Viewing SMD trajectories within VMD

Start VMD loading the trajectory just generated:

vmd da.psf da_smd.dcd

Position the molecule (rotate, translate, scale) so that you have the view of the entire length of the molecule.

Change the representation: Select the menu item Graphics$\rightarrow$ Representations. In the Graphical Representations window, set Drawing Method to Ribbons. The Ribbon representation is good for viewing the overall structure, but you may explore any other representations or even multiple views.

Use the scroll bar at the bottom of the VMD Main window to browse through the trajectory.

Figure: Deca-Alanine in ribbon representation, loaded into VMD.

An important structural change during the helix-coil transition is the breaking of hydrogen bonds. You can monitor hydrogen bonds using VMD.

Choose CPK from Drawing Methods. This will change the representation of the molecule from Ribbon to CPK.

Now let's show hydrogen bonds:

1. In the Graphics Representations window, click Create Rep.

2. In the Selected Atoms text entry, delete the word all, type name N O, and hit the Enter key. (Hydrogen bonds are formed between N and O atoms.)

3. Select HBonds from Drawing Method.

4. Change the parameters to the following: Distance Cutoff: 4.0, Angle Cutoff: 40, Line Thickness: 10.

You should see several hydrogen bonds.

Figure: Deca-alanine in CPK representataion. Hydrogen-Bonds are highlighted.

Again using the scroll bar at the bottom of the VMD Main window, browse through the trajectory. Observe the hydrogen bond breaking as the molecule is stretched.

Once you are done, quit VMD (the menu item File $\rightarrow$ Quit).