Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins

Authors:
TSUTOMU IKEGAMI;TOYOKAZU ISHIDA;DMITRI G. FEDOROV;KAZUO KITAURA;YUICHI INADOMI;HIROAKI UMEDA;MITSUO YOKOKAWA;SATOSHI SEKIGUCHI
Affiliations:
National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology;National Institute of Advanced Industrial Science and Technology
Venue:
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Year:
2005

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Abstract

A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the fragments and pairs of the fragments were conducted to obtain the electronic state of the system. The calculation at RHF/6-31G* level of theory took 72.5 hours with 600 CPUs. The CPUs were grouped into several workers, to which the calculations of the fragments were dispatched. An uneven CPU grouping, where two types of workers are generated, was shown to be efficient.