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.

Simulation Setup

Add polymers, restraints, equilibration stages, or export to GROMACS.

Analysis Workflows

Pick the right analysis plugin and get results in a few commands.

HPC & Job Submission

Submit simulations or analysis jobs via SLURM.

Plots & Troubleshooting

Adjust themes, colors, and figure sizes for publication-quality output.

Simulation Setup

Build and configure your enzyme-polymer conjugate systems.

Run on SLURM clusters — from individual jobs to daisy-chained workflows.

These analysis plugins are well-tested and recommended for production use. See also Tutorial: Measure Surface Accessibility with the SASA Plugin for a guided SASA walkthrough.

Warning

These workflows are available in PolyzyMD but their interpretation is still evolving. Treat results as exploratory, not settled science.

Customize publication-quality figures and debug common issues.