Reference for “Loading a Trajectory in VMD” Software: VMD 1.9.1 Loading a VMD model: 1. 2. 3. 4. 5.
In the window titled “VMD Main,” click “File” on the menu bar. On the drop-down menu, select “New Molecule.” Click the browse button, next to the “Filename” line. Select the desired “.dcd” file and click load. Repeat Steps 3 and 4 for the corresponding “.psf” file. NOTE: You may load the .dcd and .psf file in any order, but you have to load both. The .dcd and .psf files absolutely must have the same number of atoms.
Changing atomic visual representations: 1. 2. 3. 4.
On the window titled “VMD Main” click the “Graphics” option on the menu bar. On the drop-down menu, select “Representations.” In the “Graphical Representations” window, click “Create Rep”. With this new Representation line highlighted in green, click on the “Selections” tab underneath the “Selected Atoms” box. 5. Double-click the desired “Keyword” of the representation you wish you select. NOTE: Two of the more helpful keywords are “segname” and “resid”. Each is shown in the corresponding video accompanying these written instructions. 6. On the right-hand side of the screen, click on the desired “Value” of the representation you wish to create. NOTE: Alternative to step 5 and step 6, when you are comfortable with VMD, you can simply type the desired keyword and value into the line underneath “Selected Atoms.” 7. Click enter. IT IS IMPORTANT TO CLICK ENTER AT THIS TIME TO SAVE YOUR CURRENT CHANGES. 8. Click the “Draw style” tab underneath the “Selected atoms” line. 9. Click the drop-down menu associated with “Drawing Method” and select the desired representation viewing method. 10. You can repeat steps 3 – 10 to create as many representations of the molecule as you wish.