GROMACS Wizard tutorials

Use these tutorials to prepare, minimize, equilibrate, simulate, and analyze molecular systems with GROMACS Wizard in SAMSON.

GROMACS Wizard integrates GROMACS workflows directly into SAMSON. It ships with a compatible GROMACS build, so you can start without installing GROMACS separately, and it can also use a custom local GROMACS installation when needed.

Who this is for

Use this tutorial family if you want to:

• prepare molecular systems for GROMACS simulations
• run energy minimization, equilibration, and production molecular dynamics
• work with protein-ligand systems, periodic boundary conditions, batch computations, or cloud jobs
• continue into advanced workflows such as center-of-mass pulling, umbrella sampling, and PMF analysis

Before you start

• Add the GROMACS Wizard Extension from SAMSON Connect.
• Restart SAMSON so the extension is downloaded and installed.
• If you are new to molecular dynamics in SAMSON, follow the recommended path below in order.
• The tutorials often use the 1AKI structure as an example, but you can apply the same route to your own systems.

Recommended path

Follow this sequence for a standard molecular dynamics workflow:

1. Pre-processing - load and prepare the starting molecular system before GROMACS setup.
2. Step 1: Prepare - define the model, simulation box, solvent, ions, and output files.
3. Step 2: Energy Minimization - relax the prepared system before equilibration.
4. Step 3: NVT Equilibration - equilibrate temperature at constant volume.
5. Step 4: NPT Equilibration - equilibrate pressure and density.
6. Step 5: Production Molecular Dynamics Simulation - run the production molecular dynamics simulation and inspect results.

Common workflows

• Periodic boundary conditions - choose box shapes and satisfy minimum-image constraints during system preparation.
• Protein-ligand systems - parametrize a ligand, combine it with a protein, and prepare the complex.
• Adding custom index groups - create custom groups for pulling, analysis, or advanced simulation setup.
• Batch computations - prepare and run the same workflow across multiple systems or conformations.
• Launching computations in the Cloud - submit, monitor, download, and import GROMACS Wizard cloud jobs.
• Using custom GROMACS version and performance parameters - configure a custom GROMACS installation and tune local performance.

Advanced workflows

• Coarse-grained systems - prepare coarse-grained systems for later minimization, equilibration, and simulation.
• COM pulling - perform center-of-mass pulling simulations.
• Umbrella Sampling - generate umbrella sampling projects from trajectories, conformations, or paths.
• Potential of Mean Force analysis - compute a PMF with weighted histogram analysis after umbrella sampling.
• Applying custom parameters - apply custom parameters when the standard preparation workflow is not enough.

What you can skip

If you only need a specific task, such as cloud jobs, custom index groups, or custom performance settings, you can jump directly to that page. For simulation tasks that depend on prepared input files, complete the recommended path up to the required starting point first.

Installing GROMACS Wizard

To install GROMACS Wizard:

1. Sign in on SAMSON Connect.
2. Open the GROMACS Wizard Extension page.
3. Click Add to add the extension to your account.
4. Restart SAMSON so the extension is downloaded and installed.

You can check whether GROMACS Wizard is installed in Home > Apps > Biology, in Interface > Preferences > Updates > SAMSON Extensions, or under User > My Extensions when you are signed in at SAMSON Connect.

Related tutorials

• Protein preparation and validation - prepare protein structures before simulation.
• Create molecular boxes with Molecular Box Builder - build molecular boxes and lipid-layer systems.
• Interactive Modeling Universal Force Field - perform interactive force-field based modeling.
• Pathlines - visualize motion of the center of mass of an atomic system.

Next step

Start with Pre-processing if you are following the full molecular dynamics path.