Parallel molecular dynamics simulations of biomolecular systems

1998 ◽  
pp. 296-303 ◽  
Author(s):  
Alexander Lyubartsev ◽  
Aatto Laaksonen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

Full-neighbor-list based numerical reproducibility method for parallel molecular dynamics simulations

2019 ◽  
Vol 85 ◽  
pp. 109-118
Author(s):  
Liyang Xu ◽  
Xiaoguang Ren ◽  
Qian Wang ◽  
Xinhai Xu ◽  
Xuejun Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Neighbor List ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

PS38 Hierarchical parallel molecular dynamics simulations of nanomaterials deformation on a Cell-based cluster

2008 ◽  
Vol 2008 (0) ◽  
pp. _PS38-1_-_PS38-2_
Author(s):  
Takayuki Matsuno ◽  
Akio Ishii ◽  
Hajime Kimizuka ◽  
Shigenobu Ogata
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
A Cell ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems

2015 ◽  
Vol 17 (15) ◽  
pp. 9959-9972 ◽  
Author(s):  
Juan Torras
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Active Zones ◽  
Dynamics Simulations

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented.

Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

1995 ◽  
Vol 117 (14) ◽  
pp. 4193-4194 ◽  
Author(s):  
T. E. III Cheatham ◽  
J. L. Miller ◽  
T. Fox ◽  
T. A. Darden ◽  
P. A. Kollman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Systems ◽  
Particle Mesh Ewald ◽  
Ewald Method ◽  
Dynamics Simulations

Pseudorandom number generator for massively parallel molecular-dynamics simulations

1994 ◽  
Vol 50 (2) ◽  
pp. 1607-1615 ◽  
Author(s):  
Brad Lee Holian ◽  
Ora E. Percus ◽  
Tony T. Warnock ◽  
Paula A. Whitlock
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Massively Parallel ◽  
Pseudorandom Number ◽  
Pseudorandom Number Generator ◽  
Number Generator ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

PARALLEL MOLECULAR DYNAMICS SIMULATIONS OF ORGANIC MATERIALS

1994 ◽  
Vol 05 (02) ◽  
pp. 295-298 ◽  
Author(s):  
STEVE PLIMPTON ◽  
BRUCE HENDRICKSON
Keyword(s):  
Molecular Dynamics ◽  
Parallel Algorithms ◽  
Molecular Dynamics Simulations ◽  
Parallel Algorithm ◽  
Communication Cost ◽  
Dynamics Model ◽  
Organic Systems ◽  
Intel Paragon ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

A new parallel algorithm suitable for molecular dynamics simulations of organic systems is presented. It reduces the communication cost and memory requirements of other commonly-used parallel algorithms by a factor of [Formula: see text] where P is the number of processors. The algorithm has been implemented in a CHARMM-like molecular dynamics model and its performance on 1024-processor nCUBE 2 and Intel Paragon machines is discussed.

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