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

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.