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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.

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  • $\begingroup$ 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 $\endgroup$ Apr 13, 2016 at 2:53
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    $\begingroup$ 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

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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.
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    $\begingroup$ 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
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    $\begingroup$ 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. $\endgroup$ Apr 13, 2016 at 14:33
  • $\begingroup$ @AndersMB Send an e-mail to the Avogadro e-mail list or to me privately. $\endgroup$ 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. $\endgroup$ Apr 15, 2016 at 20:01

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