Continue a Weighted Ensemble MD Simulation

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/Molecular Dynamics

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Enhanced Sampling

  • Solution-based/Target Identification/Target Preparation/Pocket Detection

  • Solution-based/Hit to Lead/Target Preparation/Cryptic Pocket Detection

  • Role-based/Computational Chemist

  • Task-based/Target Prep & Analysis/Pocket Detection


This floe extends a weighted ensemble molecular dynamics simulation up to a given number of iterations. Note that the job can cost a few thousand dollars if the number of iterations is too high (>500).

Promoted Parameters

Title in user interface (promoted name)

Input Data

Collection (collection): Protein sampling data generated in the first round of weighted ensemble MD simulation.Simulation data generated in this run will be added to this input collection

  • Required

  • Type: collection_source

  • Default: Protein Sampling Data

Output Data

Output Dataset (a3_data_out): Output dataset containing the current iteration number, simulation settings, and a reference design unit. This dataset contains only 1 record, and can be viewed on the Orion Analyze page to track the total number of iterations that have been completed.

  • Required

  • Type: dataset_out

  • Default: Protein Sampling Summary Table

Failure Report (failure_report): Output report to generate upon failure.

  • Type: string

  • Default: Protein Sampling Failure Report

Weighted Ensemble Parameters

Additional Iterations (iterations):

Number of additional iterations to be run. Check the “Iteration Number” field on the Protein Sampling Dataset for the current number of iterations to determine the additional number of iterations that needs to be run. Note that the job can cost a few thousand dollars if this parameter is too high (>500). See documentation for more details.

  • Required

  • Type: integer

  • Default: 50

Advanced Weighted Ensemble Parameters

Log Verbosity (verbosity): verbose level

  • Type: string

  • Default: debug

  • Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]