Starting a molecular dynamics simulation can feel like a file-format problem disguised as a science problem: there are several preparation steps, each produces inputs for the next, and it is not always obvious where to begin. Skipping ahead can leave you without the prepared files a later task depends on.
GROMACS Wizard brings a sequence of GROMACS workflows into SAMSON. The key is to treat the process as a chain: prepare the starting structure, set up the system, relax it, equilibrate it, and only then run production dynamics. This route helps you keep track of what each stage is for—and where to resume if you only need part of the workflow.
Follow the dependency chain
- Pre-process the starting system. Begin with the structure you want to simulate and prepare it before GROMACS setup. The tutorials use the 1AKI structure as an example, but the same route can be applied to your own systems.
- Prepare the simulation system. Define the model and set up the simulation box, solvent, ions, and output files. These choices establish the system that the subsequent simulation steps will use.
- Minimize the energy. Relax the prepared system before equilibration. This is the next stage in the recommended sequence, not a substitute for system preparation.
- Equilibrate in two stages. NVT equilibration adjusts temperature at constant volume. NPT equilibration then addresses pressure and density. Keeping these stages in order makes the intended progression explicit.
- Run production molecular dynamics. Once the recommended preparation and equilibration path is complete, run the production simulation and inspect the results.
In short: Pre-processing → Prepare → Energy Minimization → NVT → NPT → Production MD.
Know when you can jump ahead
You do not have to follow every tutorial for every task. If your immediate goal is a cloud job, a custom index group, or performance settings, you can go straight to the relevant page. But first check what that task depends on: simulation work that needs prepared input files still requires you to complete the workflow up to the appropriate starting point.
The same distinction is useful for specialized systems. The tutorial collection includes separate routes for protein–ligand systems, periodic boundary conditions, coarse-grained systems, and batch computations. Advanced topics include center-of-mass pulling, umbrella sampling, and potential of mean force analysis. These are options for particular modeling goals, rather than extra steps every user must add to a standard simulation.
Remove installation friction
GROMACS Wizard includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If you need one, the extension can also use a custom local GROMACS installation. To install the extension, sign in to SAMSON Connect, add GROMACS Wizard, and restart SAMSON so it can be downloaded and installed.
A practical way to stay oriented is to write down your immediate goal, identify the prepared inputs it requires, and follow the sequence only as far as needed. For the full set of tutorials and the recommended route, learn more in the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.