of the largest molecule ever simulated (an hydrated beta-galactosidase with 413039 atoms) show the interest of such a parallel programming environment.
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