Flex-Protein Ligand Energy
- This cube calculates intermolecular protein ligand energy for a flexible protein.
Input design units are read from the intake port, and energies are emitted through the success port.
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 Non bonded interactions cutoff (cutoff) type: decimal: Non-bonded VdW and Coulomb interactions cutoffDefault: 40.0 , Max: 100.0 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 Force Field (ff_type) type: string: Built-in force field model to be used.Default: ff14sb_sageChoices: ff14sb_sage, ff14sb_parsley, mmff94, mmff94s, mmff_amber, mmffs_amber Flexibility range (flex_range) type: decimal: Portion of the protein to be considered flexible, measured as the distance between initial positions of the ligand atoms and the protein atomsDefault: 2.0 , Min: 0.5, Max: 10.0 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 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 Optimization type (opt_type) type: string: Type of optimization to performDefault: poseCartesianChoices: cartesian, poseCartesian Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32 Components to keep as the ‘protein’ (protein_mask) type: string: DU components to use as the ‘protein’.Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘solvent’, ‘other_ligands’, ‘other_cofactors’]Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined, cofactors, excipients, polymers, post_translational, other_proteins, other_nucleics, other_ligands, other_cofactors Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Solvent model (solvent_model) type: string: Solvent model to be usedDefault: Gas-phaseChoices: Gas-phase, Sheffield, PB Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Field parameters
Energy field (energy_field) type: Field Type: Float: Protein-ligand intermolecular energyDefault: Energy (kcal/mol) Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log fieldDefault: Extended Log Field None (in_du_field) type: Field Type: Chem.DesignUnit:Record:Default: designunit Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field
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
Parallel Flex-Protein Ligand Energy
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