If you’ve ever tried to simulate a molecular system locally using GROMACS and noticed your entire system becoming sluggish—or worse, freezing—you’re not alone. Molecular dynamics simulations are computationally intensive, and unless configured properly, they can push your CPU to its limits, disrupting your workflow and other applications.
Fortunately, the GROMACS Wizard extension for SAMSON includes features that allow you to control how many threads GROMACS uses for local jobs. This gives you a valuable way to optimize performance without sacrificing system usability.
Why Thread Management Matters
GROMACS is fast because it leverages parallelism. When run locally, it can exploit all available CPU cores to do more work in less time. But that’s not always desirable—running too many threads can slow down your entire computer, especially if it uses shared CPU cycles for other tasks.
By default, GROMACS Wizard avoids this by reserving some CPU power for your operating system and other programs. But did you know you can fine-tune this even further?
Where to Find These Settings
From the GROMACS Wizard window, clicking the Settings button at the top gives access to thread management and performance parameters:
Here, you can set the desired number of threads to use for local simulations.
How Thread Settings Work
- If you set the value to
0, GROMACS will auto-detect and use all available threads. - If you input a specific number (e.g.,
4), GROMACS will limit itself to that many threads.
To enhance performance, GROMACS Wizard also enables thread pinning (-pin on) when you choose a non-zero value less than the number of logical cores. Pinning binds each thread to a specific CPU core, reducing overhead from thread migration and improving efficiency.
When and Why to Change Thread Count
You might want to reduce the number of threads in cases such as:
- You’re running simulations in the background while working on other tasks like data analysis or writing reports.
- Your system has limited CPU resources and high load from unrelated applications.
- You want to prioritize stability and responsiveness over simulation speed.
Alternatively, setting all threads active might be helpful when:
- You’re running a long simulation overnight or on an isolated machine.
- You want maximum throughput and are not using the computer for anything else.
Bonus: Add Further Performance Parameters
Besides thread count, advanced users can tweak additional performance inputs such as ntmpi (number of MPI threads), ntomp (OpenMP threads), pme (PME tuning), and maxh (maximum runtime in hours). These can be added directly in the settings interface and passed to the gmx mdrun command.
For a deeper dive into performance tuning options, the official GROMACS Manual explains a wide range of command-line flags that can help improve efficiency depending on your system architecture.
To learn more about thread configuration and performance settings in GROMACS Wizard, visit the official SAMSON documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.