Permeability WEMD Setup

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

Calculation Parameters

  • Bin Size (Membrane) (bin_size_membrane) type: decimal: The width of WE bins along z in membrane (Angstrom).
    Default: 0.5 , Min: 0.01, Max: 5.0
  • Bin Size (Water) (bin_size_water) type: decimal: The width of WE bins along z in (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
  • Grouping History Length (group_history_length) type: integer: The number of iterations that walkers share in order to be put into the same group. Grouping is disabled if empty.
    Default: 10
  • 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: 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
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • 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
  • Recycling State (tstate) type: decimal: The progress coordinate beyond what the walkers will be recycled.
    Default: 35.0
  • Log Verbosity (verbosity) type: string: verbose level
    Default: debug
    Choices: info, warning, error, debug, ddebug

Field parameters

  • Bins Field (bins_field) type: Field Type: JSONObject: Field containing the binning scheme for running a WE simulation.
    Default: Bins
  • Box Edges Field (box_edges_field) type: Field Type: FloatVec: Field containing the solvated molecule and the membrane.
    Default: Box Edges
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • Reweighting Bins Field (reweight_bins_field) type: Field Type: JSONObject: Field containing the binning scheme for reweighting a WE simulation.
    Default: Reweighting Bins
  • Target State Definition Field (tstate_def_field) type: Field Type: String: Field containing the definitions of target states.
    Default: Target State Definition
  • User-Defined Configuration Field (user_configs_field) type: Field Type: JSONObject: Field containing the user-defined configuration for running the WEMD simulation.
    Default: User-Defined Configuration
  • WEMD Addon Files Field (we_addon_field) type: Field Type: DirectoryTree: Field containing the addon files for running the WEMD simulation.
    Default: WEMD Addon Files

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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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