ontology: EDAM (1.25)
topics:
  - Computational chemistry
scopes:
  - summary:
      function:
        - Molecular dynamics
      input:
        - data: Molecular structure data
          format: [PDB]
        - data: Forcefield parameters
          format: [GROMACS itp, GROMACS top]
      output:
        - data: Trajectory data
          format: [XTC]
  - gmx_energy:
      function:
        - Energy analysis
      input:
        - data: Energy data
          format: [EDR]
      output:
        - data: Energy analysis output
          format: [XVG]
  - gmx_trjconv:
      function:
        - Trajectory conversion
      input:
        - data: Trajectory data
          format: [XTC, TRR, GRO, PDB]
      output:
        - data: Converted trajectory data
          format: [XTC, TRR, GRO, PDB]
  - gmx_mdrun:
      function:
        - Molecular dynamics simulation
      input:
        - data: Molecular structure data
          format: [PDB, GRO]
        - data: Topology data
          format: [TOP, TPR]
      output:
        - data: Trajectory data
          format: [XTC, TRR]
        - data: Log data
          format: [LOG]