A production molecular dynamics run is the step where an equilibrated system begins generating the trajectory you want to inspect and analyze. But starting the run is only part of the job: choosing the right input, carrying forward compatible settings, and deciding what to import afterward can all affect how useful the results are.
This workflow focuses on those practical decisions in SAMSON’s GROMACS Wizard. It is especially useful if you want to avoid a preventable setup mismatch or finish a run only to discover that you imported the wrong portion of the trajectory.
Start with the equilibrated system
Before launching production MD, complete NPT equilibration and confirm that the equilibrated system is the one you intend to continue simulating. In the Wizard’s Simulate tab, the input can be either a GRO file from equilibration or a previous production run, or a batch project from an equilibration or production run.
If you are continuing directly from the previous step, use the auto-fill button to populate the input path from the preceding successful project. This helps reduce path-selection mistakes. You can also browse for a GRO file yourself with the … button.
Check the settings that should carry forward
The Parameters section includes commonly adjusted controls such as the integration time step and number of steps. Other GROMACS options are available through All…. Defaults are provided, but it is worth checking the settings that connect production to the preceding equilibration stages.
In particular, ensure that the temperature coupling parameters match those used for NVT equilibration. If velocity generation is enabled, check that its temperature is consistent as well. The pressure coupling parameters should correspond to those used during NPT equilibration. Position-restraint options (POSRES*) are filled automatically based on the input system.
For the tutorial’s short demonstration run, the instructions use 50,000 steps so the calculation finishes quickly. Treat that as a tutorial setting, not a general recommendation for every scientific question: choose a run length appropriate to your system and simulation goals. If you need to restore the advanced settings, use Reset. You can also load parameters from an MDP file or save the current parameters to one.
Choose where the calculation runs
The Wizard offers three routes: generate inputs for use elsewhere, simulate locally on your PC, or simulate in the cloud. Local simulation is a straightforward choice for a run suited to your machine. Cloud simulation may suit larger systems, but it requires computing credits. Generating inputs is useful when you want to run the prepared project on a local cluster.
When running locally, progress is shown in the Output window. The job manager lets you continue using SAMSON and GROMACS Wizard during the calculation, and the Local jobs button provides access to job status. If you launch multiple jobs or a batch job, check their state there rather than expecting a single completion prompt.
Import only what you need
After the run, the import dialogs let you choose whether to bring in the complete trajectory, only its last frame, or a selected range of frames. They also offer options for periodic-boundary-condition treatment and for centering the system—for example, on the protein. Consider what you plan to inspect: a full trajectory is useful when you need to explore motion over time, while importing fewer frames can be more convenient when you only need a representative structure or a portion of the run.
The import dialogs also ask about generating RMSD and radius-of-gyration plots. If you do not want to import the trajectory, clicking Cancel does not delete the simulation results; the plot can still be generated. Results remain available in the configured results folder, in a folder named with the launch date and time and a step suffix such as _md.
Once loaded, the two standard plots show radius of gyration and RMSD for the selected structures. Pulling simulations generate two additional plots for pull force and coordinates. Use these plots as a first look at the run, then inspect the trajectory in the context of your simulation question. Figures can be saved with the Save button at the top of the plot.
A reliable production workflow is less about clicking through quickly and more about preserving continuity: start from the intended equilibrated system, verify coupling settings, select a run length for your purpose, and make deliberate import choices. For the full walkthrough, see the GROMACS Wizard production MD documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.