# How-To Guides

How-to guides help you accomplish a specific task. Use this section when you
already know your goal and need the shortest practical route to it.

## Core Simulation Tasks

- [Run PolyzyMD on SLURM Clusters](../tutorials/hpc_slurm.md)
- [Add Distance Restraints](../tutorials/restraints.md)
- [Set Up Equilibration Stages](../tutorials/equilibration.md)
- [Add Polymers to a Simulation](../tutorials/polymers.md)
- [Generate Polymers from SMILES](../tutorials/dynamic_polymers.md)
- [Export a System to GROMACS](../tutorials/gromacs_export.md)
- [Troubleshoot Common Problems](../tutorials/troubleshooting.md)

## Analysis Tasks

Stable workflows:

- [Run RMSF Analysis](../tutorials/analysis_rmsf_quickstart.md)
- [Run Distance Analysis](../tutorials/analysis_distances_quickstart.md)
- [Run Contacts Analysis](../tutorials/analysis_contacts_quickstart.md)
- [Compare Simulation Conditions](../tutorials/analysis_compare_conditions.md)
- [Run Catalytic Triad Analysis](../tutorials/analysis_triad_quickstart.md)

Experimental workflows:

- [Experimental: Analyze Binding Preference](../tutorials/analysis_binding_preference.md)
- [Experimental: Analyze Binding Free Energy](../tutorials/analysis_binding_free_energy.md)
- [Experimental: Analyze Polymer Affinity](../tutorials/analysis_polymer_affinity.md)
- [Experimental: Analyze Exposure Dynamics](../tutorials/analysis_exposure_dynamics.md)

## Recipe Collections

- [Contacts Cookbook](../tutorials/analysis_contacts_cookbook.md)
- [Broken Molecule Debugging](../tutorials/broken_molecules_debugging.md)

<!-- IMAGE OPPORTUNITY: Add an annotated comparison project tree showing
`comparison.yaml`, `results/`, and `figures/`, or an example SLURM submission
flow diagram for HPC users. -->

```{toctree}
:hidden:
:maxdepth: 1

Run PolyzyMD on SLURM Clusters <../tutorials/hpc_slurm>
Add Distance Restraints <../tutorials/restraints>
Set Up Equilibration Stages <../tutorials/equilibration>
Add Polymers to a Simulation <../tutorials/polymers>
Generate Polymers from SMILES <../tutorials/dynamic_polymers>
Export a System to GROMACS <../tutorials/gromacs_export>
Troubleshoot Common Problems <../tutorials/troubleshooting>
Run RMSF Analysis <../tutorials/analysis_rmsf_quickstart>
Run Distance Analysis <../tutorials/analysis_distances_quickstart>
Run Contacts Analysis <../tutorials/analysis_contacts_quickstart>
Compare Simulation Conditions <../tutorials/analysis_compare_conditions>
Run Catalytic Triad Analysis <../tutorials/analysis_triad_quickstart>
Experimental: Analyze Binding Preference <../tutorials/analysis_binding_preference>
Experimental: Analyze Binding Free Energy <../tutorials/analysis_binding_free_energy>
Experimental: Analyze Polymer Affinity <../tutorials/analysis_polymer_affinity>
Experimental: Analyze Exposure Dynamics <../tutorials/analysis_exposure_dynamics>
Contacts Cookbook <../tutorials/analysis_contacts_cookbook>
Broken Molecule Debugging <../tutorials/broken_molecules_debugging>
```