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A supercomputer makes the difference

Originally published in the Union College Magazine, Winter 2013

The IBM intelligent cluster, gifted to Union by the company in 2011, is advancing research on campus in notable ways.

The first paper published using the machine, by Janet Anderson in the journal Biophysical Chemistry, analyzed the way protein G rotates in aqueous solution, by predicting properties measured in nuclear magnetic resonance experiments from molecular dynamics simulations.

During each of five simulations, the positions and velocities of 10,000 protein and water atoms were calculated using the NAMD program on the supercomputer. Each simulation consisted of 20,000,000 iterations, each iteration representing a femtosecond of time (there are 10 15 femtoseconds in one second).

"Computer simulations are helpful in understanding molecular behavior that is invisible to the eye, and to interpret the results of experiments," Anderson said. "These 20,000,000 steps of protein motion, equivalent to 200 nanoseconds of molecule time, would normally have taken months on a desktop computer. They took only 13 days on the cluster.

This speed-up is impressive. The method used in our paper would not have worked with shorter simulations because the molecule would not have had enough time to tumble."