Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

2005 ◽  
Vol 49 (2.3) ◽  
pp. 475-487 ◽  
Author(s):  
F. Suits ◽  
M. C. Pitman ◽  
J. W. Pitera ◽  
W. C. Swope ◽  
R. S. Germain
Keyword(s):  
Molecular Dynamics ◽  
Scientific Results ◽  
Blue Gene

scholarly journals Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

2006 ◽  
pp. 846-854 ◽  
Author(s):  
Blake G. Fitch ◽  
Aleksandr Rayshubskiy ◽  
Maria Eleftheriou ◽  
T. J. Christopher Ward ◽  
Mark Giampapa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strong Scaling ◽  
Blue Gene

Reactive Molecular Dynamics Simulations, Data Analytics and Visualization

2015 ◽  
Vol 1756 ◽  
Author(s):  
Priya Vashishta ◽  
Rajiv K. Kalia ◽  
Aiichiro Nakano ◽  
Ying Li ◽  
Ken-ichi Nomura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Production ◽  
Density Functional ◽  
Silica Surface ◽  
Hydrogen Gas ◽  
Divide And Conquer ◽  
List Type ◽  
Reactive Molecular Dynamics ◽  
Production Of Hydrogen ◽  
Blue Gene

ABSTRACTMultimillion-atom reactive molecular dynamics (RMD) and large quantum molecular dynamics (QMD) simulations are used to investigate structural and dynamical correlations under highly nonequilibrium conditions and reactive processes in nanostructured materials under extreme conditions. This paper discusses four simulations:1.RMD simulations of heated aluminum nanoparticles have been performed to study the fast oxidation reaction processes of the core (aluminum)-shell (alumina) nanoparticles and small complexes.2.Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We have used billion-atom RMD simulations on a 163,840-processor Blue Gene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated.3.Our QMD simulation reveals rapid hydrogen production from water by an Al superatom. We have found a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production.4.We have introduced an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large QMD simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786,432 cores for a 50.3 million-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16,661 atoms was performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles.

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

2008 ◽  
Vol 52 (1.2) ◽  
pp. 177-188 ◽  
Author(s):  
S. Kumar ◽  
C. Huang ◽  
G. Zheng ◽  
E. Bohm ◽  
A. Bhatele ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
L System ◽  
Blue Gene
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