User Guide# Introduction Workflow overview CLI Workflow Simulation Setup ChemicalSystems, Components and Thermodynamic Cycles Chemical Systems Components Thermodynamic Cycles See Also Creating Atom Mappings Generating Mappings Visualising Mappings Scoring Mappings Creating and using Protocols Settings and creating Protocols Using Protocols Defining the Ligand Network Generating Ligand Networks Alchemical Networks: Planning a Simulation Campaign See Also Alchemical Networks: Creation Python API Alchemical Network Planners Command-line interface Execution Execution with Quickrun Executing within a job submission script See Also Protocols and the Execution Model Theory Working with Results Working with individual results From command line execution From Python execution See Also Working with networks of results Converting relative results to absolute estimates Gathering using the command line Using cinnabar directly See also CLI Interface CLI basics Customising CLI planning with yaml settings Customising the atom mapper Customising the network planner Details of Specific Protocols Relative Hybrid Topology Protocol Overview Scientific Details The Hybrid Topology approach The lambda schedule Simulation overview Simulation Steps Simulation details Getting the free energy estimate Analysis Energetic and replica exchange analysis Structural analysis See Also References Absolute Solvation Protocol Overview Scientific Details Partial annhilation scheme The lambda schedule Simulation overview Simulation steps Simulation details Getting the free energy estimate See Also References Plain MD Protocol Overview Scientific Details Simulation Steps and Outputs Performance consideration for gas phase MD simulations See Also References