A molecular dynamics project can feel like a collection of unrelated setup tasks: prepare a structure, define a box, add solvent and ions, choose simulation stages, then work out how to inspect the results. The risk is not just getting stuck—it is starting a later step before the files and system it depends on are ready.
A useful way to reduce that friction is to treat the workflow as a sequence of handoffs. Each stage should leave you with the prepared inputs needed by the next one. GROMACS Wizard brings these stages into SAMSON, and includes a compatible GROMACS build so you can begin without installing GROMACS separately. If your work requires it, the extension can also use a custom local GROMACS installation.
Think in stages, not settings
For a standard molecular dynamics workflow, the recommended path has six stages. The first is pre-processing: load and prepare the starting molecular system before GROMACS setup. Next, prepare the simulation model by defining the model, simulation box, solvent, ions, and output files. These are distinct tasks, so keeping them grouped in the preparation stage helps make the transition from a molecular structure to a simulation-ready system easier to follow.
- Pre-processing: prepare the starting system.
- Prepare: define the model, box, solvent, ions, and output files.
- Energy minimization: relax the prepared system.
- NVT equilibration: equilibrate temperature at constant volume.
- NPT equilibration: equilibrate pressure and density.
- Production molecular dynamics: run the production simulation and inspect results.
The order matters because each stage has a different purpose. Minimization is not the production run; it is the relaxation step that comes first. NVT and NPT equilibration are also separate stages, with different conditions and aims. Keeping those distinctions visible makes it easier to understand where a project is, and what kind of output to look for before proceeding.
A practical checkpoint at every handoff
Before moving forward, pause and ask three simple questions: Have I completed the task this stage is meant to handle? Do I have the starting files needed for the next stage? Am I following the standard route, or does my system need a specialized workflow? These questions do not replace the individual tutorials; they help you navigate them without treating every page as a mandatory step for every project.
For example, the tutorial family often uses the 1AKI structure, but the same route can be applied to your own systems. If you are building a protein–ligand system, consult the dedicated protein-ligand workflow. If your setup needs a particular box shape or minimum-image constraints, review periodic boundary conditions while preparing the system, rather than treating box selection as an afterthought.
When it is fine to skip ahead
Not every user needs to run the full sequence. If your immediate task is cloud submission, custom index groups, or local performance settings, you can go directly to the relevant tutorial. The important distinction is whether that task depends on prepared simulation inputs. When it does, first complete the workflow up to the required starting point. This prevents a common source of confusion: opening an advanced task and discovering that it assumes a system or files you have not prepared yet.
For repeated systems or conformations, the batch computations tutorial covers running the same workflow across multiple inputs. For calculations that continue beyond a standard production run, the tutorial set also includes umbrella sampling and PMF analysis. These are extensions of the basic route, not substitutes for preparing the starting system.
Start with the next useful step
If you are new to GROMACS Wizard, begin with pre-processing and follow the recommended path in order. If you already have a prepared system, jump to the page that matches your next task and check its required starting point. The complete tutorial index is available in the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.