A3b. Protein Sampling (for Cryptic Pockets): 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.

Promoted Parameters

Title in user interface (promoted name)

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. See documentation for more details.

  • Required

  • Type: integer

  • Default: 50


Protein Sampling (Weighted Ensemble MD Simulation) Dataset (data_in): This is a ‘Protein Sampling Dataset’ output generated by ‘A3a. Protein Sampling (for Cryptic Pockets): Run a Weighted Ensemble MD Simulation’ or ‘A3b. Protein Sampling (for Cryptic Pockets): Continue a Weighted Ensemble MD Simulation’. The dataset should come from the most recent Protein Sampling job run for a given protein.

  • Required

  • Type: data_source


Output Dataset (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 Dataset

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

  • Type: string

  • Default: Protein Sampling Failure Report