Proceedings of the 2nd International Conference on Computer Science and Electronics Engineering

Research and Analysis the Performance of NAMD- Molecular Dynamics Simulation Based Multi-core +GPU

Authors
Yang Zhang, Wen Bo Chen, Qi Feng Bai, Lian Li
Corresponding Author
Yang Zhang
Available Online March 2013.
DOI
https://doi.org/10.2991/iccsee.2013.72How to use a DOI?
Keywords
GPU,NAMD,CUDA, molecular stimulation , Performance analyses, NVIDIA Tesla C2050
Abstract
Nowadays, the GPU can provide about one order of magnitude accelerated over CPU code and even more, so it can be used in large scale science computing applications. The paper based on NVIDIA Tesla C2050 and dual-core CPU server through use NAMD 2.9 simulates three differences molecule number proteins: Beta2- adrenergic receptor, SET9 and Ubiquitin. Through the comparison and analyses the results of the simulations experiment, we can conclusion that the difference systems of molecule will lead to the difference GPU accelerated. The computing times of four GPU is nearly half of the time used by 1 GPU; and this is especially true in the case of macromolecules. Furthermore, from the GPU’s memory utilization rate, the larger the protein system is, the higher the memory use of the GPU is. NVIDIA Tesla C2050 is can satisfy an even larger system simulation. The paper provides the best options for application of this software use the GPU and multi-core framework, a reference to building large scale molecule stimulations platforms, and a solution to science application of large molecule stimulation.
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Proceedings
Proceedings of the 2nd International Conference on Computer Science and Electronics Engineering
Part of series
Advances in Intelligent Systems Research
Publication Date
March 2013
ISBN
978-90-78677-61-1
ISSN
1951-6851
DOI
https://doi.org/10.2991/iccsee.2013.72How to use a DOI?
Open Access
This is an open access article distributed under the CC BY-NC license.

Cite this article

TY  - CONF
AU  - Yang Zhang
AU  - Wen Bo Chen
AU  - Qi Feng Bai
AU  - Lian Li
PY  - 2013/03
DA  - 2013/03
TI  - Research and Analysis the Performance of NAMD- Molecular Dynamics Simulation Based Multi-core +GPU
BT  - Proceedings of the 2nd International Conference on Computer Science and Electronics Engineering
PB  - Atlantis Press
SN  - 1951-6851
UR  - https://doi.org/10.2991/iccsee.2013.72
DO  - https://doi.org/10.2991/iccsee.2013.72
ID  - Zhang2013/03
ER  -