Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method

2003 ◽  
Vol 24 (5) ◽  
pp. 582-592 ◽  
Author(s):  
Takashi Amisaki ◽  
Shinjiro Toyoda ◽  
Hiroh Miyagawa ◽  
Kunihiro Kitamura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Fast Multipole Method ◽  
Hardware Accelerator ◽  
Fast Multipole ◽  
Nonbonded Interactions ◽  
Multipole Method ◽  
Dynamics Simulations

Large Scale Molecular Dynamics Simulations of a Liquid Crystalline Droplet with Fast Multipole Implementations

1998 ◽  
Vol 538 ◽  
Author(s):  
Zhiqiang Wang ◽  
James Lupo ◽  
Soumya S. Patnaik ◽  
Alan McKenney ◽  
Ruth Pachter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Liquid Crystalline ◽  
Fast Multipole Method ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Fast Multipole ◽  
Multipole Method ◽  
Dynamics Simulations

AbstractThe Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in our group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4'-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.

Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations

2021 ◽  
Vol 42 (15) ◽  
pp. 1073-1087
Author(s):  
Yoshimichi Andoh ◽  
Shin‐ichi Ichikawa ◽  
Tatsuya Sakashita ◽  
Noriyuki Yoshii ◽  
Susumu Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Fast Multipole Method ◽  
Fast Multipole ◽  
Molecular Dynamics Calculations ◽  
Multipole Method
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