Permeability - Run Permeability SimulationΒΆ

A floe that calculates the passive membrane permeability of a drug-like molecule.

Promoted Parameters

  • temperature (decimal) : Temperature (Kelvin)
    Default: 308.0
  • hmr (boolean) : Give hydrogens more mass to speed up the MD
    Default: False
  • prep_cpu_count (integer) : The number of CPUs to run the preparation cubes (energy minimization, etc.)
    Default: 8 Min: 1 Max: 128
  • spot_policy (string) : Control cube placement on spot market instances
    Default: Allowed
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • prod_time (decimal) : Length of MD run in nanoseconds
    Default: 0.1
  • verbosity (string) : The level of logging verbosity
    Default: debug
    Choices: error, warning, info, debug, ddebug
  • bin_size_membrane (decimal) : Bin size in membrane in Angstrom
    Default: 0.5 Min: 0.01 Max: 5.0
  • bin_size_water (decimal) : Bin size in water in Angstrom
    Default: 2.0 Min: 0.01 Max: 5.0
  • mab_bin_size_membrane (decimal) : The maximal bin size (Angstrom) for the MAB scheme in membrane
    Default: 1.5 Min: 0.01 Max: 5.0
  • mab_bin_size_water (decimal) : The maximal bin size (Angstrom) for the MAB scheme in water
    Default: 3.0 Min: 0.01 Max: 5.0
  • mab (boolean) : Whether or not to enable the Minimal, Adaptive Binning (MAB) scheme
    Default: True
  • out (dataset_out) : Output dataset to write to
  • ligand_ff (string) : Force field to be applied to the ligand
    Default: OpenFF_1.3.1
    Choices: Gaff_1.81, Gaff_2.11, OpenFF_1.1.1, OpenFF_1.2.1, OpenFF_1.3.1, OpenFF_2.0.0, Smirnoff99Frosst
  • prep_only (boolean) : Prepare the system without running the WESTPA simulation
    Default: False
  • n_basis (integer) : A set of Omega conformers used as input to permeability
    Default: 20
  • in (data_source) : The dataset(s) to read records from
  • iterations (integer) : Number of iterations for the WESTPA simulation.
    Default: 500 Min: 1 Max: 5000
  • iteration_interval (decimal) : Length of each WESTPA iteration in picoseconds.
    Default: 100.0
  • restart (boolean) : Restart (as opposed to resume) the WE simulation. The preparation would still be skipped if it has already been done.
    Default: False
  • reweighting (boolean) : Whether or not to reweight the trajectory segments to reduce the relaxation time in steady-state simulations using the WESS method. This parameter will be set to the value specified here when resuming a simulation.
    Default: True
  • walkers_per_bin (integer) : Number of trajectories per bin for the WESTPA simulation
    Default: 5 Min: 2 Max: 100
  • report_interval (decimal) : Trajectories saving interval for the WESTPA run in picoseconds.
    Default: 20.0
  • reweighting_period (integer) : The period of reweighting the trajectory segments in terms of the number of iterations.No reweighting when set to 0. This parameter will be set to the value specified here when resuming a simulation.
    Default: 50
  • reweighting_window (decimal) : The fraction of previous iterations used for estimating the transition rates for reweighting. This parameter will be set to the value specified here when resuming a simulation.
    Default: 0.75 Max: 1.0
  • cleanup (boolean) : Clean up intermediate data. The output record can still be used for resuming a simulation or analysis
    Default: True
  • deep_cleanup (boolean) : Remove WESTPA data to save space for permeability results. WARNING: if this option is turned on, the output record cannot be used by the analysis floe.
    Default: False
  • ref_perm (string) : This can be a value determined by an experiment or determined by other methods as a reference for comparison. The reference value should have a unit of cm/s and then converted to the log scale. An error can be included in a pair of parentheses, if available. Example input: -6.0 (0.1)
  • ref_src (string) : Source of the reference permeability coefficient, which can be the type of the experiment or the name of the method that used to determine permeability
  • mol_id (string) : This can be any identification number (e.g., CHEMBL ID) associated with the molecule

Extra Required Parameters

  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field