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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.

Yoda
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  • 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 http://www.paraview.org/gallery/ – CoffeeIsLife Apr 13 '16 at 02:53
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    This might help: http://molecularmodelingbasics.blogspot.dk/2009/06/force-is-strong-in-this-one.html – Jan Jensen Apr 13 '16 at 06:39
  • @JanJensen The link to the jmol application is dead, unfortunately. – Yoda Apr 13 '16 at 07:33
  • 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". – shrx Apr 15 '16 at 08:33

1 Answers1

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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.
pentavalentcarbon
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    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? – Yoda Apr 13 '16 at 05:47
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    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. – Geoff Hutchison Apr 13 '16 at 14:33
  • @AndersMB Send an e-mail to the Avogadro e-mail list or to me privately. – Geoff Hutchison Apr 13 '16 at 14:33
  • @GeoffHutchison e-mail sent, not sure whether you received it or not? – Yoda Apr 15 '16 at 10:33
  • @AndersMB I did. I'm knee deep in other work right now - probably take me about a week to get to it. – Geoff Hutchison Apr 15 '16 at 20:01
  • @GeoffHutchison Is it possible to change the color of the force vectors? – Yoda Jun 02 '16 at 09:28
  • @AndersMB - No, but it's a good suggestion for 1.2.1... – Geoff Hutchison Jun 02 '16 at 15:43