Solvation¶
The solvation cube solvates a given solute input system by a periodic box of a solvent or a selected mixture of solvents. The solvents can be specified by comma separated smiles strings of each solvent component or selected keywords like tip3p for tip3p water geometry. For each component the user needs to specify its molar fractions as well. The solution can be neutralized by adding counter-ions. In addition, the ionic solution strength can be set adding salt. The cube requires a record as input with a solute molecule to solvate and produces an output record with the solvated solute.
Calculation Parameters¶
Automated Box Size Reduction (auto_reduce_box) type: boolean: If the input record specifies ‘gentle restraints’ to prevent protein tumbling, automatically reduce the size of the simulation boxDefault: True Periodic Box shape (box_shape) type: string: Periodic box shape selection: cubic or rectangularDefault: cubicChoices: cubic, rectangular Close solvent (close_solvent) type: boolean: If Checked/True solvent molecules will be placed very close to the soluteDefault: False 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 density (density) type: decimal: Solution density in g/mlDefault: 1.03 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 Minimum distance between atoms (distance_between_atoms) type: decimal: The minimum distance between atoms in ADefault: 2.0 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 Molar fractions (molar_fractions) type: string: Molar fractions of each solvent components. The molar fractions are specifiedas comma separated molar fractions strings e.g. 0.5,0.2,0.3Default: 1.0 Neutralize solute (neutralize_solute) type: boolean: Neutralize the solute by adding Na+ and Cl- counter-ions based onthe solute formal chargeDefault: True Padding distance (padding_distance) type: decimal: The padding distance between the solute and the box edge in ADefault: 8.0 Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32 Random Seed from System Time (random_seed_from_system_time) type: boolean: If turned on, the seed for Packmol’s random number generator will be generated from the system time. If turned off, a fixed default seed will be used.Default: False salt (salt) type: string: Salt type. The salt is specified as list of smiles strings. Each smiles string is the salt component dissociated in the solution e.g. Na+, Cl-Default: [Na+], [Cl-] Salt concentration (salt_concentration) type: decimal: Salt concentration in millimolarDefault: 50.0 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 solvents (solvents) type: string: Select solvents. The solvents are specified as comma separated smiles stringse.g. [H]O[H], C(Cl)(Cl)Cl, CS(=O)C or special keywords like tip3pDefault: tip3p Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required verbose (verbose) type: boolean: Output Packmol logDefault: False
Field parameters¶
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 Solvation
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