A molecular dynamics run is rarely just a matter of pressing “simulate.” Before a trajectory can be useful, the starting structure has to be prepared, a model and simulation box defined, and the system taken through minimization and equilibration. It is easy to lose track of what comes next—or to open a later tutorial before its input files are ready.
The GROMACS Wizard tutorials in SAMSON offer a practical sequence for moving from a molecular structure toward a production simulation. The key is to treat the process as a chain of dependent stages: each step prepares the system for the next, rather than being an isolated button to click.
Follow the dependency chain
- Pre-process the starting structure. Begin by loading and preparing the molecular system. The tutorial uses the
1AKIstructure as an example, but the route can also be applied to your own systems. - Prepare the simulation system. Define the model, simulation box, solvent, ions, and output files. These choices establish the system that later stages will work with.
- Minimize energy. Relax the prepared system before moving on to equilibration.
- Equilibrate at constant volume (NVT). This stage focuses on temperature while the volume is held constant.
- Equilibrate at constant pressure (NPT). Continue by equilibrating pressure and density.
- Run production molecular dynamics. Once the preceding stages are complete, run the production simulation and inspect its results.
This order helps answer a useful question at each stage: What has to exist before I can start the next task? If a tutorial depends on prepared input files, complete the relevant earlier stages first. If your immediate need is a standalone task—such as configuring performance settings or submitting a cloud job—you can jump directly to that tutorial instead.
Choose a route that matches the system
The standard sequence is only one part of the tutorial collection. For a protein-ligand project, the dedicated workflow explains how to parametrize a ligand, combine it with a protein, and prepare the complex. If the system needs periodic boundary conditions, the corresponding guide covers box shapes and minimum-image constraints during preparation. These are useful places to pause and check that the workflow matches the system you are actually building.
Other tutorials address needs that often arise after the basic setup is understood. Custom index groups can be created for pulling, analysis, or advanced simulation setup. Batch computations provide a route for applying a workflow across multiple systems or conformations. For jobs that should run in the cloud, the cloud guide covers submitting, monitoring, downloading, and importing jobs. You can also configure a custom local GROMACS installation and tune local performance parameters when needed.
Know when to move beyond the standard path
Some projects require additional methods rather than a different version of the basic sequence. The advanced tutorials cover coarse-grained systems, center-of-mass pulling, umbrella sampling, and Potential of Mean Force analysis. Custom parameters are available for cases where the standard preparation workflow is not enough. In particular, the PMF tutorial follows umbrella sampling, so it makes sense to approach those pages in that order when building that type of analysis.
GROMACS Wizard includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If you do need a custom local version, the settings tutorial explains that option. To install the extension, add GROMACS Wizard from SAMSON Connect, then restart SAMSON so the extension is downloaded and installed.
A simple way to avoid getting lost is to write down your intended route before starting: identify the system type, follow the preparation steps it needs, and only then choose the simulation or analysis workflow. For the complete tutorial sequence and links to each guide, visit the GROMACS Wizard tutorials.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.