Gas Phase Ligand Entropy¶
This cube calculates gas-phase entropy of ligand conformation ensembles using the MMFF force field.
The calculated entropic components are added to the intake port record and emitted through the success port.
Parameter Details¶
Calculation Parameters¶
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 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
Field parameters¶
Configurational Entropy field (conf_ent_field) type: Field Type: Float: Configurational entropy of the conformer ensembleDefault: Configurational Entropy None (in_mol_field) type: Field Type: Chem.Mol: None (out_mol_field) type: Field Type: Chem.Mol: Rotational Entropy field (rot_ent_field) type: Field Type: Float: Rotational entropy of the conformerDefault: Rotational Entropy Total Entropy field (tot_ent_field) type: Field Type: Float: Total entropy of the conformer ensembleDefault: Total Entropy Vibrational Entropy field (vib_ent_field) type: Field Type: Float: Vibrational entropy of the conformerDefault: Vibrational Entropy
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
Parallel Gas Phase Ligand Entropy
The parallel version adds these extra parameters.
Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.Default: 1 , Min: 1, Max: 65535 Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work itemDefault: 10 , Min: 1, Max: 100 Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this CubeDefault: True Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this CubeDefault: 1000 , Min: 1 Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this CubeDefault: 0