DocumentCode
536171
Title
Parallel molecular dynamics simulation of lysozyme hydration on IBM blade center cluster
Author
Sha, Feng ; Wei, Ying ; Wei, Tao
Author_Institution
Network Inf. Center, Xiamen Univ. of Technol., Xiamen, China
Volume
2
fYear
2010
fDate
29-31 Oct. 2010
Firstpage
479
Lastpage
482
Abstract
A new Beowulf Clusters with IBM blade HS22 and DELL PC 755 has been built to perform parallel atomistic MD simulations. Lysozyme hydration was used as a model system to evaluate the system performance with different numbers of CPUs and nodes with AMBER suite. The efficiency reaches around 70% of the theoretical value. From our simulation, about 771 water molecules are found to be bound on lysozyme surface at 300K within the first hydration shell within first hydration shell.
Keywords
biology computing; digital simulation; molecular biophysics; parallel processing; Beowulf clusters; Dell PC 755; HS22 IBM blade; IBM blade center cluster; first hydration shell; lysozyme hydration simulation; parallel molecular dynamics simulation; Biological system modeling; Computational modeling; Computers; Proteins; Temperature measurement; AMBER; Bewulf Culstetrs; Lysozyme Hydration; Parallel Atomistic MD Simulation;
fLanguage
English
Publisher
ieee
Conference_Titel
Intelligent Computing and Intelligent Systems (ICIS), 2010 IEEE International Conference on
Conference_Location
Xiamen
Print_ISBN
978-1-4244-6582-8
Type
conf
DOI
10.1109/ICICISYS.2010.5658262
Filename
5658262
Link To Document