Feedback on Verification Plan

[PaulWAyers]

1. Being able to write the molecule in z-matrix format is not enough to identify rotatable bonds. In a ring compound, there are "missing dihedrals" in the rings. Derrick's software will automatically generate all dihedrals if you like. The number of rotatable bonds is very often (much!) different from the number of dihedrals in the z matrix -- it can be bigger but also can be (much) smaller. E.g., in a linear hydrocarbon C_{n} H_{2n+2} you have n-1 rotatable bonds but 3n dihedrals in the z-matrix. For a branched isomer of the same hydrocarbon the mismatch can be even worse.

2. If you keep a list of dihedral angles, then for molecules without symmetry, different lists of dihedrals are different conformers. For molecules with symmetry you could label "equivalent dihedrals" either automatically (hard) or manually (easy) or us the RMSD trick to find two conformers that are equivalent by symmetry.

3. Page 3. As before, your list of dihedrals from a z-matrix will not be adequate. Certainly different atom permutations gives different (and terrible!) dihedrals in a z-matrix. But that's irrelevant....you just can't make a dihedral angle list in this way. Derrick has an automated way to do this though.....based on the (standard) approach for finding (redundant) internal coordinates in Dalton and Gaussian.

4. 4.4 Can link to cardbordlint (or whatever it is called now) repo.

5. 5.1.1.2 For a lot of the Dunning (cc-pVXZ) basis sets K is missing. So that makes this "basis set missing test" easy. There is not only the Basis Set Exchange but a (nicer) porcelain available through MolSSI.

6. 5.1.1.2 With very bad geometries a conformer may still be findable, even the best. If the rotatable bonds are located correctly things should still work....no matter how bad it is. On the other hand, if you enter cubane (no rotatable bonds) when you want a different isomer, then all hell will break loose....

7. Probably for these tests should give very specific molecules/molecular geometries to test on. It won't be too hard, I think.....

Overall the issue I see is algorithmic and specificity. Simple tests using (substituted) hydrocarbons or small di/tri-peptides would suffice. For amino acids, actually, we have an exhaustive list of conformers (and their relative stability) in hand (work with Chunying, Farnaz, Ramon, etc.).