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
Description
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
Inputs
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
Outputs
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