VMD - Visual Molecular Dynamics - Quick Help

Help is available for the following topics:

VMD Text Commands
VMD Command-Line Options
VMD Environment Variables

For the latest news about VMD, please see the VMD home page. VMD is one component of the MDScope software, which includes also the program NAMD (a portable, parallel molecular dynamics program) and the MDCOMM software to enable communication betweenVMD and NAMD. For further information on MDScope, please see the Theoretical Biophysics group home page.

For a complete description on how to install, use, or modify VMD, please see the VMD Installation Guide, the VMD Users Guide, or the VMD Programmers Guide.

Please send bug reports, comments, or suggestions to vmd@ks.uiuc.edu.

VMD Text Command Summary

VMD understands commands which start with the following words; click on a command for a more complete synopsis. Items marked as (optional) may not be available in the current version of VMD.

animate: Play/Pause/Rewind a molecular trajectory.
axes: Position a set of XYZ axes on the screen.
color: Change the color assigned to molecules, or edit the colormap.
debug: Turn on/off printing of debugging messages.
display: Change various aspects of the graphical display window.
echo: Turn on/off echoing of text commands to the console.
exit: Quit VMD.
external: Connect to an external VMD command source (optional).
help or ?: Display this help file with an HTML viewer.
journal: Turn on/off logging a VMD session to a log file.
label: Turn on/off labels for particular atoms, bonds, angles, or dihedral angles.
light: Control the light sources used to illuminate graphical objects.
log: Same as journal.
menu: Control or query the on-screen GUI menu forms.
mol: Load, modify, or delete a molecule in VMD.
mol: Same as mol .
mouse: Change the current state (mode) of the mouse.
play: Start executing text commands from a specified file.
quit: Same as exit .
remote: Set up VMD to connect to or start a remote simulation program (optional).
render: Output the currently displayed image (scene) to a file.
rock: Rotate the current scene continually at a specified rate.
rot: Rotate the current scene around a given axis by a certain angle.
rotate: Same as rot .
rotation: Same as rot .
run: Same as play .
scale: Scale the current scene up or down.
sim: Control the state of a remote simulation after it is connected (optional).
simulation: Same as sim .
stage: Position a checkerboard stage on the screen.
stop: Same as exit .
tool: Control the appearance and function of 3D pointers (tools).
tracker: Initialize and control external spatial tracking devices.
trans: Translate the objects in the current scene.
translate: Same as trans .
user: Add user-customized commands to the graphics display pop-up menu.
wait: Specify a number of seconds to wait before reading another command.

VMD Command-Line Option Summary

When started, the following command-line parameters may be given to VMD. Note that if a command-line parameter does not start with a dash (-), and is not part of another option, it is assumed to be a PDB filename. Thus, the command

vmd molecule.pdb

will start VMD and load a molecule from the file molecule.pdb.

-? | -h

Print a summary a command-line options to the console.

-e filename

After initialization, execute the text commands in filename, and then resume normal operation.

-psf filename

Load the specified molecule (in PSF format) at startup. The PSF file only contains the molecular structure; a PDB or DCD file must also be specified when this option is used.

-pdb filename

Load the specified molecule (in PDB format) at startup.

-dcd filename

Load the specified trajectory file (in binary DCD format) at startup. The DCD file only contains atomic coordinates; a PDB or PSF file must also be specified when this option is used.

-disp < win | text | cave | none>

Specify the type of graphical display to use. The possible display devices include:

win: a standard graphics display window.
text: do not provide any graphics display window.
cave: use the CAVE virtual environment for display.
none: same as text.

It is possible to use VMD as a filter to convert coordinate files into rendered images, by using the -disp text and -e options.

-pos x y

Specify the position for the graphics display window. The position (x,y) is the number of pixels from the lower-left corner of the display to the lower-left corner of the graphics window.

-size x y

Specify the size for the graphics display window, in pixels.

-nt

Do not display the VMD title at startup.

-startup filename

Use filename as the VMD startup command script, instead of the default file.

-init filename

Use filename as the file containing VMD initialization data, instead of the default file.

-debug [level]

Turn on output of debugging messages, and optionally set the current debug level (1=few messages ... 5=many verbose messages). Note this is only useful if VMD has been compiled with debugging message included.

VMD Environment Variable Summary

Several environment variables are used by VMD to determine the location of certain files and directories. These variables include:

VMDDIR: The directory which contains the VMD data files (such as this help file) and architecture-specific executables. By default, this is /usr/local/lib/vmd.
VMDTMPDIR: The directory which VMD should use for temporary data files. By default, this is /tmp.
VMDBABELBIN: The complete path and filename for the program babel, which is used by VMD to convert molecular structure/coordinates files into PDB files which VMD can actually understand. If this is not set explicitly, the VMD startup script will attempt to find babel in the current path. If babel cannot be found or is not installed, VMD will not be able to read molecular file formats other than PDB, PSF, and binary DCD files. The program babel may be obtained via anonymous ftp from the University of Arizona Biotechnology ftp server, joplin.biosci.arizona.edu.
VMDHTMLVIEWER: The name of the HTML viewer (Netscape, Mosaic, whatever you prefer) that VMD should use to display HTML documents (such as this help file). By default, this is Mosaic (hey, we are at the University of Illinois, NCSA is literally right upstairs ...).

Return to the top of this document ...

VMD Documentation / Theoretical Biophysics Group, University of Illinois / vmd@ks.uiuc.edu