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.
Run PolyzyMD on SLURM Clusters
Add Distance Restraints
Set Up Equilibration Stages
Add Polymers to a Simulation
Generate Polymers from SMILES
Export a System to GROMACS
Troubleshoot Common Problems
Stable workflows:
Run RMSF Analysis
Run Distance Analysis
Run Contacts Analysis
Compare Simulation Conditions
Run Catalytic Triad Analysis
Experimental workflows:
Experimental: Analyze Binding Preference
Experimental: Analyze Binding Free Energy
Experimental: Analyze Polymer Affinity
Experimental: Analyze Exposure Dynamics
Contacts Cookbook
Broken Molecule Debugging