A first look at the command-line interface

Overview

Teaching: 10 min
Exercises: 5 min

Questions

• How to start VMD in text mode?

• How to use VMD commands?

Objectives

• Learn how to use basic VMD commands

• Learn to write loops in VMD

• Learn how to get help on VMD commands

Introducing VMD commands

Starting VMD in text mode.

The VMD program can also be used in text mode. Everything you can do in VMD interactively can also be done with commands and scripts. In text mode you interact with VMD using commands. The command-line interface is more flexible than GUI and it allows VMD to read commands from script files. With commands, you can use options than are not available in GUI, and you can run VMD non-interactively. Command-line access to VMD functions is very useful in HPC environment for batch jobs. The text mode is typically used for analyzing MD simulations and rendering animations.

How to start vmd in text mode? If graphical display is not available VMD will automatically fallback into text mode. When you are running analysis scripts on a system with graphical display you may want to enforce text mode to prevent VMD from opening GUI. To do so start vmd with the option -dispdev text.

• The command-line interface
  • is more flexible than GUI
  • allows VMD to read commands from script files.
  • offers options than are not available in GUI

To start vmd in text mode use the option -dispdev text.

Entering commands

Commands can be entered in two ways:

• in the VMD command window
• in Tk Console available under the Extensions menu

VMD command window is very basic, you can only type commands, and it is not possible to edit command lines. Tk console offers history, autocompletion, and syntax highlighting.

Let’s run our first command.

rotate

rotate usage:
rotate stop -- stop current rotation
rotate [x | y | z] by <angle> -- rotate in one step
rotate [x | y | z] by <angle> <increment> -- smooth transition

If a command is entered without any argument, VMD displays short instructions on how to use it.

rotate x by 90 1

A smooth rotation of the scene around the x axis will be performed with an increment of 1 degree by this command. The advantage of using commands to rotate is that you can precisely specify the angle by which you want to rotate. For example to get a lateral view of a membrane system with membrane in x-y plane you would type rotate x by 90 or rotate y by 90.

Try continuous rotation:

rock x by 1 180
rock off

Sometimes it is useful to set the exact dimensions of the graphical window. For example you want to make a movie in a standard HD format.

Set the exact dimensions of the graphical window.

display resize 1080 720 

Sometimes when you start VMD graphical window may be positioned incorrectly so that its menu bar is off screen and you can’t move with mouse. In this case you can reposition it with the command:

Reposition graphical window

display reposition 100 700

• Display position 0 0 corresponds to the lower left display corner.

Get to know more commands

Here are some commands you can run to see how they work:

display resetview 
display backgroundgradient on
display projection orthographic
display projection perspective
scale by 2
axes location lowerleft
axes location off

Key Points