{
  "name": "GROMACS CPU sample",
  "summary": "gmx pdb2gmx on a two-residue peptide (CPU SIF)",
  "containers": [
    "gromacs/2026.09"
  ],
  "steps": [
    {
      "id": "s1",
      "kind": "slurm-cpu",
      "name": "pdb2gmx",
      "script": "jobs/s1.sh",
      "after": [],
      "container": "gromacs/2026.09",
      "use_slurm": false,
      "copies": [],
      "shape": {
        "cpus": 4,
        "mem": "8G",
        "nodes": 1
      }
    }
  ],
  "files": {
    "jobs/s1.sh": "#!/bin/bash\nset -euo pipefail\napptainer exec /tmp/image.sif gmx pdb2gmx -f pep.pdb -o pep.gro -p pep.top -water none -ff amber99sb -ignh\nls -l pep.gro pep.top\n",
    "pep.pdb": "ATOM      1  N   ALA A   1       0.000   0.000   0.000  1.00  0.00           N\nATOM      2  CA  ALA A   1       1.458   0.000   0.000  1.00  0.00           C\nATOM      3  C   ALA A   1       2.009   1.420   0.000  1.00  0.00           C\nATOM      4  O   ALA A   1       1.251   2.389   0.000  1.00  0.00           O\nATOM      5  CB  ALA A   1       1.979  -0.761  -1.214  1.00  0.00           C\nATOM      6  N   ALA A   2       3.329   1.531   0.000  1.00  0.00           N\nATOM      7  CA  ALA A   2       4.000   2.820   0.000  1.00  0.00           C\nATOM      8  C   ALA A   2       5.500   2.700   0.000  1.00  0.00           C\nATOM      9  O   ALA A   2       6.100   1.650   0.000  1.00  0.00           O\nATOM     10  CB  ALA A   2       3.600   3.600   1.214  1.00  0.00           C\nEND\n"
  },
  "spans": []
}