Abstract
We describe in this paper a domain decomposition molecular dynamics algorithm for use on distributed memory parallel computers which is capable of handling systems containing rigid bond constraints and three- and four-body potentials as well as non-bonded potentials. The algorithm has been successfully implemented on the Fujitsu 1024 processor element AP1000 machine. The performance has been compared with and benchmarked against the alternative cloning method of parallel processing [D. Brown, J.H.R. Clarke, M. Okuda and T. Yamazaki, J. Chem. Phys., 100 (1994) 1684] and results obtained using other scalar and vector machines. Two parallel versions of the SHAKE algorithm, which solves the bond length constraints problem, have been compared with regard to optimising the performance of this procedure.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
