Starting a molecular dynamics simulation can feel like a collection of disconnected tasks: prepare a structure, choose a model, add solvent and ions, relax the system, and finally run the simulation. The difficult part is often not any one step—it is knowing what should come first, and which steps you can safely skip.
GROMACS Wizard in SAMSON organizes these tasks into a sequence, from initial system preparation through production molecular dynamics. Thinking of the process as a series of checkpoints helps make the workflow easier to follow and makes it clearer where a task-specific tutorial fits.
Follow the sequence when you are starting from a structure
For a standard workflow, the recommended route is:
- Pre-processing: load and prepare the starting molecular system before setting it up for GROMACS.
- Prepare: define the model and simulation box, add solvent and ions, and set output files.
- Energy minimization: relax the prepared system before equilibration.
- NVT equilibration: equilibrate temperature at constant volume.
- NPT equilibration: equilibrate pressure and density.
- Production molecular dynamics: run the production simulation and inspect results.
The order matters because later stages use the prepared inputs and system state from earlier stages. Minimization is not a substitute for preparing the system, and production is not the first stage to jump into when its required inputs have not yet been created. If you are following the full path, begin with pre-processing and move forward in sequence.
Use each stage as a checkpoint
Rather than treating the workflow as one long operation, think of each stage as a point to confirm that you have reached the intended starting condition for the next one. Preparation defines the simulation system; minimization relaxes it; equilibration proceeds in two distinct conditions—constant volume for NVT, then pressure and density for NPT—before production. This mental model can help you locate where to return if you need to revise an earlier choice.
The example tutorials often use the 1AKI structure, but the documentation notes that the same route can be applied to your own systems. The sequence is a guide to the workflow, not a requirement to use that example structure.
Branch off only when your task calls for it
Not every simulation project has the same needs. If you are working with a protein and ligand, the protein-ligand systems tutorial covers ligand parametrization, combining the ligand with a protein, and preparing the complex. For box geometry and minimum-image constraints, see periodic boundary conditions.
Other focused tasks include batch computations across multiple systems or conformations, and cloud jobs for submitting, monitoring, downloading, and importing computations. These can be useful entry points when you already have the appropriate inputs. If a task depends on prepared simulation files, first complete the workflow up to the starting point it requires.
Check installation before troubleshooting the workflow
GROMACS Wizard is an extension that integrates GROMACS workflows into SAMSON. It includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started; a custom local installation can also be used when needed. To install the extension, sign in to SAMSON Connect, add GROMACS Wizard to your account, and restart SAMSON so it can be downloaded and installed.
That gives you a simple starting rule: if you are new to the process, follow the standard sequence; if you have a specific goal, open its focused tutorial and check whether it depends on earlier preparation. For the full tutorial map and additional workflows, learn more in the GROMACS Wizard documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.