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» Large Scale Simulation of Parallel Molecular Dynamics
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CPHYSICS
2008
121views more  CPHYSICS 2008»
13 years 8 months ago
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations
A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principlesbased reactive force fields (ReaxFF) des...
Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, ...
ICA3PP
2005
Springer
14 years 1 months ago
GridMD: Program Architecture for Distributed Molecular Simulation
In the present work we describe architectural concepts of the distributed molecular simulation package GridMD. The main purpose of this work is to underline the construction patter...
Ilya Valuev
IBMRD
2008
52views more  IBMRD 2008»
13 years 8 months ago
Massively parallel molecular dynamics simulations of lysozyme unfolding
Ruhong Zhou, Maria Eleftheriou, Chung-Chau Hon, Ro...
IPPS
2008
IEEE
14 years 2 months ago
Model-guided performance tuning of parameter values: A case study with molecular dynamics visualization
In this paper, we consider the interaction between application programmers and tools that automatically search a space of application-level parameters that are believed to impact ...
Yiinju L. Nelson, Bhupesh Bansal, Mary W. Hall, Ai...
CPHYSICS
2006
124views more  CPHYSICS 2006»
13 years 8 months ago
Collision-free spatial hash functions for structural analysis of billion-vertex chemical bond networks
State-of-the-art molecular dynamics (MD) simulations generate massive datasets involving billion-vertex chemical bond networks, which makes data mining based on graph algorithms s...
Cheng Zhang, Bhupesh Bansal, Paulo S. Branicio, Ra...