IBM叶片中心簇上溶菌酶水合作用的平行分子动力学模拟

2010 IEEE International Conference on Intelligent Computing and Intelligent Systems Pub Date : 2010-12-06 DOI:10.1109/ICICISYS.2010.5658262

Feng Sha, T. Wei, Ying Wei

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引用次数: 1

摘要

采用IBM刀片HS22和DELL PC 755构建了一个新的Beowulf集群，用于执行并行原子MD模拟。以溶菌酶水合作用为模型系统，利用AMBER套件对不同cpu数和节点数的系统性能进行评价。效率达到理论值的70%左右。模拟结果表明，在300K温度下，溶菌酶表面约有771个水分子结合在第一水化壳内的第一水化壳内。

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

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.

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2010 IEEE International Conference on Intelligent Computing and Intelligent Systems

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