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JSON Configuration

Each build writes a config.json file inside the output folder.

This file stores the full build configuration and allows full reproducibility of the system.

📄 Example Configuration

{
    "output_name": "outputs/OpenBuilder-2026-05-15_00-47-52",
    "selected_ff": "martini_v3",
    "base_folder": "",
    "selected_module": "membrane_with_cg_protein",
    "box_x": 10.0,
    "box_y": 10.0,
    "box_z": 20.0,
    "box_type": "rectangular",
    "solvation": "solv:W pos:NA neg:CL salt_molarity:0.18",
    "salt_molarity": 0.18,
    "n_systems": 4,
    "pdb_path": "outputs/OpenBuilder-2026-05-15_00-47-52/simulations/R0004/protein.pdb",
    "itp_path": "outputs/OpenBuilder-2026-05-15_00-47-52/toppar/protein.itp",
    "abs_lip_vals": false,
    "entries": [
        [
            "POPC",
            0.3,
            0.25,
            0.6,
            0.6
        ],
        [
            "CHOL",
            0.3,
            0.5,
            0.6,
            0.6
        ],
        [
            "PSM",
            0.4,
            0.25,
            0.6,
            0.6
        ]
    ],
    "z_method": "Height above Membrane",
    "distance_to_mem": 2.0,
    "randomize_pos": true,
    "randomize_pos_every": true,
    "randomize_rot": true,
    "randomize_rot_every": true,
    "protein_params": {
        "R0001": {
            "cx": -0.2634,
            "cy": -0.3105,
            "cz": 5.5903,
            "rx": 140.6176,
            "ry": 154.579,
            "rz": -117.2219
        },
        "R0002": {
            "cx": 1.7503,
            "cy": 0.6474,
            "cz": 5.9287,
            "rx": 72.6335,
            "ry": -121.346,
            "rz": -131.9327
        },
        "R0003": {
            "cx": -1.6669,
            "cy": 1.3716,
            "cz": 5.8229,
            "rx": 17.8925,
            "ry": -115.151,
            "rz": 177.4764
        },
        "R0004": {
            "cx": -0.9433,
            "cy": -1.1002,
            "cz": 5.914,
            "rx": -169.1105,
            "ry": 45.0814,
            "rz": -55.516
        }
    }
}

🧠 Explanation of Key Fields

🧱 System

  • selected_module
  • "membrane"

  • "membrane_with_cg_protein"

  • selected_ff

  • Force field (currently martini_v3)

📦 Box

  • box_x, box_y, box_z → size in nm
  • box_type → currently "rectangular"

🧂 Solvation

  • solvation → string passed to COBY
  • salt_molarity → numeric version (used internally)

🔁 Replicas

  • n_systems → number of independent systems generated

🧬 Protein

  • pdb_path → protein structure
  • itp_path → topology

These are automatically copied into:

user_inputs/

📍 Placement

  • z_method
  • "Absolute z position"

  • "Height above Membrane"

  • distance_to_mem

  • Used only for height-based placement

🎲 Randomization

  • randomize_pos
  • randomize_pos_every
  • randomize_rot
  • randomize_rot_every

Controls variability across replicas.

🧬 Membrane Composition

Each lipid entry follows:

[lipid_name, upper, lower, apl_upper, apl_lower]

Example:

["POPC", 0.5, 1.0, 0.6, 0.6]

Relative mode (abs_lip_vals = false)

  • Values must sum to 1.0 per leaflet

Absolute mode (abs_lip_vals = true)

  • Values are lipid counts (integers)

⚠️ Notes

  • membrane_string is generated automatically → do not edit
  • entries is an internal field
  • output_name is set automatically

🚀 Reuse

python app.py --no-gui outputs/OpenBuilder-xxxx/config.json