Yes, @Juanes was reporting this as well, e.g. Conformer analysis: error in structures? - #3 by ghutchis
I opened an issue for this: Handling vibrations along trajectories · Issue #2764 · OpenChemistry/avogadrolibs · GitHub
The central issue is that vibrations are handled by generating multiple 3D coordinates, and there’s not currently support for handling vibrations for multiple steps.
While there are some good ways to handle this particularly in the context of multiple properties per coordinate / conformer block (Add new properties for conformers · Issue #2577 · OpenChemistry/avogadrolibs · GitHub) it’s not something I wanted to jam in right before the 2.0 release. (It’ll require some work in the underlying data structures as well as the UI.)
So the robust solution I’m proposing is:
- Avogadro can store multiple vibrational sets connected with different coordinate sets (i.e., there’s a list of vibrations / frequencies connecting with different geometries)
- When you select a particular coordinate set, you’ll get the vibrations connected with that
This is particularly important for things like an IRC or NEB-TS calculation in which you might want to verify that the start / end geometries are minima, and the TS has only one imaginary frequency.