生体系における大規模分子シミュレーション(<特集>地球シミュレータ(続))

概要

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The prediction of the three-dimensional structures of proteins with the input of only the amino-acid sequence information (prediction from the first principles) is believed to be impossible with the presently available computation power. We present the results of the protein folding simulations on the Earth Simulator. Our simulations are based on generalized-ensemble algorithms, in particular, the replica-exchange molecular dynamics (REMD). We chose a small protein with 56 amino acids (B1 domain of streptococcal protein G). We performed a REMD simulation of protein G in a sphere of water of radius 50 angstroms. The total number of water molecules was 17,187 (the total number of atoms was 52,416 including the protein atoms). Using 112 nodes of the Earth Simulator, we performed a REMD simulation of this system with 224 replicas. The REMD simulation was successful in the sense that we observed a random walk in potential energy space that suggests that a wide conformational space was sampled. This is the largest system that the REMD simulation was successfully performed. We observed the formation of native-like secondary structures (α-helix and β-strands).
日本応用数理学会の論文
2006-09-26