Page Comparison

Compute resources

• What are OpenFF’s available compute resources? Are there shared allocations on e.g. XSEDE or is everything run on local/institutional resources?

  • Local resources, most datasets finish in < 1 week

  • Entos OrbNet Denali training dataset (available in QCEngine soon)

• For shared resources, what is the process for approving for QM calculations?

Status of peptide datasets

• Peptide unconstrained Optimization dataset. Looks like 6689/6709 complete from this PR.

• Peptide TorsionDrive dataset. Looks like 823/845 complete from this PR.

• PEPCONF dataset. Looks like 2892/7560 complete from this PR.

  • Need additional compute spec for second-order SCF methods for many calculations

• Is there documentation on how the conformations were chosen for Dave Cerutti’s datasets?

  • From mdgx, not reproducible

• Are we planning to troubleshoot errored calculations or are these datasets complete enough as is?

  • Small error rate is expected and acceptable

Expense of QC datasets

• What is the expected cost (in wall time or core-hours) of each conformation in an Optimization dataset and a 1-D TorsionDrive dataset? How does cost scale with number of atoms or electrons?

  • 25 heavy atoms, 700 torsions, completed in ~1 month

  • 140 optimizations per TorsionDrive for large molecules

• How do you decide the number of conformations per molecule?

  • 10 conformations per molecule

• What is the cost of a 2-D TorsionDrive? Is a 2-D TorsionDrive with spacing N-by-N equivalent to N 1-D TorsionDrives with spacing N?

  • 1-4 interactions complicate optimization trajectories

• What is the expected cost of including an implicit solvent model, e.g. PCM?

  • Very slow in psi4; including polarizability in MM model may be more expedient

Feasibility of peptide datasets

• 20 canonical amino acids + 7 alternate protonation/tautomers

  • Pilot datasets with ANI-2X, few days wall time

  • New version of ANI from Simon

• Optimization datasets for PTMs

  • Complete set of filtered SMILES strings from Ligand EXPO

• 1-D TorsionDrives of backbone torsions and χ₁ for all dipeptides

• 1-D TorsionDrives of backbone torsions and χ₁ for subset of Ace-X-Y-Z-Nme tetrapeptides

• 2-D TorsionDrives of backbone torsions for subset of dipeptides