I'm forced into using GAMESS-UK for an older software package. Using a cs-symmetry molecule, I've noticed that GAMESS will reorient the molecule before running a standard SCF calculation. This is related to the algorithm the software uses to process the symmetry of the molecule. For instance, If I were to input my molecule as having C1 symmetry, no reorientation would occur; the scf calculation would run using the exact same coordinates from the input file.
For some molecules, I've noticed a rotation for the reorientation as large as about 45°. For other molecules, it might only rotate 5° from my input coordinates. This for the same system of molecules—all cs symmetry, same functional groups, only the alkyl backbone has a variable number of carbons. As a result of this, my molecular axis is being defined differently across my various output integral files. It'd be more convenient for me if that were possible to avoid.
I'd like to better understand what conditions determine the reorientation of the molecule. I realize Gamess-UK is old, so any kind of symmetry algorithm from other computational software would also be useful to know about. Maybe I can see if it's similar to the one I'm encountering.
Does anyone know how computational software determines the reorientation of input coordinates prior to a calculation?