A production molecular dynamics run is the part where a prepared, equilibrated system begins generating the trajectory you want to study. But starting the run is not always the hardest part. It is easy to select the wrong input, carry over inconsistent settings, or finish the simulation and then be unsure what to import or inspect.
A reliable workflow makes each decision visible: confirm the starting structure, check the parameters that should match equilibration, choose where to run, and decide how to handle the results. The steps below follow the GROMACS Wizard workflow in SAMSON, with particular attention to common points where a small oversight can lead to an unhelpful run.
1. Start from the system you actually equilibrated
Before setting up production MD, complete NPT equilibration and confirm that the equilibrated system is the one you intend to continue simulating. The production step can take either a GRO file from equilibration or an equilibrated batch project as input. It can also continue from the output of a previous production run.
If you are continuing from the immediately preceding successful step, use the auto-fill button to populate the input path. This reduces the chance of manually selecting an old or unrelated file. If you need a different starting point, browse for the GRO file yourself and verify that it belongs to the intended system.
2. Treat equilibration settings as continuity checks
The parameters shown in the Simulate tab include commonly adjusted settings such as the integration time step and the number of steps. More advanced GROMACS parameters are available through All…, and position-restraint options are populated automatically based on the input system.
Before launching, check the settings that should carry through from equilibration:
- Temperature coupling: ensure it corresponds to the NVT equilibration settings.
- Velocity generation: if enabled, make sure its temperature is consistent with the NVT setup.
- Pressure coupling: ensure it corresponds to the NPT equilibration settings.
These checks help preserve continuity between preparation and production rather than treating the production step as an unrelated run. If you have a project-specific parameter set, the advanced-parameters window can reset to defaults, load an MDP file, or save parameters to an MDP file. SAMSON also saves modified parameters when it closes, so review them rather than assuming a new session starts from untouched defaults.
For the tutorial, the maximum number of steps is set to 50,000 so the example finishes quickly. Treat that as a tutorial setting, not a universal production-run recommendation: choose the number of steps and time step to match your simulation goal.
3. Pick the execution route that fits the job
GROMACS Wizard offers three routes. Generate inputs creates a project you can run elsewhere, for example on a local cluster. Simulate locally runs on your PC using the shipped GROMACS version or one specified in the settings. Simulate in the cloud is an option for larger systems that need more resources than are available locally; cloud execution requires computing credits.
For a local run, progress appears in the Output window, and the Local jobs button lets you check job status. You can continue using SAMSON and GROMACS Wizard while calculations are running.
4. Make the result import match the question
When a run finishes, the import dialogs let you choose whether to load the whole trajectory, only the last frame, or a range of frames. You can also select periodic-boundary-condition treatment and choose what to center the system on, such as the protein. These choices affect what you bring into the working view; the results remain available in the results folder even if you cancel trajectory import.
Production runs can generate plots for radius of gyration and RMSD. The RMSD plot compares the selected structures—for example, the backbone—to the corresponding structure in the initial equilibrated system. If the run involved pulling, plots for pull force and coordinates are generated as well. The figures are saved when the job finishes and results are loaded, and the Save button lets you save a plot separately.
A useful final check is to ask whether the input, parameter choices, and imported frames all match the analysis you plan to do next. That simple habit makes it easier to distinguish a simulation that merely ran from one whose outputs are ready for your workflow.
For the complete walkthrough, see the GROMACS Wizard production MD documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.