Here we compare the benchmarks of Sage 2.1.0 (unconstrained) between YAMMBS and the original benchmarking script used during the development of Sage 2.1.0.
The original benchmarks of Sage 2.1.0 were taken from here. These benchmarks use a geometry optimization convergence threshold of 5e-9 kJ/mol/nm^2. ddE is defined with respect to the lowest energy QM conformer, and ddE’s between the lowest energy conformers are excluded as they are definitionally zero.
The YAMMBS benchmarks were calculated as follows. The MoleculeStore object was generated with this commit of the YAMMBS package, which optimizes the molecules using a convergence threshold of 5e-9 kJ/mol/nm^2. The ddE’s, TFD’s, and ICRMSD’s were calculated using this commit of the YAMMBS package, which has revised the ddE definition to be consistent with the old benchmarking script (defined with respect to the lowest energy QM conformer, and ddE’s between the lowest energy conformers are excluded) and uses mapped SMILES to create molecules for TFD analysis. The RMSD’s have been calculated using the same commit as the ddE and TFD, but with a modified RMSD function that uses all atoms to calculate the RMSD, in order to be consistent with the RMSD definition in the old benchmarks. YAMMBS typically uses a heavy-atom-only RMSD, which is much faster to compute.
DDE
The DDE’s are nearly identical between YAMMBS and the old benchmark (“og” in the figures).
RMSD
When comparing the all-atom RMSD’s between the two codes, the calculated RMSD benchmarks are nearly identical.
TFD
The TFD metric is nearly the same between the two sets of scripts.
