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Parallel molecular dynamics simulation of lysozyme hydration on IBM blade center cluster

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3 Author(s)
Feng Sha ; Network Inf. Center, Xiamen Univ. of Technol., Xiamen, China ; Tao Wei ; Ying Wei

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.

Published in:

Intelligent Computing and Intelligent Systems (ICIS), 2010 IEEE International Conference on  (Volume:2 )

Date of Conference:

29-31 Oct. 2010

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