Permeability - Continue Permeability Simulation (Optional)¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Solution-based/Hit to Lead/Properties/Permeability
Solution-based/Small Molecule Lead-opt/ADME & Tox/Permeability
Product-based/Molecular Dynamics/WESTPA
Product-based/Molecular Dynamics/OpenMM
Task-based/Molecular Dynamics
Task-based/ADME & Tox Assessment
Description
The Floe can be used to continue a permeability simulation until it reaches a target number of iterations. The Floe takes a collection generated by the Permeability - Run Permeability Simulation floe as the input. By default, the simulation is set up to extend the simulation up to 500 iterations, which may cost a few thousand dollars.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Collection (in): Collections to use as input to a floe
Required
Type: collection_source
Outputs
Output Dataset (out): Output dataset to write to
Required
Type: dataset_out
Default: Permeability Simulation
Failure Report (fail_report): Output report to generate upon failure
Type: string
Default: Permeability Simulation Failure Report
Weighted Ensemble Parameters
Iterations (iterations): Number of iterations for the WE simulation.
Required
Type: integer
Default: 500
Reweighting (reweighting): 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.
Required
Type: boolean
Default: True
Choices: [True, False]
Advanced Weighted Ensemble Parameters
Reweighting Period (reweighting_period): 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.
Required
Type: integer
Default: 50
Reweighting Window Size (reweighting_window): 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.
Required
Type: decimal
Default: 0.75
Miscellaneous Parameters
Log Verbosity (verbosity): verbose level
Type: string
Default: debug
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]