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 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 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-evaluatedDefault: 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 secondsDefault: 60Choices: 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 CPUDefault: 32 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: 35.0 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 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 fieldDefault: 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 reportDefault: 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 addressDefault: 64
- Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 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-evaluatedDefault: 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 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