WESTPA 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 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 Grouping History Length (group_history_length) type: integer: The number of iterations that walkers share in order to be putinto 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 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 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required Recycling State (tstate) type: decimal: The progress coordinate beyond what the walkers will be recycled.Default: 40.0 Log Verbosity (verbosity) type: string: verbose levelDefault: debugChoices: info, warning, error, 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 Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field None (in_mol_field) type: Field Type: Chem.Mol: Initial Progress Coordinates Field (init_pcoords_field) type: Field Type: InitPCoordArray: Field containing the initial progress coordinates of basis states.Default: Initial Progress Coordinates Integrator Field (integrator_field) type: Field Type: String: Field containing the OpenMM integrator.Default: Integrator Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field WESTPA Project Files Field (project_files_field) type: Field Type: DirectoryTree: Field containing a dictionary of extra files needed for running the WESTPA simulation. (WESTPA simulation root directory).Default: WESTPA Project Files 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 Related Files Field (runseg_files_field) type: Field Type: DirectoryTree: Field containing a dictionary of extra files needed for propagating each segment. (links under the “traj_segs” folder).Default: Simulation Related Files 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 User-Defined Configurations Field (user_configs_field) type: Field Type: JSONObject: Field containing a dictionary of user-defined configurations (west.cfg).Default: User-Defined Configurations
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 addressDefault: 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 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