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Computation


The picture is a close-up of the thioester bond between Ubc13, an E2 enzyme, and ubiquitin, a protein used for post-translational modification. There is a lysine poised to attack, which will result in thioester bond cleavage and the transfer of ubiquitin to the substrate lysine. The image was generated by VMD and is a snapshot of a QM/MM simulation via the CP2K software package.
Points of Contact: Tom DeVore (540.568.6672)
Isaiah Sumner (540.568.6670)

Computation has become an indispensable tool for the modern chemist. Simulations of chemical and biochemical processes routinely provide atomic-level detail that is difficult or impossible for traditional experimental techniques to achieve. Therefore, the JMU Department of Chemistry and Biochemistry operates a high performance computing cluster, named Faust, that is dedicated to computational chemistry. Faust is composed of eight, Dell R420 compute nodes and a Dell R720 head node. Each compute node has two, 1.9GHz six-core Intel Xeon processors and 48 GB of memory, whereas the head node has two, 2.2GHz eight-core Intel Xeon processors and 64 GB of memory. In total, Faust has 10TB of shared disk space for data storage. The cluster is parallelized with a 10 GbE interconnect and the HPL-Linpack benchmark clocked Faust running at 617 GFLOPS on all eight compute nodes. Software running on this cluster includes Gaussian09, Amber12, CP2K, GaussView5 and VMD enabling calculations for electronic structure, molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and molecular visualization manipulation and analysis.