Tutorials and scripts for scientific visualization

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Web Molecular Dynamics (three.js)

VMD Visualization

In VMD you can save the representations you selected so that you can automatically apply them to any trajectory.

Adding simulation box

pbc set {a b c alpha beta gamma} -all
pbc box_draw -shiftcenterrel  {x y z}


pbc set {35 35 40 90 90 90} -all
pbc box_draw -shiftcenterrel  {0 0 0}

If you are gonna use this command from the command-line then you would need to load the pbctools package first or the pbc command will not be recognized.

package require pbctools
pbc set {35 35 40 90 90 90} -all
pbc box_draw -shiftcenterrel  {0 0 0}

More on adding a box and pbctools

Rendering an image

Images can be rendered with render command in VMD.


render <method> <filename>


render TachyonInternal snapshot.rgb

Rendering multiple frames

We can use a for loop and the render command to render all images in the trajectory file as follows:

for {set i 0} {$i < $num} {incr i} {
  # go to the given frame
  animate goto $i
  # force display update
  display update
  # take the picture
  render TachyonInternal [format snapshot.%04d.rgb $i]

Here image files with names such as snapshot.0000.rgb, snapshot.0001.rgb, snapshot.0002.rgb, ... are generated.

VMD Render Documentation

Creating a movie from images

Following line would read all files formatted as shapshot.<number>.rgb using the rendering script above.

exec convert shapshot.*.rgb movie.gif

Adding delay, looping multiple times

exec convert -delay 10 -loop 2 shapshot.*.rgb movie.gif

Generating movies from the command line

You can generate a movie using a VMD ‘tcl script file. These files can be generated easily using a visualization state. Once you create a template with the representations you like, save it as a visualization state. The file you save is basically a list of instructions (tcl script) that tells VMD how to represent your molecules. Adding the necessary instructions to render images in a frame and convert to movie you can generate a script that would read your trajectory file and output an animated movie without even loading VMD. Moreover, you can even add that scipt at the end of your MD simulation so it would generate a movie directly after the simulation is finished.

Running tcl script with VMD from the command line

vmd -dispdev text -eofexit < input.tcl > output.log

VMD Command-Line Options