A simple coupled potential QM/MM/MD simulation.

(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

Using VMD with AMBER - SECTION 1

By Ross Walker

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

1) Loading VMD and Customizing the Initial Window Layout

Before we start looking at some AMBER trajectories you should ensure that VMD is correctly installed on your machine and working correctly. When you issue the command 'VMD' it should load without error messages. If you can't get VMD to work please refer to the VMD website for further info.

Lets start by customizing the way VMD starts up so that we have a similar display layout. (If you are confident navigating your way around VMD you can skip this step.)

Since most people will be using single display machines to run this tutorial, we will step through creating a startup script for a single display.

VMD's initial layout is controlled by a file called .vmdrc. Here is a .vmdrc file you can use to obtain what I consider to be a good initial layout.

vmdrc

# turn on lights 0 and 1
light 0 on
light 1 on
light 2 off
light 3 off

# position the stage and axes
axes location off
stage location off

# position and turn on menus
menu main on
menu graphics on
menu files on

menu main move 5 196
menu graphics move 5 455
menu files move 800 750

display projection orthographic

If you have a file called .vmdrc in your home directory (check with cd ~, ls -la) either delete it or rename it. Then save the file above as ".vmdrc" in your home directory. (Note the dot before the vmdrc).

This file is sourced automatically by VMD on load and does several things. First of all, it switches on lights 0 and 1. It then turns off the Axis. This I feel creates a cleaner OpenGL window. It also sets the display projection mode to orthographic, which in my opinion gives much better depth perception and less distortion when rotating on a screen that does not have an exact 4 by 3 ratio, e.g. my screen which has a resolution of 1280x1024. Finally it turns on the main menu, the graphics menu and the file menu. It then moves these to suitable locations on the screen. Note: this is designed for a screen resolution of 1280x1024. If your resolution is different you may need to play around with the numbers on the 3 move lines to get a layout that is reasonable.

Now run VMD and it should come up with a layout similar to that below:

>vmd

We are now ready to try loading some molecules.

CLICK HERE TO GO TO SECTION 2