I am trying to use the RMSD Trajectory Tool in VMD Main window. You select EXTENSION --> ANALYSIS --> RMSD Trajectory Tool. I want to use RMSD on ubiquitin.psf. So what I do is I load ubiquitin.psf using the Molecule File Browser on VMD (the specific file is in the 1-1-build directory), and then I load the trajectory file into the ubq.psf. The trajectory file is called equilibration.dcd. In the RMSD Trajectory Tool window, I click on Add all and ubiquitin.psf appears in the "id" box. I then "select" it, and there is a blue horizontal bar that appears across ubiquitin.psf. I then check the "Plot" box. I then click on ALIGN and then on RMSD. But what happens when I click on RMSD is that the error message Frame out of range (max is -1) appears. And when I click on File --> Plot data, the error No data available to plot yet appears. Can someone help me out with this? I don't get it. (And one more thing, how do you view a DCD file? You certainly cannot view it with Notepad).
