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. 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’]