VMD

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. VMD [49] is a molecular visualization program that provides interactive biomolecular display and analysis capabilities. VMD incorporates scripting and plugin interfaces for user-extensibility and automation of complex tasks. (http://www.ks.uiuc.edu/Research/vmd/) VMD runs on all major operating systems and supports computers ranging from laptops to supercomputers. VMD utilizes advanced hardware technologies including stereoscopic displays, six-degree-of-freedom input devices with haptic feedback, multiprocessor and clustered rendering systems, OpenGL, programmable shading, and 64-bit processors. In the past year, VMD has been extended with new structure building tools that assist biomedical researchers with building all-atom molecular models and preparing simulations. VMD now processes structures with multiple conformations, special bonds, biological unit transformations, and can automatically regenerate some types of missing information. A new volumetric map generation tool synthesizes volumetric density and occupancy maps from molecular dynamics trajectories for use in analysis and visualization. New graphical representations allow researchers to visualize very large molecular models with reduced detail and efficient rendering algorithms. Several new plugins provide additional molecular and volumetric file format support. More than 10,300 new users registered and downloaded VMD 1.8.3 since the previous progress report. As of April, 2006, over 17,200 unique users had registered and downloaded this version. Three plugin updates were released for VMD 1.8.3 since the previous progress report. Over 11,400 unique users have downloaded developmental versions of VMD since the last progress report. The latest version, VMD 1.8.4, was released on April 16, 2006. Ongoing VMD developments include additional tools for structure building, multiple sequence alignment, and simulation analysis, new and improved graphical representations, and multiprocessor performance improvements. The next release of VMD is planned for the summer of