In my DFT calculations on nanoflakes of 2D quantum dots, I observe a few small negative frequencies in the range of 10–30 cm⁻¹, even after full convergence. I have used both effective core potentials (ECPs) and a large basis set (def2-TZVP). The IR spectrum in that region is nearly flat, and the associated vibrational modes appear to involve soft, floppy motion.

I also slightly displaced the geometry along the fluctuating directions (corresponding to those modes), but the re-optimized structure yields similar results with no significant changes.

Is it generally acceptable in this case to proceed with the current configuration, or is further refinement necessary?

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