Running a molecular dynamics (MD) production simulation can be a major milestone in the modeling of biomolecular systems. But this important step often becomes a source of confusion, especially when it comes to choosing the right input files and making sure all parameters are in sync with previous steps like equilibration. Small mismatches in temperature coupling, pressure settings, or even coordinate files can lead to wasted compute time or non-physical results.
If you are using the GROMACS Wizard in SAMSON, here’s a focused guide on how to correctly set up and launch a production MD simulation with minimal risk of mistakes.
💡 Select the Right Input — And Let SAMSON Help You
A key source of friction is selecting the correct input structure for the production run. GROMACS Wizard in SAMSON provides two options:
- The path to a previously generated GRO file (from NPT Equilibration or a previous production run).
- A complete batch project that already includes minimized and equilibrated structure(s).
If you’re working within a consistent project flow, simply click the Auto-fill button: 
. This will pull the latest relevant structure without needing to manually browse to the file.
🔧 Matching Parameters: Avoid Silent Misconfigurations
GROMACS expects consistency between phases. If your production run’s thermodynamic settings differ from equilibrium phases, you might not get physically meaningful results. SAMSON provides a reminder for this:
Important
Please ensure that the temperature coupling matches your NVT equilibration phase.
And verify that the pressure coupling matches your NPT phase too.
To look under the hood, click the All… button to unlock more advanced GROMACS parameters:
Got changes you want to save or reuse? You can load or export the configuration as an .mdp file.
Tip
- To reset parameters to defaults, click Reset.
- To load from a previous project, use Load from file….
- To save your current set, click Save as….
🚀 Choose Where to Run
You can launch the simulation:
- Locally on your machine
- In the Cloud with computing credits
- Or only generate input files for use elsewhere
Use the job manager to monitor progress. Simulations run in separate threads so you can keep using SAMSON for other tasks.
📊 What Happens After?
Once the run is complete, SAMSON prompts you to import results and review plots like RMSD and radius of gyration. Even if you decline to import the full trajectory, you’ll still get useful insights from generated plots.
Wrapping Up
Taking the time to correctly configure your production MD run can mean the difference between useful data and a frustrating re-run. Thanks to SAMSON’s GROMACS Wizard, many of these steps are made easier, faster, and less error-prone.
To learn more details, visit the full documentation page on Running Production MD Simulations with GROMACS Wizard in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.