Tuesday October 27, 2009
This one-day workshop introduced researchers to the newly released version (v.2.2) of Desmond software from D. E. Shaw Research, used for molecular dynamics simulations of biological molecules. Attendees learned the basic concepts underlying Desmond, and how to run simulations and analyze results. The workshop was co-hosted by the National Resource for Biomedical Supercomputing (NRBSC) and the Pittsburgh Supercomputing Center (PSC), with instructors from D. E. Shaw Research, the NRBSC, and the PSC. Topics included preparing structure files, setting system constraints, specifying force fields, and post-simulation analysis. A hands-on lab session provided an opportunity to work with Desmond on local workstations and large scale PSC systems.
The workshop was geared toward life science researchers but was also 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 was recommended.