# RMSD analysis of trajectory (DCD file) using VMD

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.