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
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;
Conference_Titel :
Intelligent Computing and Intelligent Systems (ICIS), 2010 IEEE International Conference on
Conference_Location :
Xiamen
Print_ISBN :
978-1-4244-6582-8
DOI :
10.1109/ICICISYS.2010.5658262
