Ensemble-space visualization improves perception of 3D state of molecular dynamics simulation
Israel J. Huff, Chris Weigle, David C. Banks · 2008
Large-scale molecular dynamics (GD) simulations are some of the primary applications running on today's supercomputers. These simulations frequently compute the interactions of millions of atoms over millions of time steps, and petascale simulations will target billion atom simulations in the near future. Visualizing the state of such large-scale simulations poses a significant challenge for both data reduction and perception. Standard tools for 3D visualization of MD simulations -- such as direct visualization of the molecules in their simulated physical arrangement -- eventually grow so dense (with more atoms than screen pixels) that only the volumetric shape of the simulation domain is apparent, rather than its detailed content.