(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

TUTORIAL B2 - SECTION 8

Using VMD with AMBER

By Ross Walker

Updated for VMD 1.9.2
[by Aditi Munshi and Ross Walker]

8) Following system parameters over the course of a trajectory.

We have two more useful things we should look at in this tutorial. The first is to use VMD's label tools to watch how the distance between two atoms changes during our trajectory.

Let's start by making our currently loaded trajectory a little prettier. Click Graphics->Representations to bring up the "Graphical Representations" menu if it is not already up. Next click "Create Rep" and change the Drawing method to "Ribbons" and the Coloring method to "ResType". Then hit "Create Rep" again and change the Drawing method to "H bonds" and then change the "Line thickness" to 3 so things are easier to see. Also change the "Distance Cutoff" to 4.2 angstroms. This is a little long for what would be considered a regular hydrogen bond but it is just for demonstration purposes since this trajectory is not long enough for any real hydrogen bonds to form. Your window should now look something like this:

Detected hydrogen bonds will now appear as dashed lines between the two atoms involved. If you play through the trajectory you will see that they are formed in places and then broken and then reformed. In this way, you can visually track the presence of hydrogen bonds over a trajectory. Note that if this was an explicit solvent simulation, you would probably want to change the selected atoms for each of the 3 representations we have from "all" to "all not water". This is especially true with the HBonds case. Otherwise you will be swamped with dotted lines between all of the hydrogen bonded water molecules.

Finally we will add a bond label between the two ends of out peptide chain. This will allow us to monitor the distance between the chain ends as we run through our simulation. Go to the "VMD Main" window and select Mouse->Label->Bonds. This will change the mouse left click action to bond selection.

Then go to the "OpenGL" window and click on one atom on each end of the peptide chain. You should see a dashed line with the distance between them displayed. If you get things wrong you can use the Graphics->Labels tool to delete labels so that you can create them again. Note: The bond, angle and dihedral label options don't actually refer to bonds, angles and dihedrals. The labels you add don't actually have to be between bonded atoms. Bond means distance between any two atoms (in angstroms), angle means angle between any 3 atoms (in degrees) and dihedral means dihedral angle between any 4 atoms (in degrees).

Now play through the trajectory and you should see the value change and the TRPcage peptide starts to fold up. We don't really learn a lot about the system here but this is only designed to show you some of the things VMD can do. Over a much longer production simulation we could learn a lot more and measure more relevant parameters.


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(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015