A molecular dynamics workflow can feel like a chain of unrelated setup screens: prepare a structure, define a box, add solvent, minimize, equilibrate, and finally run production. The difficult part is often knowing what must happen first—and when it is safe to skip ahead.
GROMACS Wizard brings these stages together in SAMSON. A useful way to approach the workflow is to treat each stage as a handoff: the next step depends on the system and files prepared in the previous one. That simple idea helps prevent a common frustration: reaching a simulation step before its required starting point is ready.
Follow the workflow in order
- Pre-process the starting system. Begin by loading and preparing the molecular system before setting up GROMACS. The tutorials often use the 1AKI structure as an example, but the same general route can be applied to your own systems.
- Prepare the simulation system. Define the model and simulation box, configure solvent and ions, and specify output files. These choices establish the system that later stages will work with.
- Minimize energy. Energy minimization relaxes the prepared system before equilibration. It is a separate step, not a substitute for the temperature and pressure equilibration that follows.
- Equilibrate at constant volume (NVT). This stage equilibrates temperature while volume is held constant.
- Equilibrate at constant pressure (NPT). Next, equilibrate pressure and density.
- Run production molecular dynamics. Once the preceding stages are complete, run the production simulation and inspect the results.
Thinking in terms of handoffs is useful: before moving on, make sure you have completed the preceding stage and have the prepared inputs needed for the next one. The tutorial sequence provides a clear starting route, rather than asking you to choose among every available feature at once.
Branch only when your system needs it
Not every project is a standard protein simulation. If you are working with a protein–ligand complex, the dedicated workflow covers ligand parametrization, combining the ligand with a protein, and preparing the complex. If your setup requires periodic boundary conditions, consult that tutorial for box shapes and minimum-image constraints during system preparation.
Other tutorials address more specific needs: custom index groups for pulling or analysis, batch computations across systems or conformations, and cloud jobs that can be submitted, monitored, downloaded, and imported. Advanced workflows include coarse-grained systems, center-of-mass pulling, umbrella sampling, and potential of mean force analysis. These are useful branches when your research question calls for them, but they do not need to distract from the standard preparation-to-production path.
When can you skip ahead?
If you only need a focused task—such as configuring performance settings, creating custom index groups, or launching cloud jobs—you can go directly to its tutorial. But if that task depends on prepared simulation files, first complete the workflow up to the required starting point. This distinction can save time: skip unrelated tutorials, not prerequisites.
To get started, add the GROMACS Wizard Extension through SAMSON Connect and restart SAMSON so it can be installed. The extension includes a compatible GROMACS build, so a separate GROMACS installation is not required to begin; a custom local installation can also be used when needed.
For the complete tutorial sequence and links to each workflow, visit the GROMACS Wizard tutorials.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.