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.

Related Cubes

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 box
    Default: True
  • Periodic Box shape (box_shape) type: string: Periodic box shape selection: cubic or rectangular
    Default: cubic
    Choices: cubic, rectangular
  • Close solvent (close_solvent) type: boolean: If Checked/True solvent molecules will be placed very close to the solute
    Default: False
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • density (density) type: decimal: Solution density in g/ml
    Default: 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 A
    Default: 2.0
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 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-evaluated
    Default: 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 seconds
    Default: 60
    Choices: 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. 0.5,0.2,0.3
    Default: 1.0
  • Neutralize solute (neutralize_solute) type: boolean: Neutralize the solute by adding Na+ and Cl- counter-ions based onthe solute formal charge
    Default: True
  • Padding distance (padding_distance) type: decimal: The padding distance between the solute and the box edge in A
    Default: 8.0
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 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 millimolar
    Default: 50.0
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 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 tip3p
    Default: tip3p
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • verbose (verbose) type: boolean: Output Packmol log
    Default: False

Field parameters

  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: 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 address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 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-evaluated
    Default: 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 with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 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 instances
    Default: Prohibited
    Choices: 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 seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: 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 item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0