Starting a molecular dynamics simulation can feel like a collection of disconnected tasks: prepare a structure, choose a box, add solvent, minimize, equilibrate, and finally run production dynamics. The difficult part is often not any single step—it is knowing what must happen first, what depends on prepared input files, and where a specialized workflow fits.
GROMACS Wizard brings GROMACS workflows into SAMSON. It includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If you need to use a local installation, the extension can also be configured to use a custom GROMACS version.
Think in stages, not isolated buttons
A useful way to plan a simulation is to treat it as a sequence in which each stage produces the starting point for the next. This helps prevent a common source of frustration: reaching an equilibration or production step before the system and its input files are ready.
- Pre-process the starting structure. Load and prepare the molecular system before setting up the GROMACS run. The example tutorials often use the 1AKI structure, but the same overall route can be applied to other systems.
- Prepare the simulation system. Define the model and simulation box, then set up solvent, ions, and output files. These choices establish the system that later stages will work on.
- Minimize the energy. Relax the prepared system before moving into equilibration.
- Equilibrate at constant volume (NVT). This stage is used to equilibrate temperature while volume is held constant.
- Equilibrate at constant pressure (NPT). Continue by equilibrating pressure and density.
- Run production molecular dynamics. Once the earlier stages are complete, run the production simulation and inspect the results.
In other words, if you are new to the workflow, follow the sequence rather than jumping straight to production. The order gives you a practical checkpoint at each transition: a prepared system before minimization, a minimized system before equilibration, and an equilibrated system before the production run.
Choose a branch only when your system needs it
Not every project follows exactly the same route. The core sequence is a good starting point, while additional tutorials address specific requirements. For a protein-ligand complex, use the protein-ligand workflow to parametrize a ligand, combine it with a protein, and prepare the complex. If your setup depends on the shape of the periodic box or minimum-image constraints, consult the periodic-boundary-conditions tutorial during system preparation.
Other tasks are best treated as branches from the relevant point in the workflow:
- Multiple systems or conformations: use batch computations to apply a workflow across several inputs.
- Remote computation: the cloud tutorial covers submitting, monitoring, downloading, and importing GROMACS Wizard cloud jobs.
- Special analysis or simulation groups: custom index groups can be created for tasks such as pulling, analysis, or advanced setup.
- Custom computing environment: settings cover a custom GROMACS installation and local performance parameters.
- Advanced sampling: follow the tutorials for center-of-mass pulling, umbrella sampling, and potential-of-mean-force analysis when those methods are relevant to your question.
These branches are not substitutes for required preparation. If a task depends on prepared input files, complete the main workflow up to the starting point that task requires. Conversely, if you only need a specific task—such as configuring performance settings—you can go directly to its tutorial without completing every simulation stage.
A simple way to avoid setup detours
Before opening the workflow, identify what you have (a starting structure, a protein-ligand complex, or multiple conformations) and what you want to do (a standard production simulation, a batch, a cloud run, or an advanced sampling calculation). Then follow the core sequence until your system is ready for that task, and add only the relevant specialized steps. This small planning check makes it easier to tell whether a tutorial is a prerequisite or an optional branch.
To install GROMACS Wizard, add the extension from SAMSON Connect and restart SAMSON so it can be downloaded and installed. You can check for it under Home > Apps > Biology, in the SAMSON Extensions update preferences, or in your extensions on SAMSON Connect.
For the full tutorial sequence and links to each workflow, see the GROMACS Wizard tutorials.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.