The two most common approaches for dealing with imaginary frequencies in free energy computations are:
- Compute the free energy using only the modes with real valued frequencies
- Reoptimize the structure to remove any imaginary frequencies
Neither of these are ideal: 1 is not necessarily a reasonable approximation and 2 will likely distort the geometry relative to the configuration that you aim to study.
The Grimme group recently developed the Single-Point (or Biased) Hessian approach for computing free energies of non-equilibrium structures . This approach reoptimizes the geometry under a constraining potential, aiming to remove imaginary frequencies while retaining the initial structure as much as possible. From the paper, this can lead to more accurate calculations of free energy and is a more rigorous way of handling non-equilibrium structures.
Off-hand, I only know of this method being implemented in xTB, but the paper gives a description of a general implementation.
- Sebastian Spicher and Stefan Grimme
Journal of Chemical Theory and Computation 2021 17 (3), 1701-1714