A production molecular dynamics run is where an equilibrated system begins generating the trajectory you hope to analyze. It is also where small setup oversights can become frustrating: starting from the wrong structure, changing coupling settings unintentionally, or finishing a simulation without knowing where its results went.
This guide focuses on a reliable handoff from equilibration to production using GROMACS Wizard in SAMSON. The central idea is simple: verify the input, preserve the intended simulation conditions, and decide how you want to use the results before launching the job.
1. Start from the equilibrated system you actually intend to continue
Production should follow a successful NPT equilibration. Before proceeding, confirm that the equilibrated system is the one you want to simulate further. GROMACS Wizard accepts either a GRO file from the previous step or an equilibrated batch project. If you are continuing directly from the previous successful run, the auto-fill button can populate the input path for you. You can also choose a GRO file manually.
This is a useful moment to pause: an automatically filled path is convenient, but it is still worth checking that it points to the expected project or structure. A correct simulation configuration cannot compensate for an unintended starting structure.
2. Treat parameter continuity as part of the setup
The common production settings are available in the Parameters section of the Simulate tab. These include values modelers may adjust frequently, such as the integration time step and number of steps. Additional GROMACS options are available through All…, and parameters can be reset, loaded from an MDP file, or saved to one.
Two checks deserve particular attention. First, ensure that the temperature-coupling parameters correspond to those used during NVT equilibration, including the temperature used for velocity generation if velocity generation is enabled. Second, ensure that the pressure-coupling parameters correspond to those used during NPT equilibration. These checks help avoid changing the intended setup accidentally when moving between stages.
Position-restraint options (POSRES*) are filled automatically based on the input system. Still, review the broader parameter set if your workflow uses custom settings. For this tutorial, the instructions reset parameters to defaults and set the maximum number of steps to 50,000 so the run finishes quickly. That is a tutorial setting—not a general recommendation for production length. Choose the duration and other parameters for your scientific question and workflow.
3. Choose how the job will run
GROMACS Wizard offers three routes: generate inputs for use elsewhere, simulate locally on your computer, or simulate in the cloud. Local execution uses the shipped GROMACS version or a version specified in the settings. Cloud execution can suit systems that need more resources than are available locally and requires computing credits. Generating inputs is an option when you want a ready-to-use project to run, for example, on a local cluster.
If you choose Simulate locally, progress appears in the Output window. You can continue using SAMSON while the computation runs and check job status through Local jobs. For multiple jobs or a batch job, use that list to monitor their state rather than expecting a single completion prompt.
4. Decide what to import—and keep the files either way
When results are ready, dialogs let you choose options for RMSD and radius-of-gyration plots, as well as how much trajectory to import. You can select the whole trajectory, only the last frame, or a range of frames; choose periodic-boundary-condition treatment; and choose what to center the system on, such as the protein.
Importing a large trajectory may not be necessary for every immediate task. If you do not want to import it, clicking Cancel does not delete the simulation results; the plot is still generated. Results remain accessible in the results folder specified in GROMACS Wizard. Folders include the launch date and time and a step description; production MD folders use the suffix _md.
After the run, GROMACS Wizard generates radius-of-gyration and RMSD plots. RMSD is calculated for the chosen structures—for example, the backbone relative to the backbone in the initial equilibrated system. Pulling simulations can also produce plots of pull force and coordinates. You can save a plot using the Save button at the top of its figure.
A useful end-of-run routine is to confirm that the expected job finished, locate its results folder, review the plots, and inspect the trajectory using import choices suited to your next analysis. This keeps the simulation output usable without requiring you to import more frames than you need right away.
For the full workflow and interface details, see the GROMACS Wizard production MD tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.