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User Guide

The User Guide covers every feature of PRISM in detail, from preparing input files to advanced free energy calculations.

How to Use This Guide

Each page follows the same structure: a Quick Start box with the essential command, a step-by-step walkthrough, an options reference table, and links to related pages. Read the pages in order for a full tour, or jump to a specific topic.

System Building

  • Input Files

    Prepare protein PDB and ligand MOL2/SDF files for PRISM

  • Building Systems

    Build GROMACS-ready protein-ligand systems with one command

  • Force Fields

    Choose from 8+ ligand force fields and multiple protein force fields

  • Configuration

    Customize simulation parameters with CLI flags or YAML files

Running and Analysis

  • Running Simulations

    Execute EM, NVT, NPT, and production MD with GROMACS

  • Analysis Tools

    Analyze trajectories: RMSD, contacts, H-bonds, interactive HTML reports

  • Output Files

    Understand the directory structure and file formats PRISM generates

Advanced Methods

  • PMF Calculations

    Binding free energy via steered MD, umbrella sampling, and WHAM

  • Troubleshooting

    Solutions for common build, simulation, and installation errors

What's Next