I have performed a set of geometry optimizations in Orca, and I am able to successfully visualize the optimized structures in Avogadro2. However, some of the structures are at a saddle point, meaning that I would need to "chase" the imaginary mode to find the optimized structure. This brings me to the current problem: If it was a gaussian log file, I can visualize the mode in GaussView and manually modify the structure by chasing the mode. However, in Avogadro, I am unable to stop the vibration at an intermediate point to get the new structure. Are there any ways of obtaining the modified structure from Avogadro2?
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2$\begingroup$ Also, ORCA has some "compound" scripts to modulate such imaginary modes, e.g. github.com/ORCAQuantumChemistry/CompoundScripts/blob/main/… $\endgroup$– Geoff HutchisonCommented yesterday
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This came up recently on the Avogadro forum and while there's a way to do it, I understand it would be great to have a more intuitive interface.
For now:
Pick a vibrational mode in the dialog and adjust the amplitude. (For this example, I drove up the amplitude to make it clear.)
Go to the animation tool. You’ll see there are a set of animation frames – corresponding to each of the steps of the vibration out, back - one way then another.
- You should be able to pick one of the frames and then export the modified coordinates.
I'd obviously recommend using a small amplitude and taking one step along the displacement (e.g. frame 2) as indicated.
