{
    "id": "mdrun",
    "description": "Wrapper of the GROMACS mdrun module.",
    "arguments": [
        {
            "id": "config",
            "required": false,
            "description": "Configuration file for the mdrun tool",
            "filetype": "input",
            "sample": "https:\/\/raw.githubusercontent.com\/bioexcel\/biobb_md\/master\/biobb_md\/test\/data\/config\/config_mdrun.json",
            "formats": [
                ".*\\.json$",
                ".*\\.yml$",
                ".*\\.yaml$"
            ]
        },
        {
            "id": "input_tpr_path",
            "required": true,
            "description": "Path to the portable binary run input file TPR",
            "filetype": "input",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_md\/raw\/master\/biobb_md\/test\/data\/gromacs\/mdrun.tpr",
            "formats": [
                ".*\\.tpr$"
            ]
        },
        {
            "id": "output_trr_path",
            "required": true,
            "description": "Path to the GROMACS uncompressed raw trajectory file TRR",
            "filetype": "output",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_md\/raw\/master\/biobb_md\/test\/reference\/gromacs\/ref_mdrun.trr",
            "formats": [
                ".*\\.trr$"
            ]
        },
        {
            "id": "output_gro_path",
            "required": true,
            "description": "Path to the output GROMACS structure GRO file",
            "filetype": "output",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_md\/raw\/master\/biobb_md\/test\/reference\/gromacs\/ref_mdrun.gro",
            "formats": [
                ".*\\.gro$"
            ]
        },
        {
            "id": "output_edr_path",
            "required": true,
            "description": "Path to the output GROMACS portable energy file EDR",
            "filetype": "output",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_md\/raw\/master\/biobb_md\/test\/reference\/gromacs\/ref_mdrun.edr",
            "formats": [
                ".*\\.edr$"
            ]
        },
        {
            "id": "output_log_path",
            "required": true,
            "description": "Path to the output GROMACS trajectory log file LOG",
            "filetype": "output",
            "sample": "https:\/\/github.com\/bioexcel\/biobb_md\/raw\/master\/biobb_md\/test\/reference\/gromacs\/ref_mdrun.log",
            "formats": [
                ".*\\.log$"
            ]
        },
        {
            "id": "input_cpt_path",
            "required": false,
            "description": "Path to the input GROMACS checkpoint file CPT",
            "filetype": "input",
            "sample": null,
            "formats": [
                ".*\\.cpt$"
            ]
        },
        {
            "id": "output_xtc_path",
            "required": false,
            "description": "Path to the GROMACS compressed trajectory file XTC",
            "filetype": "output",
            "sample": null,
            "formats": [
                ".*\\.xtc$"
            ]
        },
        {
            "id": "output_cpt_path",
            "required": false,
            "description": "Path to the output GROMACS checkpoint file CPT",
            "filetype": "output",
            "sample": null,
            "formats": [
                ".*\\.cpt$"
            ]
        },
        {
            "id": "output_dhdl_path",
            "required": false,
            "description": "Path to the output dhdl.xvg file only used when free energy calculation is turned on",
            "filetype": "output",
            "sample": null,
            "formats": [
                ".*\\.xvg$"
            ]
        }
    ]
}