[Internal FF] SO3lr

[Benzoin96485]

A proposal for implementing a new architecture family, SO3krate and SO3lr, as internal FFs.

Article:

• Kabylda, A., Frank, J. T., Dou, S. S., Khabibrakhmanov, A., Sandonas, L. M., Unke, O. T., ... & Tkatchenko, A. (2024). Molecular Simulations with a Pretrained Neural Network and Universal Pairwise Force Fields. link
• Frank, J. T., Unke, O. T., Müller, K. R., & Chmiela, S. (2024). A Euclidean transformer for fast and stable machine learned force fields. Nature Communications, 15(1), 6539. link
• Frank, T., Unke, O., & Müller, K. R. (2022). So3krates: Equivariant attention for interactions on arbitrary length-scales in molecular systems. Advances in Neural Information Processing Systems, 35, 29400-29413. link

Code repository:

• https://github.com/general-molecular-simulations/so3lr
• https://github.com/thorben-frank/mlff

Performance on biochemistry:

• SO3lr:
  • GEMS bottom-up (gas-phase and explicitly micro-solvated protein fragments, structures with gas-phase water clusters): force and dipole error
  • AcAla₃NMe, AT-AT, Stachyose: force, dipole and hirshfield ratio error
  • AcAla₁₅NMe, Crambin top-down (fragments): force error
  • Distribution of CV of AcAla₃NMe and Stachyose
  • Secondary structures analysis of AcAla₁₅NMe
  • Hydrogen bond analysis of AcAla₁₅LysH⁺
  • Power spectrum of Crambin
  • RMSD of Crambin, and protein and carbohydrate segment of glycoprotein
  • Tail group NMR order parameters, area per lipid, bilayer thicknesses and electronic density of POPC Lipid Bilayer
• SO3krate:
  • Energy and force error of Ac-Ala3-NHMe, Stachyose, AT-AT, and AT-AT-CG-CG
  • Distribution of the radius of gyration (ROG) and Ramachandran density plots for Ac-Ala3-NHMe
  • Dynamics of Ala15

Other highlights: SO3krate reduces the scaling index w.r.t L (the highest angular momentum) in message passing and is expected to be more efficient than other SE(3)-equivariant architectures. SO3lr added the physical priors and long-range awareness in SpookyNet to SO3krate.

Notice: the official repos are written in JAX.