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Metadynamics Free Energy Surface of a Capped Dipeptide

  • Task ID: chemistry.metadynamics_for_dipeptide_in_vacuum
  • Domain: chemistry
  • Subdomain: molecular_simulation
  • Status: final
  • Benchmark set: seed42 (60 tasks)
  • Tags: metadynamics, well_tempered, free_energy_surface, val_dipeptide, dihedral_angles, enhanced_sampling, molecular_dynamics, openmm, ramachandran

Runtime and requirements

  • Estimated time: 30-120 minutes
  • Python: >=3.11
  • Packages: openmm>=8.0, numpy>=1.26.0, scipy>=1.11.0, matplotlib>=3.8.0
  • GPU required: no
  • Network required: yes

Public input and output contract

Inputs

  • dipeptide.pdb (data): Initial atomic coordinates of a capped dipeptide (ACE-X-NME) in PDB format

Outputs

  • analysis.py (code): Agent-generated simulation and analysis script
  • results/fes_2d.npy (data): 2D free energy surface F(phi, psi) in kJ/mol
  • results/minima.csv (data): Identified FES minima with positions and relative free energies
  • results/fes_plot.png (figure): 2D contour/heatmap of the free energy surface
  • results/cv_definition.txt (data): Description of collective variables used, their definitions, and rationale

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.