A molecular dynamics project can feel like a chain of small decisions: prepare the structure, choose a model, add solvent and ions, relax the system, equilibrate it, and finally run the simulation. When these steps are approached out of order, it can be difficult to tell whether a problem comes from the structure, the setup, or the simulation itself.
GROMACS Wizard in SAMSON organizes these tasks into a sequence. The practical benefit is not just having the steps in one place: it is knowing what each stage is for, and what needs to be ready before moving to the next one.
Think in stages, not one long run
A standard workflow begins before GROMACS setup. First, load and prepare the starting molecular system. Then define the simulation model and environment, including the simulation box, solvent, ions, and output files. Once the system is prepared, the usual progression is energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics.
- Pre-processing: Get the starting structure ready for the GROMACS workflow.
- Preparation: Set up the model, box, solvent, ions, and output files.
- Energy minimization: Relax the prepared system before equilibration.
- NVT equilibration: Equilibrate temperature at constant volume.
- NPT equilibration: Equilibrate pressure and density.
- Production simulation: Run the molecular dynamics simulation and inspect the results.
This sequence is useful because each stage has a distinct role. Minimization comes before equilibration; equilibration comes before production. Treating these as separate milestones also makes it easier to locate where you are in the workflow and which tutorial is relevant when you need to revisit a decision.
Use the workflow as a readiness checklist
Before starting, identify the structure you want to simulate and decide whether the standard route applies. The tutorials use the 1AKI structure as an example, but the route can also be applied to your own systems. As you progress, keep track of the stage you have completed and the files or results you need for the next one. If a later task depends on prepared input files, complete the required earlier steps first rather than jumping ahead without them.
Not every project needs every tutorial. If your immediate task is cloud computing, custom index groups, or performance settings, you can go directly to the relevant guide. But tasks that rely on an already prepared system still need the appropriate setup beforehand. This simple distinction helps avoid following a full tutorial path when you do not need it, while also avoiding skipped prerequisites.
Branch out when the system calls for it
The main sequence is only one part of the tutorial collection. For a protein-ligand system, there is a workflow for parametrizing a ligand, combining it with a protein, and preparing the complex. For periodic systems, the dedicated guide covers box shapes and minimum-image constraints during preparation. Other routes address batch computations across systems or conformations, cloud jobs, and custom GROMACS installations and performance parameters.
There are also more specialized workflows. These include preparing coarse-grained systems, center-of-mass pulling, umbrella sampling, and potential of mean force analysis. Custom parameters are covered for cases where the standard preparation workflow is not enough. These are best treated as focused branches from the basic workflow: first establish the appropriate starting point, then follow the specialized guide for the task at hand.
Getting started
To use GROMACS Wizard, add the extension from SAMSON Connect and restart SAMSON so it can be downloaded and installed. The extension includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started; a custom local installation can also be used when needed.
If you are following the full molecular dynamics route, begin with Pre-processing. For the complete set of steps and specialized workflows, see the GROMACS Wizard tutorials.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.