GridFMO Quantum chemistry of proteins on the grid

Authors:
Tsutomu Ikegamial;Jun Maki;Toshiya Takami;Yoshio Tanaka;Mitsuo Yokokawa;Satoshi Sekiguchi;Mutsumi Aoyagi
Affiliations:
Grid Technology Research Center, AIST 1-1-1 Umezono, Tsukuba 305-8568, JAPAN;Computing and Communications Center, Kyushu University 6-10-1 Hakozaki, Fukuoka 812-8581, JAPAN;Computing and Communications Center, Kyushu University 6-10-1 Hakozaki, Fukuoka 812-8581, JAPAN;Grid Technology Research Center, AIST 1-1-1 Umezono, Tsukuba 305-8568, JAPAN;RIKEN Next-Generation Supercomputer R&DCenter 2-1-1 Marunouchi, Tokyo 100-0005, JAPAN;Grid Technology Research Center, AIST 1-1-1 Umezono, Tsukuba 305-8568, JAPAN;Computing and Communications Center, Kyushu University 6-10-1 Hakozaki, Fukuoka 812-8581, JAPAN
Venue:
GRID '07 Proceedings of the 8th IEEE/ACM International Conference on Grid Computing
Year:
2007

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Abstract

A GridFMO application was developed by recoining the fragment molecular orbital (FMO) method of GAMESS with Grid technology. With the GridFMO, quantum calculations of macro molecules become possible by using large amount of computational resources collected from many moderate-sized cluster computers. A new middleware suite was developed based on Ninf-G, whose fault tolerance and flexible resource management were found to be indispensable for long-term calculations. The GridFMO was used to draw ab initio potential energy curves of a protein motor system with 16,664 atoms. For the calculations, 10 cluster computers over the Pacific rim were used, sharing the resources with other users via batch queue systems on each machine. A series of 14 GridFMO calculations were conducted for 70 days, coping with more than 100 problems cropping up. The FMO curves were compared against the molecular mechanics (MM), and it was confirmed that (1) the FMO method is capable of drawing smooth curves despite several cut-off approximations, and that (2) the MM method is reliable enough for molecular modeling.