WESTPA Setup¶
Set up WESTPA parameters, e.g. initial progress coordinate and bin boundaries.
Parameter Details¶
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 withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: 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 withDefault: 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 secondsDefault: 60Choices: 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 instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required None (tstate) type: decimal:Default: 30.0 Log Verbosity (verbosity) type: string: The level of logging verbosity.Default: debugChoices: 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 fieldDefault: 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 withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: 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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network