Running molecular dynamics simulations with GROMACS can be computationally demanding, especially on your personal machine. If you’ve ever noticed your entire system getting sluggish while simulations run, you’re not alone. GROMACS is designed to use your machine efficiently, but when integrated inside SAMSON’s GROMACS Wizard, there’s a way to fine-tune performance so you stay productive – without sacrificing simulation speed.
By default, the GROMACS Wizard in SAMSON chooses a conservative number of processing threads, so your computer remains responsive during local jobs. However, there are configurable performance parameters that you can use to tailor GROMACS execution exactly to your hardware and needs.
Adjusting the Number of Threads
The first lever you can pull is the number of threads used in local simulations. In SAMSON, this setting is found in the GROMACS Wizard Settings window, which you can access by clicking the gear icon at the top of the Wizard.
If you set the number of threads to:
- 0: GROMACS automatically uses all available logical cores. This can make simulations go faster, but may make your system unresponsive for other tasks.
- Any positive value less than your number of cores: GROMACS uses that many threads and includes
-pin onto bind threads to specific cores for better performance and stability.
Using Advanced Parameters
If you’re comfortable going deeper, the Settings window also lets you add parameters like:
ntmpi: Number of MPI ranks.ntomp: Number of OpenMP threads per MPI rank.pme: Algorithm for calculating long-range electrostatics. Options likepmeorpme-switchcan affect performance and accuracy.maxh: Maximum length in hours before simulation stops, helpful for time budgeting on shared machines.
These options replicate the command-line flexibility of gmx mdrun but are now configurable inside SAMSON. This setup is ideal for iterative testing and optimization, especially for large systems or high-throughput runs.
Note
These parameters apply only to local runs. If you’re submitting to the Cloud through SAMSON, these settings are ignored.
Why It Matters
Even experienced users of GROMACS sometimes overlook how much performance tuning can improve usability. On multi-core laptops or desktops, keeping a balance between computation and interactivity is key. Whether you’re analyzing results, tweaking systems, or reading literature on the side, small changes to thread counts and scheduling can greatly improve your workflow.
To get the most out of your machine – and your day – it’s worth exploring these simple yet powerful settings. Your operating system (and your patience) will thank you. 🧠💻
To learn more about these and other performance settings in the GROMACS Wizard, read the full section of the documentation here: 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.