Using Reycled Computers to Construct a Beowulf Cluster for Molecular Modeling

Abstract

The process of using recycled computers to construct a Beowulf cluster in order to simulate the molecular dynamics of a chemical system is explored. The cluster was assembled using used computers taken out of service due to upgrades, and would otherwise be discarded. When assembled in a cluster, the computer performed the numerically-intensive process of molecular modeling roughly four times faster than a current machine using synthetic benchmarks. The cluster was used to run a molecular modeling program NAMD. We used the cluster and NAMD to analyze an experiment to study a biologically active lipid called DOPC in the form of a monolayer. The monolayer was constructed using VMD (Visual Molecular Dynamics). It consists of DOPC molecules on the air/water interface. An energy minimization process is carried out before molecular dynamics can be calculated in order to render the system in its most probable physical state.