One common frustration among molecular modelers is the unresponsiveness of their computer when running local simulations. You’ve likely experienced it: you launch a simulation, and suddenly everything slows to a crawl. This often happens when computational tools like GROMACS run simulations using all available CPU threads, leaving no room for your OS to breathe.
Fortunately, if you use the GROMACS Wizard in SAMSON, you can easily manage this with built-in performance controls designed specifically for local jobs. Here’s how it works and how you can use these settings to maintain a smooth user experience while simulating efficiently.
Why Managing Threads Matters
GROMACS is designed to make the most of your system’s computational power. When running locally, however, it might aggressively use all your CPU threads. While this might seem ideal for performance, it can cause your entire system to freeze—especially if you’re multitasking or need responsiveness during the simulation.
To prevent this, GROMACS Wizard allows you to manually specify the number of threads to use for local simulations. By default, it uses fewer than the maximum, balancing performance and usability. If you set it to 0, GROMACS will automatically detect and use the maximum available threads—something you should use cautiously.
Where to Set These Options
Click the Settings button at the top of the GROMACS Wizard interface:
Here you’ll find a dedicated section for performance parameters. You can adjust:
ntmpi: Number of MPI threadsntomp: Number of OpenMP threadspme: Type of PME algorithm (e.g., GPU-accelerated)maxh: Maximum runtime in hours
One particularly smart option is -pin on, which GROMACS Wizard uses automatically when appropriate. This pins threads to specific logical cores for improved performance and avoids unnecessary context switching.
Avoiding Pitfalls: Cloud vs. Local Settings
Keep in mind these tweaks apply only to local jobs. If you’re running simulations in the Cloud via SAMSON, these parameters won’t carry over. This distinction is noted in the Settings window to help you avoid confusion.
Tips for Choosing the Right Settings
🧠 Tip 1: If you want to browse the web or write reports during simulation, set thread use to about half your logical cores (e.g., 4 out of 8).
⚡ Tip 2: Use ntomp and ntmpi in tandem to fine-tune parallel performance. Consider running short benchmarks to find the sweet spot for your hardware.
🎯 Tip 3: Avoid using -maxwarn unless you fully understand the warnings. It’s tempting to bypass them, but it may lead to unstable simulations.
For a deeper look at GROMACS performance tuning in general, check the official guide here: GROMACS Manual – Performance.
To explore all the configuration options and step-by-step instructions described above, visit the original documentation page: SAMSON Documentation – GROMACS Wizard Settings.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.