VMD Publications

Peer-reviewed articles we've written on VMD and the algorithms it employs:

• Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories. John E. Stone, Kirby L. Vandivort, and Klaus Schulten. Lecture Notes in Computer Science, 6939:1-12, 2011.

• Fast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogramming. Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer. Journal of Computational Physics, 230:3556-3569, 2011.

• GPU-accelerated computation and interactive display of molecular orbitals. John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011.

• Fast molecular electrostatics algorithms on GPUs. David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp. 43-58. Morgan Kaufmann Publishers, 2011.

• GPU algorithms for molecular modeling. John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten. In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors, Scientific Computing with Multicore and Accelerators, chapter 16, pp. 351-371. Chapman & Hall/CRC Press, 2011.

• Immersive molecular visualization and interactive modeling with commodity hardware. John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten. Lecture Notes in Computer Science, 6454:382-393, 2010.

• Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman, Guochun Shi, Kenneth Esler, Volodymyr Kindratenko, John E. Stone, and James C. Phillips. In International Conference on Green Computing, pp. 317-324, 2010.

• GPU-accelerated molecular modeling coming of age. John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten. Journal of Molecular Graphics and Modelling, 29:116-125, 2010.

• OpenCL: A parallel programming standard for heterogeneous computing systems. John E. Stone, David Gohara, and Guochun Shi. Computing in Science and Engineering, 12:66-73, 2010.

• Probing biomolecular machines with graphics processors. James C. Phillips and John E. Stone. Communications of the ACM, 52:34-41, 2009.

• GPU clusters for high performance computing. Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu. In Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on, pp. 1-8, 2009.

• Long time-scale simulations of in vivo diffusion using GPU hardware. Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida Luthey-Schulten. In Proceedings of the IEEE International Parallel & Distributed Processing Symposium, pp. 1-8, 2009.

• Visualization of cyclic and multi-branched molecules with VMD. Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain. Journal of Molecular Graphics and Modelling, 28:131-139, 2009.

• High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, and Klaus Schulten. In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, New York, NY, USA, 2009. ACM.

• Multilevel summation of electrostatic potentials using graphics processing units. David J. Hardy, John E. Stone, and Klaus Schulten. Journal of Parallel Computing, 35:164-177, 2009.

• 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. In CF'08: Proceedings of the 2008 conference on Computing Frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.

• 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 E. 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

2011:
• Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories, ISVC 2011, Las Vegas, NV (9/26/2011)

2010:
• Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware, ISVC 2010, Las Vegas, NV (12/1/2010)
• Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA, NVIDIA Booth, Supercomputing 2010, New Orleans, LA (11/16/2010)
• High Performance Computing with CUDA Case Study: Heterogeneous GPU Computing for Molecular Modeling, CUDA Tutorial, Supercomputing 2010, New Orleans, LA (11/14/2010)
• GPU and the Computational Microscope, GPU Technology Conference (09/22/2010)
• High Performance Molecular Simulation, Visualization, and Analysis on GPUs, GPU Technology Conference (09/22/2010)
• Simulating Biomolecules on GPUs with the Multilevel Summation Method, Oak Ridge National Laboratory (09/17/2010)
• High Performance Molecular Simulation, Visualization, and Analysis on GPUs, Oak Ridge National Laboratory (09/16/2010)
• Faster, Cheaper, and Better Science: Molecular Modeling on GPUs, Fall National Meeting of the American Chemical Society, Boston, MA (08/22/2010)
• OpenCL: Molecular Modeling on Heterogeneous Computing Systems, Fall National Meeting of the American Chemical Society, Boston, MA (08/22/2010)
• Quantifying the Impact of GPUs on Performance and Energy Efficiency in HPC Clusters, The Work in Progress in Green Computing(WIPGC), Chicago, IL (08/17/2010)
• Using GPUs to compute the multilevel summation of electrostatic forces, Multiscale Molecular Modeling Conference, Edinburgh, Scotland (07/02/2010)
• Molecular Visualization and Analysis on GPUs, Symposium on Application of GPUs in Chemistry and Materials Science, University of Pittsburgh (06/29/2010)

2009:
• Accelerating Molecular Modeling Applications with GPU Computing, Exhibition, Supercomputing 2009, Portland, OR (11/18/2009)
• OpenCL for Molecular Modeling Applications: Early Experiences, OpenCL BOF, Supercomputing 2009, Portland, OR (11/18/2009)
• High Performance Molecular Visualization and Analysis with GPU Computing, Beckman Institute Forum for Imaging and Visualization, University of Illinois (10/20/2009)
• GPU Accelerated Visualization and Analysis in VMD and Recent NAMD Developments, GPU Technology Conference, San Jose, CA (10/1/2009)
• GPU Accelerated Visualization and Analysis in VMD, Center for Molecular Modeling, University of Pennsylvania, (6/9/2009)
• Keynote: Accelerating Molecular Modeling Applications with GPU Computing, Second Sharcnet Symposium on GPU and Cell Computing, University of Waterloo (5/20/2009)
• Experiences with Multi-GPU Acceleration in VMD, Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters, NCSA (4/2/2009)
• High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs, Second Workshop on General-Purpose Processing on Graphics Processing Units, Washington D.C. (3/8/2009)
• High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs, IACAT Accelerator Workshop, NCSA (1/23/2009)

2008:
• GPU Computing, Cape Linux Users Group, South Africa (10/28/2008)
• Accelerating Molecular Modeling Applications with Graphics Processors, Computer Science Department, University of Cape Town, South Africa (10/23/2008)
• Accelerating Computational Biology by 100x Using CUDA, NVISION 2008 (8/26/2008)
• GPU Acceleration of Cutoff Pair Potentials for Molecular Modeling Applications, ACM Computing Frontiers 2008 (5/7/2008)
• 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)

2001-2007:
• 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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