14
$\begingroup$

I perform my calculations in Q-Chem and would like to make short movies of IR modes. As of now, I render them with IQmol, but I believe graphics properties (colors and resolution) can be much better. Yet, CYLView cannot understand Q-Chem outputs unfortunately.
What visualization software can be used with a variety of atom/bond styles and adjustable resolution?

$\endgroup$
  • 5
    $\begingroup$ Something being more user friendly is largely opinion and user specific. The answer I gave below is difficult if you're not familiar with VMD, but once you know VMD you can automate a lot of things making it easy. Normally it's not that important to have good looking frequency movies because they won't be published. Therefore I'd stick with IQMol or even MOLDEN! If you set molden_format True in Q-Chem it will create Freqency output with which you can easily visualize the frequency spectrum and vibrations $\endgroup$ – Cody Aldaz Jun 26 at 0:56
13
$\begingroup$

VMD Normal Mode Wizard

If you're goal is to create high quality visualizations of vibrations I recommend VMD. It's highly customizable in terms of colors, resolution, and representation.

The setup however, is a little bit painful as the normal mode (NMD) input file has to be specially prepared in atomic units and has a special format (see below).

The official details can be found here.

One benefit however, is that the in addition to creating a movie which you can show in your presentation you can create static images like this which show the vibration vector

enter image description here

Here is my "NMD" file which was used in VMD to create this image.

names C C C C H H H H H H C C C C H H H H H H
coordinates 0.419783 -0.742862 0.883452 -0.036356 0.490734 0.325996 0.251234 0.764637 -1.047649 0.039963 -0.211417 -2.131132 0.176898 -0.924957 1.920794 0.324685 -1.620253 0.262458 -0.109550 1.336747 0.988139 0.216590 1.797666 -1.352741 -0.135041 -1.246035 -1.916959 0.240780 0.062286 -3.148909 2.889548 1.383592 2.407869 2.645651 0.115596 2.054427 2.219184 -0.415514 0.727746 2.398198 0.407775 -0.493158 3.167189 1.622583 3.418802 2.857201 2.206403 1.717940 2.728662 -0.638593 2.822578 2.541096 -1.440669 0.600368 2.721145 1.425776 -0.398300 2.693411 -0.087720 -1.397883
mode 0.029 -0.016  0.006 0.018 0.034 -0.077  0.045 0.058 0.153 -0.012  -0.073  -0.082  -0.002  -0.001  0.000 -0.003  -0.001  0.001 0.003 0.001 0.000 -0.015  0.001 0.001 -0.002  0.002 -0.001  0.004 -0.002  0.001 0.000 -0.000  -0.001  0.003 0.000 -0.000  -0.027  -0.016  0.020 -0.050  0.018 -0.021  -0.000  0.000 -0.000  0.000 0.000 -0.000  -0.000  0.000 -0.000  0.004 0.000 0.001 0.004 -0.003  0.001 -0.000  -0.001  -0.002
mode 0.002 0.005 0.003 -0.028  -0.027  0.083 0.138 0.009 -0.050  -0.023  -0.011  -0.013  -0.002  0.001 -0.000  -0.000  0.000 -0.001  -0.003  -0.001  -0.000  -0.003  -0.001  0.001 -0.000  0.000 -0.000  0.001 0.000 0.001 -0.000  0.001 -0.000  -0.000  -0.002  -0.000  0.002 -0.002  0.005 -0.102  0.033 -0.036  0.000 -0.000  0.000 0.000 -0.000  -0.000  0.000 0.000 0.000 -0.000  -0.000  0.001 0.012 -0.003  0.003 0.008 -0.001  0.002
| cite | improve this answer | |
$\endgroup$
  • $\begingroup$ Thank you, Cody! $\endgroup$ – Dmitry Eremin Jun 26 at 21:18
9
$\begingroup$

Jmol

The Jmol package is able to do what you want. You can produce the animations below just using point & click with your mouse.

But you can also use its scripting capabilities to work with batch files, and make the process all automatic.

As it is coded in Java, you can used in any operative system.

Here are some examples. Below the results for $CH_4$ ($T_d$ symmetry):

$o_1 = 3025.5\, cm^{-1}$ ($A_1$ Symmetry)

enter image description here

$o_2 = 1582.7\, cm^{-1}$ ($E$ Symmetry)

enter image description here

$o_3 = 3156.8\, cm^{-1}$ ($F_2$ Symmetry)

enter image description here

$o_4 = 1367.4\, cm^{-1}$ ($F_2$ Symmetry)

enter image description here

| cite | improve this answer | |
$\endgroup$
  • 1
    $\begingroup$ @CodyAldaz here you have an example (with some instructions) and here you have the scripting code. $\endgroup$ – Camps Jun 26 at 11:22

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

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