VMD Publications

Journal and conference articles we've written on VMD

• GPU acceleration of cutoff pair potentials for molecular modeling applications. Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-Mei W. Hwu. Proceedings of the 2008 Conference On Computing Frontiers, 2008. In press.

• GPU computing. John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips. Proceedings of the IEEE, 96:879-899, 2008.

• Continuous fluorescence microphotolysis and correlation spectroscopy using 4Pi microscopy. Anton Arkhipov, Jana Hüve, Martin Kahms, Reiner Peters, and Klaus Schulten. Biophysical Journal, 93:4006-4017, 2007.

• Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.

• A system for interactive molecular dynamics simulation. John Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten. In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pp. 191-194, New York, 2001. ACM SIGGRAPH.

• Speech/gesture interface to a visual-computing environment. Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten. IEEE Computer Graphics and Applications, 20:29-37, 2000.

• A visual computing environment for very large scale biomolecular modeling. Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of the 1997 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pp. 3-12. IEEE Computer Society Press, 1997.

• Speech/gesture interface to a visual computing environment for molecular biologists. R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips, M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of 13th ICPR 96, volume 3, pp. 964-968, 1996.

• VMD - Visual Molecular Dynamics. William Humphrey, Andrew Dalke, and Klaus Schulten. Journal of Molecular Graphics, 14:33-38, 1996.

VMD talks
• GPU Acceleration of Molecular Modeling Applications Linux Clusters Institute, NCSA (5/1/2008)
• Accelerating Molecular Modeling Applications with Graphics Processors SIAM Conference on Parallel Processing for Scientific Computing (3/12/2008)
• Tutorial: High Performance Computing on GPUs with CUDA (Supercomputing 2007)
• GPU Acceleration of Scientific Applications Using CUDA
  • AstroGPU 2007, Institute for Advanced Study, Princeton University (11/09/2007)
• ECE 498AL1: Programming Massively Parallel Processors
  • Case Studies: Ion Placement Tool, VMD (10/15/2007)
  • CUDA Student Project Pages
• ECE 498AL: Programming Massively Parallel Processors
  • Case Studies: Ion Placement Tool, VMD (3/14/2007)
• Visualization of Nano-Scale Structures
  • Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006
  • University of Texas Health Science Center at Houston, 4/20/2006
• VMD: Algorithms and Methods for Large Scale Biomolecular Visualization
  • San Diego Supercomputer Center, 9/12/2005
• Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware
  • ITG Forum at University of Illinois at Urbana-Champaign, 2/15/2005
  • CS Colloqium at University of Missouri-Rolla, 2/22/2005
  • Purdue University Envision Center, 2/25/2005
• VMD: Biomolecular Visualization and Analysis
  • INRIA/CNRS ARC Docking Project, Nancy France, 12/8/2004
• VMD: Biomolecular Visualization and Analysis
  • The Scripps Research Institute (while at Siggraph 2003)
• Biomolecular Visualization with the CAVE and VMD
  • 2001 CAVE Programming Workshop, Swedish Royal Institute of Technology
• A System for Interactive Molecular Dynamics
  • Presented at ACM Siggraph I3D 2001, matches paper below.

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
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