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.
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 ...