Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.
A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.
Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, 223-8522, Japan.
Yutaka
Y
Maruyama
Norio
N
Yoshida
Hiroto
H
Tadano
Daisuke
D
Takahashi
Mitsuhisa
M
Sato
Fumio
F
Hirata
D005583:Fourier Analysis; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D011108:Polymers / Q000737:chemistry*; D013816:Thermodynamics
D010455:Peptides; D010940:Plant Proteins; D011108:Polymers; C093336:chymotrypsin inhibitor 2
3D-FFT; 3D-RISM theory; massively parallel machine