Paper Citing NAMD - Abstract
Krone, Michael; Bidmon, Katrin; Ertl, Thomas
Interactive Visualization of Molecular Surface Dynamics
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 15:1391-1398, NOV-DEC 2009
Molecular dynamics simulations of proteins play a growing role in various fields such as pharmaceutical, biochemical and medical research. Accordingly, the need for high quality visualization of these protein systems raises. Highly interactive visualization techniques are especially needed for the analysis of time-dependent molecular simulations. Beside various other molecular representations the surface representations are of high importance for these applications. So far, users had to accept a trade-off between rendering quality and performance-particularly when visualizing trajectories of time-dependent protein data. We present a new approach for visualizing the Solvent Excluded Surface of proteins using a GPU ray casting technique and thus achieving interactive frame rates even for long protein trajectories where conventional methods based on precomputation are not applicable. Furthermore, we propose a semantic simplification of the raw protein data to reduce the visual complexity of the surface and thereby accelerate the rendering without impeding perception of the protein's basic shape. We also demonstrate the application of our Solvent Excluded Surface method to visualize the spatial probability density for the protein atoms over the whole period of the trajectory in one frame, providing a qualitative analysis of the protein flexibility.
