Run 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 uses weighted ensemble molecular dynamics to sample the conformational dynamics of a target protein. Sampling is enhanced along a given set of normal modes. Note that the job can cost a few thousand dollars if the number of iterations for the simulation is too high (>500).
Promoted Parameters
Title in user interface (promoted name)
Input Data
Protein Normal Mode Records (mode_data_in): A dataset containing the normal modes along which to promote sampling. These records come from a ‘’Protein Normal Modes’’ output generated by ‘Calculate Normal Modes’. To ensure the selection of specific modes, this dataset should contain only one or two records. In the presence of more than two modes, the top two modes from the input dataset will be selected.
Required
Type: data_source
Solvated and Equilibrated Protein (du_data_in): The ‘Solvated and Equilibrated Protein’ dataset output from the ‘Solvate and Equilibrate Target Protein’ floe.
Required
Type: data_source
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
Collection Name (a3a_collection_name): Name of the collection to create
Required
Type: collection_sink
Default: Protein Sampling Data
Failure Report (failure_report): Output report to generate upon failure.
Type: string
Default: Protein Sampling Failure Report
Weighted Ensemble Parameters
Iterations (a3a_iterations): Number of iterations for the WE simulation. Suggested values: 50 iterations (total) for proteins with <200 residues; 100 iterations (total) for proteins with <600 residues. Note that the job can cost a few thousand dollars if this parameter is too high (>500).
Required
Type: integer
Default: 50
Iteration Interval (Tau) (a3a_iteration_interval): Length of each WE iteration in picoseconds.
Type: decimal
Default: 100.0
Advanced Weighted Ensemble Parameters
Number of Frames Per Iteration (a3a_frames_per_iteration): Number of frames saved in each WE iteration.
Type: integer
Default: 5
Number of Bins per Dimension (a3a_nbins): The number of bins along each normal mode. Either a single value or a sequence of values (one for each mode) may be provided. Bin placement is controlled by the Minimal Adaptive Binning (MAB) scheme (P.A. Torrillo, A.T. Bogetti, L.T. Chong, J. Phys. Chem. A 2021, 125, 7, 1642–1649).
Required
Type: integer
Default: [10]
Trajectories Per Bin (a3a_walkers_per_bin): Number of trajectories per bin for the WEMD simulation.
Required
Type: integer
Default: 10
Smallest Allowed Weight (Log) (a3a_smallest_allowed_log_weight): The smallest allowed weight for splitting in logarithmic scale.
Required
Type: decimal
Default: -310.0
Log Verbosity (verbosity): verbose level
Type: string
Default: debug
Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]