Using Reycled Computers to Construct a Beowulf Cluster for Molecular Modeling
MetadataShow full item record
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.
Advisor: Maria Bohorquez ; Timothy Urness
Showing items related by title, author, creator and subject.
Horvath, Ryan; McVey, Sean; Love, DeCarlos; Nesheim, Skyler (2007-05-31)The Drake University Virtual Reality Project is an ongoing endeavor with the primary goal of producing a working CAVE system, which is a virtual, immersive 3D theater. The Drake Virtual Reality Project utilizes low cost ...
Ionization Of The Hydrogen Molecular Ion By Ultrashort Intense Elliptically Polarized Laser Radiation DuToit, Ryan (2013-04-17)We report results for the single- and multi-photon ionization of the H2 + ion irradiated by ultrashort elliptically polarized laser pulses with central photon energies from the ionization threshold up to 300 eV. Using the ...
DuToit, Ryan (2012-04-23)We investigate how the simplest molecular ion, Dihydrogen (H2 +), reacts when exposed to an intense ultrashort laser pulse. We use a computer code written in parallel FORTRAN, which is run on a Drake-owned cluster. The ...