deepdrivemd.sim.openmm_stream.config

pydantic settings deepdrivemd.sim.openmm_stream.config.OpenMMConfig

Show JSON schema

{
   "title": "OpenMMConfig",
   "description": "Auto-generates configuration file for MD tasks.",
   "type": "object",
   "properties": {
      "experiment_directory": {
         "title": "Experiment Directory",
         "default": "set_by_deepdrivemd",
         "env_names": "{'experiment_directory'}",
         "type": "string",
         "format": "path"
      },
      "stage_idx": {
         "title": "Stage Idx",
         "default": 0,
         "env_names": "{'stage_idx'}",
         "type": "integer"
      },
      "task_idx": {
         "title": "Task Idx",
         "default": 0,
         "env_names": "{'task_idx'}",
         "type": "integer"
      },
      "output_path": {
         "title": "Output Path",
         "default": "set_by_deepdrivemd",
         "env_names": "{'output_path'}",
         "type": "string",
         "format": "path"
      },
      "node_local_path": {
         "title": "Node Local Path",
         "default": "set_by_deepdrivemd",
         "env_names": "{'node_local_path'}",
         "type": "string",
         "format": "path"
      },
      "pdb_file": {
         "title": "Pdb File",
         "default": "set_by_deepdrivemd",
         "env_names": "{'pdb_file'}",
         "type": "string",
         "format": "path"
      },
      "initial_pdb_dir": {
         "title": "Initial Pdb Dir",
         "default": ".",
         "env_names": "{'initial_pdb_dir'}",
         "type": "string",
         "format": "path"
      },
      "solvent_type": {
         "default": "implicit",
         "env_names": "{'solvent_type'}",
         "allOf": [
            {
               "$ref": "#/definitions/MDSolvent"
            }
         ]
      },
      "top_suffix": {
         "title": "Top Suffix",
         "default": ".top",
         "env_names": "{'top_suffix'}",
         "type": "string"
      },
      "simulation_length_ns": {
         "title": "Simulation Length Ns",
         "default": 10,
         "env_names": "{'simulation_length_ns'}",
         "type": "number"
      },
      "report_interval_ps": {
         "title": "Report Interval Ps",
         "default": 50,
         "env_names": "{'report_interval_ps'}",
         "type": "number"
      },
      "dt_ps": {
         "title": "Dt Ps",
         "default": 0.002,
         "env_names": "{'dt_ps'}",
         "type": "number"
      },
      "temperature_kelvin": {
         "title": "Temperature Kelvin",
         "default": 310.0,
         "env_names": "{'temperature_kelvin'}",
         "type": "number"
      },
      "heat_bath_friction_coef": {
         "title": "Heat Bath Friction Coef",
         "default": 1.0,
         "env_names": "{'heat_bath_friction_coef'}",
         "type": "number"
      },
      "reference_pdb_file": {
         "title": "Reference Pdb File",
         "env_names": "{'reference_pdb_file'}",
         "type": "string",
         "format": "path"
      },
      "openmm_selection": {
         "title": "Openmm Selection",
         "default": [
            "CA"
         ],
         "env_names": "{'openmm_selection'}",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "mda_selection": {
         "title": "Mda Selection",
         "default": "protein and name CA",
         "env_names": "{'mda_selection'}",
         "type": "string"
      },
      "threshold": {
         "title": "Threshold",
         "default": 8.0,
         "env_names": "{'threshold'}",
         "type": "number"
      },
      "in_memory": {
         "title": "In Memory",
         "default": true,
         "env_names": "{'in_memory'}",
         "type": "boolean"
      },
      "bp_file": {
         "title": "Bp File",
         "default": "md.bp",
         "env_names": "{'bp_file'}",
         "type": "string",
         "format": "path"
      },
      "adios_cfg": {
         "title": "Adios Cfg",
         "default": "adios.xml",
         "env_names": "{'adios_cfg'}",
         "type": "string",
         "format": "path"
      },
      "adios_xml_sim": {
         "title": "Adios Xml Sim",
         "default": "adios.xml",
         "env_names": "{'adios_xml_sim'}",
         "type": "string",
         "format": "path"
      },
      "compute_rmsd": {
         "title": "Compute Rmsd",
         "default": true,
         "env_names": "{'compute_rmsd'}",
         "type": "boolean"
      },
      "divisibleby": {
         "title": "Divisibleby",
         "default": 2,
         "env_names": "{'divisibleby'}",
         "type": "integer"
      },
      "outliers_dir": {
         "title": "Outliers Dir",
         "default": ".",
         "env_names": "{'outliers_dir'}",
         "type": "string",
         "format": "path"
      },
      "pickle_db": {
         "title": "Pickle Db",
         "default": ".",
         "env_names": "{'pickle_db'}",
         "type": "string",
         "format": "path"
      },
      "copy_velocities_p": {
         "title": "Copy Velocities P",
         "default": 0.5,
         "env_names": "{'copy_velocities_p'}",
         "type": "number"
      },
      "current_dir": {
         "title": "Current Dir",
         "default": ".",
         "env_names": "{'current_dir'}",
         "type": "string",
         "format": "path"
      },
      "zcentroid_atoms": {
         "title": "Zcentroid Atoms",
         "default": "",
         "env_names": "{'zcentroid_atoms'}",
         "type": "string"
      },
      "compute_zcentroid": {
         "title": "Compute Zcentroid",
         "default": false,
         "env_names": "{'compute_zcentroid'}",
         "type": "boolean"
      },
      "ligand": {
         "title": "Ligand",
         "default": -1,
         "env_names": "{'ligand'}",
         "type": "integer"
      },
      "multi_ligand_table": {
         "title": "Multi Ligand Table",
         "default": ".",
         "env_names": "{'multi_ligand_table'}",
         "type": "string",
         "format": "path"
      },
      "adios_xml_file": {
         "title": "Adios Xml File",
         "default": ".",
         "env_names": "{'adios_xml_file'}",
         "type": "string",
         "format": "path"
      },
      "top_file1": {
         "title": "Top File1",
         "default": ".",
         "env_names": "{'top_file1'}",
         "type": "string",
         "format": "path"
      },
      "model": {
         "title": "Model",
         "default": "cvae",
         "env_names": "{'model'}",
         "type": "string"
      }
   },
   "definitions": {
      "MDSolvent": {
         "title": "MDSolvent",
         "description": "An enumeration.",
         "enum": [
            "implicit",
            "explicit"
         ],
         "type": "string"
      }
   }
}