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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
ICS
2009
Tsinghua U.
14 years 2 months ago
Dynamic topology aware load balancing algorithms for molecular dynamics applications
Molecular Dynamics applications enhance our understanding of biological phenomena through bio-molecular simulations. Large-scale parallelization of MD simulations is challenging b...
Abhinav Bhatele, Laxmikant V. Kalé, Sameer ...
PPOPP
2006
ACM
14 years 1 months ago
Performance characterization of molecular dynamics techniques for biomolecular simulations
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
JCC
2010
113views more  JCC 2010»
13 years 6 months ago
MDLab: A molecular dynamics simulation prototyping environment
Molecular dynamics (MD) simulation involves solving Newton’s equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a...
Trevor M. Cickovski, Santanu Chatterjee, Jacob Wen...
FPL
2008
Springer
180views Hardware» more  FPL 2008»
13 years 9 months ago
Compiled hardware acceleration of Molecular Dynamics code
The objective of Molecular Dynamics (MD) simulations is to determine the shape of a molecule in a given biomolecular environment. These simulations are very demanding computationa...
Jason R. Villarreal, Walid A. Najjar