For a complete description on how to install, use, or modify VMD, please see the VMD Installation Guide, the VMD User's Guide, or the VMD Programmer's Guide.
Please send bug reports, comments, or suggestions to vmd@ks.uiuc.edu.
animate:
Play/Pause/Rewind a molecular trajectory.
forward: Play animation forward.
for: Same as forward.
reverse: Play animation backward.
rev: Same as reverse.
pause: Pause animation.
prev: Go to previous frame.
next: Go to next frame.
skip n: Set stride to n+1 frames.
delete all: Delete all frames from memory.
speed n: Set animation speed to n.
style once: Set to play animation once.
style loop: Set to loop through animation continuously.
style rock: Set to play animation foward and back continuously.
goto start: Go to first frame.
goto end: Go to last frame.
goto n: Go to frame n.
read filename [beg nb] [end ne] [skip ns] [molecule_number]: Read data for molecule_number from filename, beginning with frame nb, ending with frame ne, with a stride of ns+1.
write filename [beg nb] [end ne] [skip ns] [molecule_number]: Write data from molecule_number to filename, beginning with frame nb, ending with frame ne, with a stride of ns+1.
delete [beg nb] [end ne] [skip ns] [molecule_number]: Delete data for molecule_number, beginning with frame nb, ending with frame ne, with a stride of ns+1.
readdel filename [beg nb] [end ne] [skip ns] [molecule_number]: Read data for molecule_number from filename, beginning with frame nb, ending with frame ne, with a stride of ns+1, overwriting existing data.
axes:
Position a set of XYZ axes on the screen.
location < off | origin | lowerleft | lowerright | upperleft | upperright >: Position axes.
color:
Change the color assigned to molecules, or edit the colormap. All color
values are in the range 0 ... 1.
category name color: Set color of object specified by category and name to color.
scale method < RGB | RWB | BlkW >: Set type of scale to use for coloring objects by values.
RGB: red...green...blue
RWB: red...white...blue
BlkW: black...gray...white
scale midpoint x: Set midpoint of color scale to x, in the range 0 ... 1.
scale min x: Set minimum of color scale to x, in the range 0 ... 1.
scale max x: Set maximum of color scale to x, in the range 0 ... 1.
change < alpha | shininess | rgb | ambient | diffuse | specular > color: Reset given property of color to default value.
change < alpha | shininess | rgb | ambient | diffuse | specular > color othercolor: Set given property of color to match othercolor.
change < alpha | shininess > color value: Set given (scalar) property of color to value.
change < rgb | ambient | diffuse | specular > color r g b: Set given (3-valued) property of color to r g b.
debug:
Turn on/off printing of debugging messages. This will have no effect
if VMD was compiled without the debugging option.
< on | off >: Turn debug on or off.
level n: Set debug level to n.
display:
Change various aspects of the graphical display window.
reshape: Reshape the display.
resetview: Reset the view.
eyesep value: Set the eye separation to value.
focallength value: Set the focal length to value.
height value: Set the screen height to value.
distance value: Set the screen distance to value.
antialias < on | off >: Turn antialiasing on or off.
depthcue < on | off >: Turn depth cueing on or off.
stereo < off | sidebyside | crystaleyes >: Change the
stereo mode.
nearclip < set | add > value: Add to or set near clipping plane position.
farclip < set | add > value: Add to or set far clipping plane position.
echo:
Turn on/off echoing of text commands to the console.
< on | off >: Turn echoing on or off.
exit:
Quit VMD.
confirm: Ask user before quitting.
[now]: Quit without asking.
external:
Connect to an external VMD command source (optional).
< on | begin | start >: Turn on external command interface.
< off | end | stop >: Turn off external command interface.
help or ?:
Display this help file with an HTML viewer.
[command]: Jump to help for command.
journal:
Turn on/off logging a VMD session to a log file. This will create a log
file with commands for all the actions taking during the session. The log
file may be played back later by using the
play command.
filename: Turn on logging to filename.
off: Turn off logging.
label:
Turn on/off labels for particular atoms, bonds, angles, or dihedral angles.
add category [atom1 ... atomN]:
Add a label involving the N atoms to the given category.
list category: list all labels in the given
category.
show category [ all | label_number ]:
Turn on labels in the given category.
hide category [ all | label_number ]:
Turn off labels in the given category.
delete category [ all | label_number
]: Delete labels in the given category.
graph category label_number
[command]: Show a graph of a label from the given category.
The data will be written to a file, and the specified command will be run to
graph the data. %s in the command string will be replaced by the
temporary filename.
light:
Control the light sources used to illuminate graphical objects. There are
four light sources, numbered 0 to 3.
light_number on: Turn a light on.
light_number off: Turn a light off.
light_number highlight:
Display a line indicating the position of a light source.
light_number unhighlight:
Hide the line indicating the position of a light source.
light_number rot < x | y | z > angle: Rotate a light (at infinity) angle degrees about a given axis.
log:
Same as journal.
menu:
Control or query the on-screen GUI menu forms.
menu_name on: Turn a menu on.
menu_name off: Turn a menu off.
menu_name loc: Print the location of a menu.
menu_name move x y: Turn a menu on.
mol:
Load, modify, or delete a molecule in VMD. In the following,
molecule_number is a string describing which molecules are
affected by the command. It is of the form < m1|m2|....|mN >, where
mN is one of the following: all, top, active, inactive, displayed, on, off,
fixed, free, or one of the unique integer ID codes assigned to
the molecules when they are loaded.
< new | load > structure_file_type structure_file [coordinate_file_type coordinate_file]: Load a new molecule from given file(s).
list [ all | top | active | displayed | none | molecule_number ]: Print information about molecules.
color color_method: Change the default
atom coloring method setting.
representation rep_method: Change the default
rendering method setting.
selection select_method: Change the default
atom selection setting.
modcolor rep_number molecule_number
color_method:
Change the current coloring method for the given representation in
the given molecule.
modstyle rep_number molecule_number
rep_method:
Change the current rendering method (style) for the given representation in
the given molecule.
modselect rep_number molecule_number
select_method:
Change the current atom selection for the given representation in
the given molecule.
addrep: Using the current default settings for the atom
selection, coloring, and rendering methods, add a new representation to the
top molecule.
delrep rep_number molecule_number:
Deletes the given representation from the specified molecule.
delete < all | top | active | displayed | none | molecule_number >: Delete molecules
active < all | top | active | displayed | none | molecule_number >: Make molecules active.
inactive < all | top | active | displayed | none | molecule_number >: Make molecules inactive.
on < all | top | active | displayed | none | molecule_number >: Turn molecules on.
off < all | top | active | displayed | none | molecule_number >: Turn molecules off.
fix < all | top | active | displayed | none | molecule_number >: Fix molecules.
free < all | top | active | displayed | none | molecule_number >: Unfix molecules.
top molecule_number: Set the top molecule.
molecule:
Same as mol.
mouse:
Change the current state (mode) of the mouse.
mode 0: Set mouse mode to rotation.
mode 1: Set mouse mode to translation.
mode 2: Set mouse mode to scaling.
mode 3 N: Set mouse mode to rotate light
N.
mode 4 N: Set mouse mode to picking mode
N.
play:
Start executing text commands from a specified file, instead of from the
console. When the end of file is reached, VMD will resume reading commands
from the previous source. This command may be nested, so commands being
read from one file can include commands to read other files.
filename: Execute commands from filename.
quit:
Same as exit.
remote:
Set up VMD to connect to or start a remote simulation program (optional).
cancel: Cancel the current remote simulation setup.
run: Start a new remote simulation running, using the
current setup parameters.
list [ all | jobs | apps | parameters ]: List properties of remote simulations.
initialize computer [username]:
Make an initial connection to the provided remote computer (using the
given username, or the current username if it is not specified). This
will contact the MDComm daemon there and retrieve a list of remote
applications and running jobs.
new application: Begin setting the parameters
in order to run a new simulation using the specified program (application).
attach job: Attach to a remote job which has
been previously started by VMD, and left running.
readoptions filename: Read parameter settings
from the given file for the current remote simulation setup.
writeoptions filename: Write out the current
parameter settings to a file, for use later by the readoptions
command.
setoption option [value]: Change the
current setting for the given option the specified value. This is used when
setting the initial parameters before starting the simulation.
render:
Output the currently displayed image (scene) to a file.
list: List the available rendering methods.
method filename: Render the global scene to filename using method.
method filename command: Render the global scene to filename, then execute `command'. Any %s in `command' are replaced by the
filename.
rock:
Rotate the current scene continually at a specified rate.
off: Stops rocking.
< x | y | z > by step: Rock around the given axis at a rate of step degrees per redraw.
< x | y | z > by step n: Rock around the given axis at a rate of step degrees per redraw for n steps, reverse, and repeat.
rot:
Rotate the current scene around a given axis by a certain angle.
stop: Stop all rotation, same as rock off.
< x | y | z > by angle: Rotate around the given axis angle degrees.
< x | y | z > to angle: Rotate the given axis to the absolute position angle.
< x | y | z > < by | to > angle step: Rotate at a rate of step degrees per redraw.
rotate:
Same as rot.
rotation:
Same as rot.
run:
Same as play.
scale:
Scale the current scene up or down.
by f: Multiply scene scaling factor by f.
to f: Set scene scaling factor to f.
sim:
Control the state of a remote simulation after it is connected (optional).
list: Print information about all currently connected
remote simulations. Simulations are numbered 0 ... N-1.
top sim_number: Set the top simulation.
modify parameter value:
Change a parameter for the top simulation.
patch < off | byatom | byload | bynode >:
Display the patches from a simulation (if any), coloring them by the
specified criteria, for the top simulation.
detach sim_number: Detach from a simulation,
leaving it running on the remote computer.
kill sim_number: Kill a simulation.
simulation:
Same as sim.
stage:
Position a checkerboard stage on the screen.
location < off | origin | bottom | top | left | right | behind > :
panels n: Set number of panels in stage.
stop:
Same as exit.
tracker:
Initialize and control external spatial tracking devices.
list: List running trackers.
list avail: List available trackers.
start tracker_number [on machine]: Start a tracker (possibly remote).
pause tracker_number [on machine]: Pause a tracker (possibly remote).
unpause tracker_number [on machine]: Unpause a tracker (possibly remote).
location tracker_number sensor: Print current location of sensor.
trans:
Translate the objects in the current scene.
by x y z: Translate by vector (x,y,z) in screen units.
to x y z: Translate to the absolute position (x,y,z) in screen units.
translate:
Same as trans.
user:
Add user-customized commands to the graphics display pop-up menu.
add menu name:
Add a new submenu name to the main pop-up menu. The submenu
will be initially empty, and will not appear until items are added to it.
add item name [command]:
Add a new menu item to the `User Command' submenu of the main menu. If a
command is specified, then when the menu item is selected by the user
that command will be executed as if it had been typed at the console.
add separator:
Add a separator to the end of the `User Command' submenu of the main menu.
add subitem menu name
[command]: Add an item name to the given submenu,
which must have been added already with a add menu command.
The given command will be executed when the item is selected by the user.
add subseparator menu: Add a separator to the
end of the specified submenu.
add key key [command]:
Assign the given text command to the hotkey key. When
key is then pressed while the mouse is in the display window, the
specified command will be executed.
print < menus | keys >: Print out the current
definition of the user-defined menus, or the hotkeys.
wait:
Specify a number of seconds to wait before reading another command.
time: Wait time seconds.
vmd molecule.pdb
molecule.pdb.
-? | -h
-e filename
-psf filename
-pdb filename
-dcd filename
-disp < win | text | cave | none >
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.
-disp text and -e options.
-pos x y
-size x y
-nt
-startup filename
-init filename
-debug [level]
/usr/local/lib/vmd.
/tmp.
Mosaic (hey, we are at the University of Illinois, NCSA is literally right upstairs ...).
VMD Documentation / Theoretical Biophysics Group, University of Illinois / vmd@ks.uiuc.edu