WESTPA Setup

Set up WESTPA parameters, e.g. initial progress coordinate and bin boundaries.


Calculation Parameters

  • Bin Size (Membrane) (bin_size_membrane) type: decimal: Bin size in membrane (Angstrom).
    Default: 0.5 , Min: 0.01, Max: 5.0
  • Bin Size (Water) (bin_size_water) type: decimal: Bin size in water (Angstrom).
    Default: 2.0 , Min: 0.01, Max: 5.0
  • 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
  • MAB (mab) type: boolean: Whether or not to enable the Minimal, Adaptive Binning (MAB) scheme.
    Default: False
  • MAB Bin Size (Membrane) (mab_bin_size_membrane) type: decimal: The maximal bin size (Angstrom) for the MAB scheme in membrane.
    Default: 1.5 , Min: 0.01, Max: 5.0
  • MAB Bin Size (Water) (mab_bin_size_water) type: decimal: The maximal bin size (Angstrom) for the MAB scheme in water.
    Default: 3.0 , Min: 0.01, Max: 5.0
  • 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
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • None (tstate) type: decimal:
    Default: 30.0
  • Log Verbosity (verbosity) type: string: The level of logging verbosity.
    Default: debug
    Choices: error, warning, info, debug, ddebug

Field parameters

  • Bins Field (bins_field) type: Field Type: JSONObject: Field containing the binning scheme for WESTPA.
    Default: Bins
  • Box Edges Field (box_edges_field) type: Field Type: FloatVec: Field containing the solvated molecule and the membrane.
    Default: Box Edges
  • 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
  • Extra Files Field (extra_files_field) type: Field Type: DirectoryTree: Field containing a dictionary of extra files needed to be put into the WESTPA project folder. The key is the filename and the value should be the binary content of the file.
    Default: Extra Files
  • Initial Progress Coordinates Field (init_pcoords_field) type: Field Type: InitPCoordArray: Field containing the initial progress coordinates of basis states.
    Default: Initial Progress Coordinates
  • Log Field (log_field) type: Field Type: String: Message log field
    Default: Log Field
  • Reweighting Bins Field (reweight_bins_field) type: Field Type: JSONObject: Field containing the binning scheme for the WESS plugin.
    Default: Reweighting Bins
  • Simulation Protocol (runseg.py) Field (runseg_field) type: Field Type: String: Field containing the runseg script (Python).
    Default: Simulation Protocol (runseg.py)
  • Simulation Hyperparameters (runseg_kwargs) Field (runseg_kwargs_field) type: Field Type: JSONObject: Field containing the keyword parameters for the runseg script.
    Default: Simulation Hyperparameters (runseg_kwargs)
  • 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
  • Target State Definition Field (tstate_field) type: Field Type: String: Field containing the definitions of target states.
    Default: Target State Definition

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
  • 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