2025‐02‐05 Hackathon Summary

Uses cases identified

Large Molecules:

• Reproduce SAXS output using multi-mAb AAMD simulations

  • Hard things
    • Slow loading of mAb PDB files
    • Ensure mAb PDB works as we expect (dealing with MOE built mAb, make sure all disulfide bridges are intact, easy to have multi-molecules loaded when you meant to have one large molecule)
    • Multi molecule PDB files need to work
  • Easy things
    • Analysis of trajectory ( g(r) S(q) )
    • Improve trajectory storage
    • Improve trajectory debugging

* Run a pre-built structure

• Easy things
  • Take structure "as is"

Small Molecules:

* Some use case

• Hard things
  • Support building small mol systems, like co-xstal
    • slabs, interfaces
• Easy things
  • Support easy species ratio for given pH (phcacl), given species with charges, n total, pKa, figure out ratios