When molecular modelers simulate complex systems with GROMACS, performance often becomes a bottleneck — especially on local machines. Whether you’re testing a new protocol or running multiple small systems, getting the most out of your processor can make the difference between hours and minutes. But how do you fine-tune performance without overwhelming your workstation?
The GROMACS Wizard in SAMSON offers a convenient solution by letting users control threads and additional runtime parameters directly in the interface. This blog post walks you through practical ways to manage local performance when using GROMACS through the Wizard, without diving into shell scripts or environment variables.
Why it matters 💡
By default, GROMACS tries to use the available hardware efficiently. However, in shared computing environments or personal machines running other software, full CPU use may lead to poor multitasking or even overheating. What’s more, some simulations benefit from thread pinning and domain decomposition settings that GROMACS doesn’t always get right by default.
Thread Management in GROMACS Wizard
Inside the settings panel of the GROMACS Wizard, you’ll find a section dedicated to runtime performance. Here, you can set the number of threads GROMACS should use when running local simulations.
- Set to 0: GROMACS automatically detects and uses all available threads. May not be ideal if you need your CPU for other tasks.
- Set to N (where N < total cores): This triggers the
-pin onoption, pinning threads to specific cores. Pinning can provide more consistent performance and reduce thread migration overhead.
Going Further: Additional Performance Parameters
For advanced users, the settings panel allows inclusion of customizable performance flags for the gmx mdrun command. Examples include:
-ntmpi: Number of MPI ranks-ntomp: Number of OpenMP threads per MPI rank-pme gpu: Use GPU for Particle Mesh Ewald calculations (when supported)-maxh: Maximum run time, for safe job termination
You can tailor these parameters depending on your system configuration, including hybrid CPU/GPU environments. This can boost performance but also helps avoid overloading your machine.
Note:
These performance settings apply only to local jobs. Cloud jobs already run in optimized environments and won’t use these custom options.
Thoughtful Defaults, Easy Overrides
The default SAMSON behavior keeps your system responsive by limiting CPU use. However, advanced users or those with dedicated compute nodes can override this by specifying options manually, without having to modify .mdp files or manually invoke mdrun.
This feature is particularly helpful when benchmarking or iterating over multiple parameter sets, where minimizing execution time can significantly accelerate decision-making.
To learn more or explore additional options, visit the official documentation: GROMACS Wizard Settings in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.