A molecular dynamics simulation can feel like one big task: prepare a system, choose settings, run it, and inspect the trajectory. In practice, it is a sequence of dependent steps. If the starting system is not ready, later stages may not have the inputs they need. A simple way to reduce that uncertainty is to treat the workflow as a series of checkpoints rather than jumping straight to production.
GROMACS Wizard brings these steps into SAMSON. It includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started; it can also use a custom local installation when needed.
Think in stages, not settings
The recommended route is useful because each stage prepares the ground for the next. Start by loading and preparing the molecular system. Then define the model and simulation setup, including the box, solvent, ions, and output files. Once the system is prepared, proceed through energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics.
- Pre-processing: get the starting structure ready before setting up the GROMACS workflow.
- Prepare: define the model, simulation 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 the results.
This sequence is more than a list of buttons to click. It is a useful troubleshooting map. When something is not ready for a later step, ask which earlier stage supplies the required starting point. For example, production is not the first destination: it follows system preparation and equilibration. Keeping the stages distinct also makes it easier to tell whether you are preparing an input system, relaxing it, bringing it to simulation conditions, or collecting production results.
Use the right starting point for your question
Not every project needs the same route. If your immediate task is a specific one—such as submitting a cloud job or creating custom index groups—you can go directly to that tutorial. But if the task relies on prepared simulation files, first complete the relevant earlier stages. This small check can save time spent trying to solve a downstream problem with an upstream input that is not ready.
Some projects also need a workflow beyond the standard sequence. Protein–ligand systems have a dedicated guide for parameterizing a ligand and preparing the complex. Periodic boundary conditions cover box choices and minimum-image constraints. For more advanced questions, the tutorial collection includes center-of-mass pulling, umbrella sampling, and potential-of-mean-force analysis. These are targeted paths—not steps every simulation must follow.
Before you begin
Add the GROMACS Wizard Extension from SAMSON Connect, then restart SAMSON so the extension can be downloaded and installed. The tutorials often use the 1AKI structure as an example, but the same overall route can be applied to your own systems.
A practical habit is to identify your next checkpoint before starting: What system are you preparing? Which stage are you trying to complete? What prepared input does the next stage depend on? That keeps a complex simulation workflow easier to navigate, especially when you return to a project later.
Follow the GROMACS Wizard tutorials for the full workflow and links to specialized guides.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.