Chiral inversion can happen, and often does in various enhanced sampling methods, so it is something to check for.

The best way to do that is to compute the improper dihedral, defined as the angle between two planes determined by 3 atoms: for amino acids, one plane is defined by N,CA,C and the other by N,CB,C and the angle should be ca. +120 or -120 depending on the chirality.

Besides enhanced sampling, a lack of careful model building can also cause chiral inversions, for example if there are large forces from bad contacts where some atoms are too close to each other.

Rick Venable
computational chemist