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.
Tip
If you’re new to PolyzyMD, start with Tutorials instead. These guides assume you already have a working installation and know the basics.
Add polymers, restraints, equilibration stages, or export to GROMACS.
Pick the right analysis plugin and get results in a few commands.
Submit simulations or analysis jobs via SLURM.
Adjust themes, colors, and figure sizes for publication-quality output.
Simulation Setup
Build and configure your enzyme-polymer conjugate systems.
HPC & Job Submission
Run on SLURM clusters — from individual jobs to daisy-chained workflows.
Stable Analysis Workflows
These analysis plugins are well-tested and recommended for production use. See also Tutorial: Measure Polymer Shielding with SASA for a guided SASA walkthrough.
Plots & Troubleshooting
Customize publication-quality figures and debug common issues.
Tip
Want to use the PolyzyMD artifacts to make your own plots? See Create Custom Plots from Analysis Artifacts for a post-processing workflow that reads cached analysis artifacts and sidecars. Start with Customizing Plots for Publication if you want to customize PolyzyMD’s standard analysis plots.