A molecular dynamics project can feel like a chain of unrelated setup tasks: prepare a structure, choose a box, add solvent and ions, minimize, equilibrate, and finally run production dynamics. The hard part is often knowing what needs to happen next—and which steps you can safely skip.
GROMACS Wizard brings these stages together in SAMSON. A useful way to approach the workflow is to treat each stage as a handoff: prepare the system, relax it, bring it to the conditions you want, and then run the simulation you intend to analyze. That simple map can help you avoid jumping into a later task before its required input is ready.
Think in stages, not settings
1. Pre-process the starting structure. Begin with the molecular system you want to simulate. The pre-processing tutorial covers loading and preparing the starting system before GROMACS setup. The examples often use the 1AKI structure, but the same workflow can be applied to your own systems.
2. Prepare the simulation system. Define the model and simulation box, add solvent and ions as needed, and choose output files. These decisions establish the system that later simulation steps will use. If your work involves a protein and a ligand, follow the dedicated protein-ligand workflow for ligand parametrization and complex preparation.
3. Minimize before equilibrating. Energy minimization relaxes the prepared system before equilibration. It is a distinct step in the recommended route, rather than a substitute for equilibration.
4. Equilibrate in sequence. NVT equilibration brings the system to temperature at constant volume. NPT equilibration then addresses pressure and density. Keeping these stages in order makes the purpose of each one easier to follow.
5. Run production dynamics. Once the preceding stages are complete, run the production molecular dynamics simulation and inspect the results. If you are following the standard path for the first time, use the full sequence rather than jumping straight to production.
Choose the right route for your problem
Not every project needs every tutorial. For a standard molecular dynamics workflow, follow the recommended sequence: Pre-processing, Prepare, Energy Minimization, NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics.
If you already have the inputs required for a particular task, you can go directly to a focused tutorial. For example, the periodic boundary conditions guide covers box shapes and minimum-image constraints, while the batch computations guide explains how to run a workflow across multiple systems or conformations. Cloud jobs, custom index groups, and custom GROMACS settings also have dedicated guides. The key is to check whether a task depends on prepared input files; if it does, complete the necessary earlier steps first.
Get started without a separate GROMACS installation
GROMACS Wizard includes a compatible GROMACS build, so you can begin without installing GROMACS separately. If your workflow calls for it, the extension can also use a custom local GROMACS installation. To get started, add the GROMACS Wizard Extension from SAMSON Connect and restart SAMSON so the extension is downloaded and installed.
For the complete tutorial collection and links to each workflow, visit the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.