Single Stage Workflows

The table below lists the single stage workflows that are included by default.

  • Workflow List—The name of the workflow as shown in the Workflow list of the Run Meta Workflow Panel, as well as the Load Workflow and Manage Workflows dialogs. The Help documentation for the associated panels are linked.

  • Command Option Menu—The name of the workflow as shown in the Command option menu of the Meta Workflow Builder Panel.

  • Stage Name—The default Name given to the workflow stage when you add a single stage workflow using the Append Workflow button in the Meta Workflow Builder Panel.

  • Command Help—Link to the command help for the workflow.

  • Notes—Additional information about running the stage as part of a Meta Workflow.

Workflow List Command Option Menu Stage Name Command Help Notes
Single Stage Cluster Analysis Cluster Analysis cluster cluster_analysis_driver.py Command Help  
Single Stage Diffusion Gk Diffusion Coefficient GK diffusion_vel diffusion_coefficient_gk_driver.py Command Help  
Single Stage Diffusion Msd Diffusion Coefficient MSD diffusion_msd diffusion_coefficient_msd_driver.py Command Help  
Single Stage Disorder System Single Component Disordered System Builder dsb disordered_system_builder_driver.py Command Help If the -ncells n option is included in the command, the stage produces n replicate cells as output structures. The -homogeneous option also produces multiple output structures as it creates systems with each component. Duplicate workflows are then run using each output structure produced.
Single Stage Elastic Stress Based Elastic Constants Via Stress elastic_s elastic_constants_driver2.py Command Help  
Single Stage Evaporation Evaporation evap evaporation_driver.py Command Help The Evaporation command line needs to include specific molecule numbers (-solv_mol_num) to define the solvent molecule and possibly substrates.
Single Stage Extract Clusters Extract Clusters extract extract_clusters_driver.py Command Help Can be used to extract monomers, dimers, monomer clusters or dimer clusters from a system and then run duplicate workflows on each extracted structure.
Single Stage Free Volume Free Volume Analysis freevol free_volume_analysis_driver.py Command Help  
Single Stage Macromodel Conformational Search Macromodel Conformational Search mmodel macromodel Command Help The conformational search saves all conformations within 21 kJ/mol (5.0 kcal/mol) of the lowest energy conformer and then splits the workflow to run one copy of the remaining workflow per conformation. The settings for the search are the default settings from the Macromodel Conformational Search panel if no solvent is selected.
Single Stage Penetrant Loading Penetrant Loading pload penetrant_loading_driver.py Command Help  
Single Stage Polymer Builder Polymer Builder PB polymer_builder_driver.py Command Help If the -ncells n option is included in the command, the stage produces n replicate cells as output structures, and runs duplicate workflows using each structure.
Single Stage Polymer Chain Analysis Polymer Chain Analysis pchain polymer_chain_analysis_driver.py Command Help  
Single Stage Polymer Crosslink Amide Bond Crosslink Polymers xlink polymer_crosslink_driver.py Command Help  
Single Stage Prepare For MD Prepare for MD prepmd prepare_for_md_driver.py Command Help  
Single Stage Radial Distribution Function Radial Distribution Function rdf rdf.py Command Help  
Single Stage Stress Strain Stress Strain stress stress_strain_driver.py Command Help  
Single Stage Structure Factor Structure Factor sq structure_factor_driver.py Command Help  
Single Stage Surface Tension Surface Tension surftens surface_tension_driver.py Command Help  
Single Stage Tg Thermophysical Properties tg thermophysical_properties_driver.py Command Help  
Single Stage Trajectory Density Analysis Trajectory Density Analysis density trajectory_density_analysis_driver.py Command Help  
Single Stage Viscosity Viscosity GK viscosity viscosity_gk_driver.py Command Help  

 

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