Solvation Packmol

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

  • close_solvent (boolean) : If Checked/True solvent molecules will be placed very close to the solute
    Default: False
  • density (decimal) : Solution density in g/ml
    Default: 1.0
  • distance_between_atoms (decimal) : The minimum distance between atoms in A
    Default: 2.0
  • geometry (string) : Geometry selection: box or sphere. Sphere cannot be used as periodic system along with MD simulation
    Default: box
    Choices: box, sphere
  • molar_fractions (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 (boolean) : Neutralize the solute by adding Na+ and Cl- counter-ions based onthe solute formal charge
    Default: True
  • padding_distance (decimal) : The padding distance between the solute and the box edge in A
    Default: 8.0
  • salt (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 (decimal) : Salt concentration in millimolar
    Default: 0.0
  • solvents (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
  • verbose (boolean) : Output Packmol log
    Default: False

Metrics

Cube Metric Parameters

  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Hardware Parameters

Machine hardware requirements

  • Memory (MB) (decimal) : The minimum amount of memory this cube requires in MBs
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MB) (decimal) : The amount of disk space this cube requires in MBs
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”

Parallel Solvation Packmol

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (integer) : The maximum number of messages to bundle together for a parallel cube.
    Default: 1 Min: 1 Max: 100000
  • Maximum Failures (integer) : The maximum number of times to attempt processing a work item
    Default: 10 Min: 1 Max: 100
  • Autoscale this Cube (boolean) : If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (integer) : The maximum number of concurrently running copies of this Cube
    Default: 1000 Min: 1
  • Minimum number of Cubes (integer) : The minimum number of concurrently running copies of this Cube
    Default: 0

Tip

filename: MDOrion/System/cubes.py