A molecular dynamics simulation can feel like one long task, but it is really a chain of dependent steps. A system that has not been prepared for the next stage can leave you unsure where to start—or whether a later tutorial applies to your current files. A more reliable approach is to treat the workflow as a sequence, and to branch off only when your goal calls for it.
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 needed, you can also configure a custom local installation.
Think in stages, not buttons
The standard route has six stages. Each has a distinct purpose, and following them in order helps keep the starting point for each task clear:
- Pre-process: Load and prepare the starting molecular system before setting it up for GROMACS. Begin with the Pre-processing tutorial.
- Prepare: Define the model, simulation box, solvent, ions, and output files. This is where the initial system is configured for the workflow. See Step 1: Prepare.
- Minimize energy: Relax the prepared system before equilibration. Continue with Step 2: Energy Minimization.
- Equilibrate at constant volume: NVT equilibration focuses on temperature at constant volume. Follow Step 3: NVT Equilibration.
- Equilibrate pressure and density: NPT equilibration follows NVT in the recommended path. See Step 4: NPT Equilibration.
- Run production MD: Once the earlier stages are complete, run the production molecular dynamics simulation and inspect the results. The guide is Step 5: Production Molecular Dynamics Simulation.
The practical benefit of this sequence is that it gives you a simple diagnostic question: What is the earliest stage I have not completed? If you are unsure whether to begin equilibration or production, trace the workflow back to its required starting point instead of jumping ahead. The tutorials use the 1AKI structure as an example, but the same route can be applied to your own systems.
Choose a branch only when it fits the job
Not every project needs every tutorial. Once you know the standard route, select a focused branch according to the actual challenge:
- For box geometry and minimum-image constraints, use Periodic boundary conditions.
- For a ligand combined with a protein, see Protein-ligand systems.
- For custom groups used in pulling, analysis, or advanced setup, consult Adding custom index groups.
- For repeating a workflow across systems or conformations, use Batch computations.
- For submitting and managing cloud jobs, see Launching computations in the Cloud.
- For a custom GROMACS installation or local performance settings, consult Using custom GROMACS version and performance parameters.
There are also advanced routes for specific questions: coarse-grained preparation, center-of-mass pulling, umbrella sampling, and potential of mean force analysis. These are useful when the study calls for those methods, rather than steps every standard simulation must include. The corresponding guides cover coarse-grained systems, COM pulling, umbrella sampling, and PMF analysis.
A useful starting checklist
Before opening a tutorial, name your immediate goal: prepare a system, complete a standard simulation, or solve a focused task such as running cloud jobs. Then check whether that task depends on prepared input files. If it does, follow the recommended path far enough to create the required starting point. If it does not, you can go directly to the relevant page. This small distinction saves time without skipping prerequisites.
To install GROMACS Wizard, add the extension from SAMSON Connect and restart SAMSON so it can be downloaded and installed. If you are following the full molecular dynamics path, start with Pre-processing. For the complete tutorial map, visit the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.