WORKSHOP: DESMOND TRAINING, OCTOBER 27, 2009

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This one-day workshop (9 am to 4 pm) will introduce researchers to the newly released version (v.2.2) of Desmond software from DE Shaw Research, used for molecular dynamics simulations of biological molecules. Attendees will learn the basic concepts underlying Desmond, and how to run simulations and analyze results. The workshop will be co-hosted by the National Resource for Biomedical Supercomputing (NRBSC) and the Pittsburgh Supercomputing Center (PSC), with instructors from DE Shaw Research, the NRBSC, and the PSC. Topics will include preparing structure files, setting system constraints, specifying force fields, and post-simulation analysis. A hands-on lab session will provide an opportunity to work with Desmond on local workstations and large scale PSC systems. The workshop is geared toward life science researchers but will also be of interest to anyone investigating molecular motions and interactions using computer simulation techniques. A broad familiarity with the concepts of molecular dynamics simulations and a working knowledge of Unix is recommended.