A special purpose parallel computer for molecular dynamics: motivation, design, implementation, and application

1987 ◽  
Vol 91 (19) ◽  
pp. 4881-4890 ◽  
Author(s):  
D. J. Auerbach ◽  
W. Paul ◽  
A. F. Bakker ◽  
C. Lutz ◽  
W. E. Rudge ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computer

VISUAL SIMULATION OF THE AMBER MOLECULAR DYNAMICS PROGRAM ON THE AP1000 HIGHLY PARALLEL COMPUTER

1993 ◽  
pp. 1177-1180
Author(s):  
Hiroyuki Sato ◽  
Yasumasa Tanaka ◽  
Hiroshi Iwama ◽  
Shigetsugu Kawakika ◽  
Minoru Saito ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computer ◽  
Visual Simulation

Molecular-dynamics study of the structural correlation of porous silica with use of a parallel computer

1994 ◽  
Vol 49 (14) ◽  
pp. 9441-9452 ◽  
Author(s):  
Aiichiro Nakano ◽  
Lingsong Bi ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Porous Silica ◽  
Parallel Computer ◽  
Structural Correlation

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

Cluster Molecular Dynamics on Massively Parallel Computers

1992 ◽  
Vol 278 ◽  
Author(s):  
K. M. Nelson ◽  
S. T. Smith ◽  
L. T. Wille
Keyword(s):  
Molecular Dynamics ◽  
Noble Gas ◽  
Equations Of Motion ◽  
Pair Potential ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Gas Clusters ◽  
Element Array ◽  
Small Clusters

AbstractWe report the results of computer simulations of phase transitions in noble-gas clusters. The calculations were performed on a MasPar MP-l massively parallel computer with 8,192 processing elements (PE's). We discuss the efficient implementation of molecular dynamics algorithms for small clusters on this type of architecture. The simulations are based on a classical Lennard-Jones pair potential and follow the temporal evolution of the system by numerically integrating Newton's equations of motion using the Gear algorithm. Because the number of particles is much smaller than the number of PE's, optimal partitioning of the processing element array is an essential and non-trivial task.

Ab-Initio Molecular Dynamics of Organic Compounds on a Massively Parallel Computer

1995 ◽  
Vol 408 ◽  
Author(s):  
François Gygi
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Organic Compounds ◽  
Organic Molecules ◽  
Curvilinear Coordinates ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Dynamics Simulations

AbstractWe present results of ab-initio electronic structure calculations and molecular dynamics simulations of organic molecules carried out using adaptive curvilinear coordinates, within the local density approximation of density functional theory. This approach allows for an accurate treatment of first-row elements, which makes it particularly suitable for investigations of organic compounds. A recent formulation of this method relies on a real-space approach which combines the advantages of finite-difference methods with the accuracy of adaptive coordinates, and is well suited for implementation on massively parallel computers. We used molecular dynamics simulations to obtain the fully relaxed structures of nitrosyl fluoride (FNO), and of the aromatic heterocycles furan and pyrrole. The equilibrium geometries obtained show excellent agreement with experimental data. The harmonic vibrational frequencies of furan and pyrrole were calculated by diagonalization of their dynamical matrix and are found to agree with experimental data within an rms error of 25 cm-1 and 28 cm-1 for furan and pyrrole respectively. This accuracy is comparable to that attained for smaller organic molecules using elaborate quantum chemistry methods.

Structural correlations in porous silica: Molecular dynamics simulation on a parallel computer

1993 ◽  
Vol 71 (1) ◽  
pp. 85-88 ◽  
Author(s):  
Aiichiro Nakano ◽  
Lingsong Bi ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Porous Silica ◽  
Dynamics Simulation ◽  
Parallel Computer

Centroid molecular dynamics: A quantum dynamics method suitable for the parallel computer

2000 ◽  
Vol 26 (7-8) ◽  
pp. 1025-1041 ◽  
Author(s):  
Marc Pavese ◽  
Soonmin Jang ◽  
Gregory A Voth
Keyword(s):  
Molecular Dynamics ◽  
Quantum Dynamics ◽  
Parallel Computer ◽  
Dynamics Method

scholarly journals A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

1992 ◽  
Vol 1 (2) ◽  
pp. 153-161 ◽  
Author(s):  
L.H. Yang ◽  
E.D. Brooks III ◽  
J. Belak
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Domain Decomposition Method ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Interprocessor Communication ◽  
Programming Paradigm ◽  
C Preprocessor ◽  
Large Scale Simulations ◽  
Cell Data

A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

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