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 MDDefault: 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 instancesDefault: AllowedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required prod_time (decimal) : Length of MD run in nanosecondsDefault: 0.1 verbosity (string) : The level of logging verbosityDefault: debugChoices: error, warning, info, debug, ddebug bin_size_membrane (decimal) : Bin size in membrane in AngstromDefault: 0.5 Min: 0.01 Max: 5.0 bin_size_water (decimal) : Bin size in water in AngstromDefault: 2.0 Min: 0.01 Max: 5.0 mab_bin_size_membrane (decimal) : The maximal bin size (Angstrom) for the MAB scheme in membraneDefault: 1.5 Min: 0.01 Max: 5.0 mab_bin_size_water (decimal) : The maximal bin size (Angstrom) for the MAB scheme in waterDefault: 3.0 Min: 0.01 Max: 5.0 mab (boolean) : Whether or not to enable the Minimal, Adaptive Binning (MAB) schemeDefault: True out (dataset_out) : Output dataset to write to ligand_ff (string) : Force field to be applied to the ligandDefault: OpenFF_1.3.1Choices: 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 simulationDefault: False n_basis (integer) : A set of Omega conformers used as input to permeabilityDefault: 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 simulationDefault: 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 analysisDefault: 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 reportDefault: Log Field Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field