molclaw-protein-openmm

Protein OpenMM MD and Frame Extraction

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to complete tool invocation.

Usage

1. Protein OpenMM MD

The description of tool protein_openmm_md.

Runs OpenMM-based protein molecular dynamics preparation and simulation for structure refinement workflows.
Args:
    protein_pdb (str): Absolute or relative path to input protein PDB.
    solvent_type (str): Solvent mode, 'explicit' or 'implicit', default 'explicit'.
    gb_model (str): GB model for implicit solvent mode, default 'GBn2'.
    water_model (str): Water model for explicit solvent mode, default 'tip3p'.
    force_field (str): OpenMM force field name, default 'amber14'.
    md_time (float): Production MD time in picoseconds, default 100000.0.
    platform (str): OpenMM compute platform, default 'CUDA'.
    full_md (bool): Run full MD procedure if True, default False.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable execution summary.
    command (str): The invoked command ('protein_openmm_md').
    run_dir (str | None): Final run directory under tool_result/openmm_md_result.
    work_dir (str | None): Same as run_dir for compatibility.
    trajectory_path (str | None): Path to md_traj.dcd when available.
    energy_log (str | None): Path to md.log when available.
    generated_files (List[str]): File paths relative to work_dir.
    md_time (float): Echoed requested MD time in ps.
    solvent_type (str): Echoed solvent mode.
    force_field (str): Echoed force field.
    full_md (bool): Echoed full MD mode.

How to use tool protein_openmm_md :

response = await client.session.call_tool(
    "protein_openmm_md",
    arguments={
        "protein_pdb": "/path/to/input.pdb",
        "solvent_type": "implicit",
        "gb_model": "OBC2",
        "water_model": "tip3p",
        "force_field": "amber14",
        "md_time": 1000.0,
        "platform": "CUDA",
        "full_md": True
    }
)
result = client.parse_result(response)
key_output = result["work_dir"]