A production molecular dynamics run is where a carefully prepared system starts generating the trajectory you will analyze. But getting from equilibration to a useful result involves more than pressing Simulate: you need to select the right starting structure, carry forward compatible settings, choose an execution route, and decide what to import afterward. Missing one of these steps can make a run harder to interpret or repeat.
This guide focuses on that handoff in GROMACS Wizard, with practical checks to help keep the workflow clear.
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. GROMACS Wizard accepts either a GRO file from equilibration or a previous production run, or an equilibrated batch project. If you are continuing directly from the previous step, use the auto-fill control to populate the input path from the previous successful run. You can also browse for a GRO file yourself.
This is a small but useful safeguard: selecting the intended output from the previous step helps avoid accidentally starting from an unrelated structure.
Carry forward the right conditions
The Parameters section exposes commonly adjusted settings, including the integration time step and number of steps. Other GROMACS MD settings are available through All…. Defaults are provided, but the settings should still reflect the system and workflow you want to run.
Pay particular attention to coupling settings when moving from equilibration to production. The temperature-coupling parameters should correspond to those used for NVT equilibration, as should the temperature used for velocity generation if velocity generation is enabled. Pressure-coupling parameters should correspond to those used for NPT equilibration. Position-restraint options are filled automatically based on the input system.
For the tutorial, the parameters are reset to their defaults and the maximum number of steps is set to 50,000 so the example finishes quickly. Treat that number as a tutorial setting, not as a general recommendation for scientific production runs. The appropriate simulation length depends on your research question and system.
The advanced-parameter window also offers a useful route to consistency: reset settings to defaults, load parameters from an MDP file, or save the current parameters as an MDP file. Modified parameters are saved when SAMSON closes, so check them when starting a later session if you need to confirm what is selected.
Choose where the computation should run
GROMACS Wizard offers three routes. Generate inputs prepares a project you can run elsewhere, for example on a local cluster. Simulate locally runs on your PC using the shipped GROMACS or a version specified in settings. Simulate in the cloud is an option for jobs that need more resources than are available locally; cloud launches require computing credits.
For a local run, progress appears in the Output window. You can continue using SAMSON while the job runs, and use Local jobs to check the status of local GROMACS jobs. If you launch several jobs or a batch job, use this list to follow their state rather than expecting a single completion prompt.
Decide what to import—and what to inspect
When results are ready, dialogs let you choose options for RMSD and radius-of-gyration plots, and how much trajectory data to import: the whole trajectory, only the last frame, or a selected frame range. You can also choose periodic-boundary-condition treatment and what to center the system on, such as the protein.
Importing a trajectory is not required to keep the results. If you click Cancel in the import dialog, the results are not deleted and the plot can still be generated. The result files remain in the configured results folder, in a directory named with the launch date and time and a step suffix; production MD uses _md.
After the job finishes and results are loaded, GROMACS Wizard generates plots for radius of gyration and RMSD. These offer useful first checks on the trajectory, but they are not a substitute for analysis tailored to your scientific question. If you performed a pulling simulation, pull-force and pull-coordinate plots are generated as well. Save a plot using the Save button at the top of its figure.
A quick pre-run checklist
- Confirm that the input is the intended equilibrated GRO file or batch project.
- Check temperature coupling against NVT and pressure coupling against NPT.
- Review the number of steps and other parameters rather than relying on a tutorial example value.
- Choose local execution, input generation, or cloud computing based on where the required resources are available.
- Plan which trajectory frames and plots you need for your next analysis step.
For the complete workflow and interface details, see the GROMACS Wizard production MD documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.