Simulating hiv-1 protease at its most vulnerable instant

Stony Brook University's Center for Molecular Medicine, Center for Structural Biology, provides space for researchers from different disciplines and academic departments in order to encourage collaborative research. The collaboration includes an HIV protease team, whose work is funded by the National Institutes of Health and the National Science Foundation. Stony Brook's team of scientists developed computer simulations offering insight into the mechanics of HIV-1 protease (PR). The team ran the test model on both a 128-processor Xeon cluster at the National Center for Supercomputing Applications (NCSA) and on 128 processors of an SGI Altix Bx2 system. The researchers run the calculations on NCSA's Altix 3700 Bx2, using 64 processors of the system for each of the simulations and leaving the remainder of the 1,024-processor resource available for other projects. The team developed a new set of energy parameters that were used to describe the physical forces between atoms determining the dynamic behavior.