User Guide# Introduction Workflow overview CLI Workflow Simulation Setup Preparing input structures Components, Chemical Systems and Thermodynamic Cycles Creating Atom Mappings Protocols in OpenFE Defining the Ligand Network Alchemical Networks: Planning a Simulation Campaign Execution Execution with Quickrun Parallel execution of repeats with Quickrun Optimizing GPU performance with NVIDIA MPS Task-based Execution Protocols and the Execution Model Theory Results Gathering Working with individual results Working with networks of results CLI Interface CLI basics Customising CLI planning with YAML settings Protocols Available protocols Choosing a protocol Domain of applicability See also References Under the Hood Troubleshooting Simulations Periodic box size / nonbonded cutoff errors SMIRNOFF force field parameter assignment errors NaN errors during simulation Validating your inputs with a plain MD simulation Resuming Interrupted Simulations Log Debug information JAX warnings PYMBAR_DISABLE_JAX CUDA-related errors
