Using Reycled Computers to Construct a Beowulf Cluster for Molecular Modeling

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dc.contributor.author Flemming, Creston
dc.date.accessioned 2009-06-24T13:30:19Z
dc.date.available 2009-06-24T13:30:19Z
dc.date.issued 2009-06-24T13:30:19Z
dc.identifier.uri http://hdl.handle.net/2092/957
dc.description Advisor: Maria Bohorquez ; Timothy Urness en_US
dc.description.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. en_US
dc.description.sponsorship Drake University, College of Arts and Sciences, Department of Mathematics and Computer Science, Department of Chemistry en_US
dc.language.iso en_US en_US
dc.relation.ispartofseries DUCURS 2009;21
dc.subject Used computers en_US
dc.subject Molecular dynamics en_US
dc.subject Cluster analysis--Computer programs en_US
dc.title Using Reycled Computers to Construct a Beowulf Cluster for Molecular Modeling en_US
dc.type Presentation en_US


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  • DUCURS [196]
    Poster sessions and presentation from the Drake University Conference on Undergraduate Research in the Sciences held each April at Olmsted Center on the Drake campus.

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