5
$\begingroup$

I would like to visualize molecular normal modes as vectors sitting on each atom, and not as actual vibrations. I am able to do this, in part, with Molden by copying in the vector into a file readable by Molden (extension is .geo.molden, and is generated from a Molcas calculation). The vector is represented as red lines, but they do not look very nice (see image). Also the background is black, and Molden has a limited number of ways to visualize the molecule.

Is there some other software (free) that can do this? Perhaps Avogadro, VMD, or something along these lines? Specifically I would like to be able to change to different molecular visualizations, and show the vectors as arrows with a easily distinguished color.

enter image description here Figure 1. This is what Molden can do... not very pretty!

Or possibly, after changing the background color to white with GIMP:

enter image description here Figure 2. Not really better, since the Hydrogen atoms are represented with white by Molden, as is the label text.

Improve this question
$\endgroup$
4
  • $\begingroup$ I am not sure what are your needs, but here is a program that I came across. I haven't tried it, but it looks very versatile paraview.org/gallery $\endgroup$
    – CoffeeIsLife
    Apr 13, 2016 at 2:53
  • 1
    $\begingroup$ This might help: molecularmodelingbasics.blogspot.dk/2009/06/… $\endgroup$
    – Jan Jensen
    Apr 13, 2016 at 6:39
  • $\begingroup$ @JanJensen The link to the jmol application is dead, unfortunately. $\endgroup$
    – Yoda
    Apr 13, 2016 at 7:33
  • $\begingroup$ BTW, you can change the background color (or even choose a gradient) in molden by clicking the palette icon in the main toolbar widget and selecting "Background Color" or "Background Mode". $\endgroup$
    – shrx
    Apr 15, 2016 at 8:33

1 Answer 1

Reset to default
6
$\begingroup$

As long as the output from your harmonic frequency calculation can be read directly using Avogadro, it will do exactly what you want.

Avogadro screenshot

Notice that:

  1. The normal mode of interest is selected on the right-hand side.
  2. "Force" is selected on the left-hand side; this box is present when "Display Settings..." is highlighted in the top toolbar.
Improve this answer
$\endgroup$
7
  • 2
    $\begingroup$ Avogadro cannot read geo.molden files. "Reading molecular file failed", it says. The .geo.molden file (obtained from a geometry optimization) contains the geometry and the forces, so perhaps I could construct a readable file manually? $\endgroup$
    – Yoda
    Apr 13, 2016 at 5:47
  • 1
    $\begingroup$ I'd be curious to see the Molden file. It should be readable by Open Babel. While no one has asked about reading forces from such a file, it wouldn't be hard to implement - no one has asked before. OB and Avogadro can visualize these for vibrations or for force field calculations already. $\endgroup$
    – Geoff Hutchison
    Apr 13, 2016 at 14:33
  • $\begingroup$ @AndersMB Send an e-mail to the Avogadro e-mail list or to me privately. $\endgroup$
    – Geoff Hutchison
    Apr 13, 2016 at 14:33
  • $\begingroup$ @GeoffHutchison e-mail sent, not sure whether you received it or not? $\endgroup$
    – Yoda
    Apr 15, 2016 at 10:33
  • $\begingroup$ @AndersMB I did. I'm knee deep in other work right now - probably take me about a week to get to it. $\endgroup$
    – Geoff Hutchison
    Apr 15, 2016 at 20:01

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.