Running a production Molecular Dynamics (MD) simulation can be both exciting and daunting, especially after spending valuable time setting up and equilibrating your system. But before pressing that Simulate button in the SAMSON GROMACS Wizard, it’s critical to double-check that your simulation parameters are set correctly. Otherwise, you might find out minutes—if not hours—later that the simulation needs to be redone.
If you’re like many molecular modelers, you’ve probably run into the frustration of mismatched temperature or pressure configurations, or forgotten to apply your preferred constraints. This blog post highlights a few key things to double-check when setting up your production simulation in SAMSON using the GROMACS Wizard Extension. These simple tips can save you from reruns and help you move confidently toward your results 📊.
💡 Check 1: Match Temperature and Pressure Parameters
Before running your production MD, ensure that the temperature coupling and pressure coupling parameters are carried over correctly from the NVT and NPT equilibration steps, respectively.
Important: The temperature for velocity generation (if enabled) should match your system’s equilibrated temperature. Same for pressure settings — they should align with those used during NPT equilibration.
These settings can be found in the Parameters section of the simulation tab, and additional fields are accessible via the All… button:
💡 Check 2: Use the Auto-Fill Input Path
If your production step builds on a previous equilibration, take advantage of the Auto-fill feature to automatically populate the input path:
This not only saves time but also helps avoid manual path errors that could break your setup.
💡 Check 3: Tune Advanced Parameters
Not all simulation parameters are visible at first glance. Click the All… button to access detailed GROMACS settings, especially useful if your project has custom constraints or force settings.
Tip: Use the Reset button in the Advanced Parameters window to return to safe default values, or load previously used parameters from a saved .mdp file.
💡 Check 4: Save Yourself Later – Save Configs
Your current configuration is automatically saved when closing SAMSON, making it easier to rerun or adjust settings later. Still, consider exporting your parameter set with Save as… for version control or sharing configurations among team members.
💡 Check 5: Simulate Smartly
Finally, you can choose to:
- Generate files for external execution
- Simulate locally (default GROMACS or your preferred version)
- Simulate in the cloud using credits
For most users, clicking Simulate locally is the fastest way to get results without worrying about external clusters or account setups.
To monitor progress, just open Local Jobs to view real-time status, errors, or warnings.
Wrapping Up
Taking the time to double-check these elements before launching your production MD simulation can prevent time-consuming troubleshooting later. You’ve already prepared your system through equilibration — setting up your production simulation with care is the next logical step 🧪
To learn more, read the full documentation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.