A molecular dynamics project can feel like a chain of disconnected tasks: prepare a structure, configure a system, minimize it, equilibrate it, and finally run production dynamics. The difficult part is often knowing what needs to happen next—and which steps depend on files or decisions made earlier.
GROMACS Wizard in SAMSON brings these tasks into a connected workflow. A useful way to approach it is to treat each stage as a checkpoint: finish the current stage, understand what it produces, and then move forward. That makes it easier to spot where a problem began instead of trying to troubleshoot the whole simulation at once.
Think in checkpoints, not one long setup
1. Prepare the starting structure. Begin with pre-processing: load and prepare the molecular system you intend to simulate. The tutorials use the 1AKI structure as an example, but the same overall route can be applied to your own systems. Before moving on, be clear about what system you are starting from and whether it needs a specialized workflow, such as protein-ligand preparation.
2. Define the simulation system. In the preparation stage, set up the model, simulation box, solvent, ions, and output files. These choices shape the system that later stages will work on. If periodic boundary conditions are relevant, review the guidance on box shapes and minimum-image constraints as part of this preparation work.
3. Relax before measuring dynamics. Energy minimization comes next, followed by NVT equilibration at constant volume and then NPT equilibration for pressure and density. Keeping these stages in order gives you a clear progression from preparing the system to equilibrating it, before starting production molecular dynamics.
4. Run production and inspect results. Once the preceding stages are complete, continue to production molecular dynamics and examine the results. Thinking of production as a later checkpoint can help prevent a common planning mistake: treating the production run as the entire simulation workflow.
Choose the route that matches the job
Not every project needs every tutorial. For a standard molecular dynamics workflow, follow the sequence from pre-processing through production. If you are working on a particular task—such as cloud jobs, custom index groups, or local performance settings—you can go directly to that topic. The important distinction is whether the task depends on prepared input files. When it does, complete the necessary preparation stages first.
Some projects need additional planning. Protein-ligand systems have a dedicated workflow for parametrizing a ligand and preparing the complex. Batch computations are intended for repeating a workflow across multiple systems or conformations. Cloud tutorials cover submitting, monitoring, downloading, and importing jobs. Advanced work can continue into center-of-mass pulling, umbrella sampling, and potential of mean force analysis. These are not interchangeable steps in a basic simulation sequence; they are routes to consider when the research question calls for them.
Reduce setup friction
GROMACS Wizard includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If your work calls for it, the extension can also use a custom local GROMACS installation, with settings for performance parameters.
To get started, add the GROMACS Wizard Extension from SAMSON Connect and restart SAMSON so it can be downloaded and installed. You can check whether it is available under Home > Apps > Biology, in Interface > Preferences > Updates > SAMSON Extensions, or in User > My Extensions on SAMSON Connect.
A practical habit is to write down your intended route before opening the setup: standard MD, protein-ligand, batch, cloud, or an advanced workflow. Then use the relevant tutorials as checkpoints rather than trying to absorb every option at once. For the full sequence and links to each workflow, see the GROMACS Wizard tutorials.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.