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’]