A production molecular dynamics run is where a prepared system begins generating the trajectory you want to inspect and analyze. But it is also an easy point to lose continuity: selecting the wrong starting structure, changing coupling settings unintentionally, or importing more trajectory data than you need can complicate the next steps.
A reliable approach is to treat production as a handoff. Start from the system that completed equilibration, carry forward the relevant settings, decide what you need from the run, and plan how you will review the results.
1. Confirm the starting point
Before launching, check that NPT equilibration completed successfully and that the equilibrated system is the one you intend to continue simulating. In GROMACS Wizard, production can start from a GRO file produced by equilibration or by an earlier production run. It can also start from an equilibrated batch project or a project from a previous production run.
If you are continuing from the previous step, the auto-fill control can populate the input path from the previous successful run. This reduces manual path entry, but it is still worth checking that the selected file or project is the intended one. If you prefer, browse to a GRO file yourself.
2. Preserve the equilibration settings that matter
The Parameters section contains commonly adjusted production settings, including the integration time step and number of steps. Other GROMACS parameters are available through All…, where you can review advanced options or apply custom parameters.
Two checks are especially useful before you run:
- Temperature coupling: make sure these parameters correspond to those used during NVT equilibration. If velocity generation is enabled, check that its temperature is consistent too.
- Pressure coupling: make sure these parameters correspond to those used during NPT equilibration.
Position-restraint options beginning with POSRES are filled automatically based on the input system. For a short tutorial run, the documented example resets parameters to their defaults and sets the maximum number of steps to 50,000 so the calculation finishes quickly. That value is a tutorial choice, not a universal production-run recommendation.
Need to reuse a setup? The advanced-parameters window lets you reset to defaults, load parameters from an MDP file, or save the current parameters to an MDP file. Keep in mind that modified parameters are saved when SAMSON closes, so settings may still be present the next time you open it.
3. Choose where the computation should run
GROMACS Wizard offers three routes: generate project inputs for another environment, simulate locally using the shipped GROMACS or a version configured in settings, or launch in the cloud. Cloud computing can suit systems that require more resources than are available locally, and requires computing credits.
For a local run, choose Simulate locally. Progress appears in the Output window, and the Local jobs control lets you check job status. You can continue using SAMSON and GROMACS Wizard while calculations are running.
4. Make the results useful to your next decision
When a single project finishes and there are no other projects in the local job queue, a dialog can appear with import options. With multiple jobs or a batch job, check their state under Local jobs.
During import, you can choose whether to load the whole trajectory, only its last frame, or a range of frames. You can also choose periodic-boundary-condition treatment and what to center the system on, such as the protein. These choices affect what you bring into SAMSON for inspection; they do not delete the results stored in the results folder. If you cancel trajectory import, the results remain and the plots can still be generated.
After the run, GROMACS Wizard generates plots for radius of gyration and RMSD. If the simulation includes pulling, such as in an umbrella-sampling workflow, plots for pull force and coordinates are also generated. The plots are saved when the job finishes and its results are loaded; use the figure’s Save button to save a plot separately.
A useful final habit is to check both the trajectory and the plots before deciding what to do next. Confirm that the imported frames and centering suit your inspection, then save any figures you want to keep. Production is not just a compute step: it is the point where a carefully chosen input and consistent settings become results you can review and use in further analysis.
For the complete workflow and interface details, learn more in the GROMACS Wizard production MD documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.