Extract Molecule from Record

Extract the drug molecule from a record for downstream calculation.

Main Parameters

Parameter Name

Number of Basis States

Restart Simulation

Calculation Parameters

  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Number of Basis States (n_basis) type: integer: A set of Omega conformers used as input to permeability.
    Default: 20
  • Project Name (project) type: string:
    Default: WESTPA
  • Restart Simulation (restart) type: boolean: Restart the WE simulation from the beginning.
    Default: False
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Log Verbosity (verbosity) type: string: verbose level
    Default: debug
    Choices: info, warning, error, debug, ddebug

Field parameters

  • Basis State Weights Field (bstate_weights_field) type: Field Type: FloatVec: Field containing the weights of the basis states.
    Default: Basis State Weights
  • Basis States Field (bstates_field) type: Field Type: CompressedStringVec: Field containing the data for basis states.
    Default: Basis States
  • Collection Field (collection_field) type: Field Type: LinkedResource: Field containing the collection (link) that stores the WESTPA project configurations and MD trajectory data.
    Default: Collection
  • Dry Molecule Field (dry_molecule_field) type: Field Type: Chem.Mol: Field containing the unsolvated molecule.
    Default: Dry Molecule
  • None (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Init Shard Field (init_shard_field) type: Field Type: LinkedShard: Field containing the init shard (link) that stores the WESTPA project configurations.
    Default: Init Shard
  • Integrator Field (integrator_field) type: Field Type: String: Field containing the OpenMM integrator.
    Default: Integrator
  • None (log_field) type: Field Type: String: Message log field
    Default: Log Field
  • Molecule with Membrane Field (membrane_molecule_field) type: Field Type: Chem.Mol: Field containing the solvated molecule and the membrane.
    Default: Molecule with Membrane
  • Molecule ID Field (mol_id_field) type: Field Type: String: Field containing the identification number of the molecule.
    Default: Molecule ID
  • Molecule Name Field (mol_name_field) type: Field Type: String: Field containing the name of the molecule.
    Default: Molecule Name
  • Molecule SMILES Field (mol_smiles_field) type: Field Type: String: Field containing the SMILES string for the primary molecule.
    Default: Molecule SMILES
  • Primary Molecule Field (primary_molecule_field) type: Field Type: Chem.Mol: Field containing the primary molecule.
  • Solvated Molecule (PDB) Field (solvated_molecule_pdb_field) type: Field Type: String: Field containing the solvated molecule in the PDB format.
    Default: Solvated Molecule (PDB)
  • System Field (system_field) type: Field Type: CompressedString: Field containing the OpenMM system data.
    Default: System
  • Topology Field (topology_field) type: Field Type: CompressedString: Field containing the topology data.
    Default: Topology
  • HDF5 Data (west.h5) Field (west_h5_field) type: Field Type: CompressedBlob: Field containing the WESTPA data (west.h5).
    Default: HDF5 Data (west.h5)
  • HDF5 Data Shard Field (west_h5_shard_field) type: Field Type: LinkedShard: Field holding the link to the shard that contains WESTPA data (west.h5).
    Default: HDF5 Data Shard

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network