This video shows you how to calculate the RMSD analysis of aa protein using the software VMD from the University of Illinois (http://www.ks.uiuc.edu/). VMD is a powerful tool for analysis of structures and trajectories. Numerous tools for analysis are available under the VMD Main menu item Extensions $ \rightarrow $ Analysis. In addition to these built-in tools, VMD users often use custom-written scripts to analyze desired properties of the simulated systems. VMD Tcl scripting capabilities are very extensive, and provide boundless opportunities for analysis. Example of a built-in analysis tool: the RMSD Trajectory Tool The built-in analysis tools in VMD are available under the menu item Extensions $ \rightarrow $ Analysis. These tools each features a GUI window that allow one to enter parameters and customize the quantities analyzed. In addition, all tools can be invoked in a scripting mode, using the TkConsole window. We will learn how to work with one of the most frequently used tools, the RMSD Trajectory Tool.
