Starting a molecular dynamics simulation is rarely just a matter of pressing “run.” Before the first production trajectory, a modeler needs to prepare the structure, define the system, relax it, and bring it to the intended temperature and pressure. Skipping a stage—or losing track of which files belong to which stage—can make a workflow confusing and difficult to reproduce.
GROMACS Wizard in SAMSON organizes these tasks into a clear sequence. The key idea is to treat simulation setup as a chain of dependent stages: each one prepares the system for the next. The tutorials often use the 1AKI structure, but the same overall route can be applied to other systems.
Follow the stages in order
- Pre-process the starting structure. Begin with Pre-processing. This is the point to load and prepare the molecular system before configuring it for GROMACS.
- Prepare the simulation system. In Step 1: Prepare, define the model and set up the simulation box, solvent, ions, and output files. These choices establish the system that the later stages will work on.
- Minimize energy. Step 2: Energy Minimization relaxes the prepared system before equilibration. It is a distinct stage, not a substitute for equilibration or production dynamics.
- Equilibrate at constant volume. In Step 3: NVT Equilibration, temperature is equilibrated while volume is held constant.
- Equilibrate pressure and density. Next, Step 4: NPT Equilibration handles pressure and density equilibration.
- Run production dynamics. Once the preceding stages are complete, continue to Step 5: Production Molecular Dynamics Simulation to run the production simulation and inspect results.
A simple way to avoid workflow confusion
Think of each stage as answering a different question. Is the starting structure ready? Has the simulation system been defined? Has the prepared system been relaxed? Have temperature and pressure been equilibrated? Only then is it time to run production dynamics. Keeping those questions separate makes it easier to identify where you are in the process and what needs attention before moving on.
It also helps to avoid jumping ahead. A task-specific tutorial may be useful on its own, but simulation steps depend on the appropriate prepared inputs. If you are new to the workflow, follow the recommended path from pre-processing through production rather than treating the stages as interchangeable.
Adapt the route to your system
The standard sequence is only the starting point. For example, a protein–ligand project has a dedicated protein-ligand workflow. If your preparation depends on box shape or minimum-image constraints, consult Periodic boundary conditions. Other tutorials cover batch computations, cloud jobs, custom index groups, coarse-grained systems, and advanced methods such as umbrella sampling and PMF analysis.
GROMACS Wizard includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If needed, it can also use a custom local installation; the settings tutorial explains custom versions and local performance parameters.
To install the extension, add GROMACS Wizard from SAMSON Connect and restart SAMSON so it can be downloaded and installed. For the complete tutorial map and links to each workflow, learn more in the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.