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Site Navigation

  • Installation
  • Tutorials
  • User Guide
  • Cookbook
  • Reference
    • Changelog
  • GitHub

Section Navigation

  • Introduction
  • Simulation Setup
    • ChemicalSystems, Components and Thermodynamic Cycles
    • Creating Atom Mappings
    • Creating and using Protocols
    • Defining the Ligand Network
    • Alchemical Networks: Planning a Simulation Campaign
    • Alchemical Networks: Creation
  • Execution
    • Execution with Quickrun
    • Protocols and the Execution Model Theory
  • Working with Results
    • Working with individual results
    • Working with networks of results
  • CLI Interface
    • CLI basics
    • Customising CLI planning with YAML settings
  • Details of Specific Protocols
    • Relative Hybrid Topology Protocol
    • Absolute Solvation Protocol
    • Plain MD Protocol
  • Troubleshooting Simulations
  • User Guide
  • Execution

Execution#

With a Transformation defined, the next step is to execute this. The easiest way to run it is to use the quickrun CLI tool. More advanced options are available through first considering the theory of the execution model then reading on the available Python functions.

  • Execution with Quickrun
    • Executing within a job submission script
    • See Also
  • Protocols and the Execution Model Theory

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