Show HN: Molchanica. Structural bio GUI / Rust tools | Hacker News Reader

Show HN: Molchanica. Structural bio GUI / Rust tools

github.com

1 pointthe__alchemist2 comments

This has been a passion project of mine for ~ a year. It's a collection of structural bio tools as a GUI application. Intent: "Just works". Includes party tricks like:

  - Infer ADME (drug-design) properties for small mols
  - Can view molecular dynamics trajectories like VMD, and also run them with its wn engine, or GROMACS. (Amber Force fields; inferred from any small mol/protein/nucleic acid/lipid)
  - ORCA GUI interface for quantum chem
  - 3D molecule editor with "real-time" MD
  - Building blocks exposed as open source Rust libs
  - Integration with online databases (PubChem, RCSB PDB, Drugbank etc)

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This is seriously impressive for a single project. Rust + CUDA kernels for MD, fallback to SIMD thread pools, pharmacokinetics inference, docking, and it compiles to a standalone binary? How does the MD throughput compare to GROMACS on equivalent hardware?

Ty! MD thoroughput is same OOM for both backends, but I haven't done detailed benchmarks across various molecule arrangements and config. SPME dominates the calculation for the built-in backend, with short-range Coulomb and LJ taking second place. MD accuracy is... not on the same level unfortunately, at least for proteins. Now that the backends are interchangeable with the similar config and FF params, I can hopefully narrow down what's going wrong. (I suspect SPME, again...)

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