Highlights of our Work
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Olga Svinarski and VMD
The molecular graphics program VMD has evolved to version 1.9, featuring new and improved tools for molecular cell biology. A key new tool in VMD permits visual diagnosis of the long-time dynamics of large structures. Improved computer power permits now simulation of processes like protein folding that stretch over microseconds to milliseconds. While short in human time, the process measured in terms of basic molecular motion like bond vibration is seemingly endless, involving hundreds of gigabytes of data and long hours of human attention, if not automated. VMD offers now with the Timeline tool, a convenient way of scanning such data for key "events" that signal successful process steps. Timeline can likewise assist in monitoring the dynamics of large cellular machines involving millions of atoms. VMD 1.9 sports other new tools like ParseFEP for analyzing so-called free energy perturbation calculations determining the energy arising in reaction processes as calculated with VMD's sister program NAMD. VMD includes now also a lightening fast tool to detect spatial regularities in the arrangement of small molecules in order to detect if they constitute disordered or ordered arrangements. By calculating the so-called radial distribution function the tool could identify plug formation in nanopore sensors due to precipitates that go undetected by density or visual inspection. Pleasing to the eye, molecular graphics features in VMD have been enhanced, enabling faster ray tracing, new shading features, X3D molecular scene export for display in WebGL-capable browsers including Chrome, Firefox, and Safari. See more on the VMD 1.9 release page.