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Implicit Solvent Electrostatics: Continuum Response Benchmark

  • Task ID: chemistry.implicit_solvent_pb_gb
  • Domain: chemistry
  • Subdomain: computational_biophysics
  • Status: final
  • Benchmark set: seed42 (60 tasks)
  • Tags: implicit_solvent, poisson_boltzmann, generalized_born, biomolecular_electrostatics, finite_difference, binding_energy, multi_case, surface_models, anonymous_contract, private_suite_bank, infinite_generation, rcsb_screening, pdb_redo_hidden_bank, real_biomolecule_families, nonlinear_pb, ses_native_geometry, salt_scan, temperature_scan

Runtime and requirements

  • Estimated time: 120-240 minutes
  • Python: >=3.11
  • Packages: numpy>=1.26.0, scipy>=1.11.0, matplotlib>=3.8.0
  • GPU required: no
  • Network required: no

Public input and output contract

Inputs

  • manifest.json (data): Case manifest containing case order, per-case grids, exact surface-contract metadata, binding-expression metadata, and per-case response parameters
  • sites.csv (data): Per-case entity-annotated atom table with coordinates, charges, radii, and residue labels
  • volume_a.npy (data): Per-case float volumetric tensor encoding signed-distance geometry A on the disclosed Cartesian grid
  • volume_b.npy (data): Per-case float volumetric tensor encoding signed-distance geometry B on the disclosed Cartesian grid
  • queries.npy (data): Per-case spatial query coordinates for field sampling
  • plane_spec.json (data): Per-case slice-plane definition and storage-order metadata on the case-specific grid

Outputs

  • analysis.py (code): Agent-generated electrostatics analysis script
  • results/summary_metrics.csv (data): Per-case summary metrics with one high-fidelity binding-response estimate, one distinct faster approximate estimate, and their gap
  • results/field_samples.npy (data): Per-case scalar field values sampled at the provided coordinates
  • results/field_slice.npy (data): Per-case 2D field slice on the prescribed plane
  • results/overview.png (figure): Scientific overview figure comparing the eight curated cases

Public repository files

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Provenance

This task is included in the current seed42 benchmark set at dataset revision f11a199f71fb4b854ac43a1bf548d5df519141a9.

This page is generated only from files tracked in the public ASI-Bench repository at commit f18382f03faf. Submission bundles, run logs, private scoring configuration, and private reference answers are not read by this page generator.