Running molecular dynamics simulations can be demanding on your hardware. It’s common to see users overwhelmed by lagging systems or jobs that fail due to poor performance settings. If you’re using GROMACS Wizard in SAMSON, there’s a simple way to avoid these frustrations—by understanding and configuring additional performance parameters for local jobs.
By default, GROMACS Wizard automatically limits the number of threads used during local simulations. This is done deliberately to ensure that simulations don’t freeze your operating system or slow down other applications. While this behavior is helpful, you might want to fine-tune the performance settings to get better simulation times without compromising system usability.
Managing Thread Usage
GROMACS Wizard allows you to control how many threads are used when running local simulations:
- If you set the number of threads to
0, GROMACS guesses the optimal number and uses all logical cores available. This might be fastest but could make your system unresponsive. - If you use a non-zero value (e.g. 4 on an 8-core machine), GROMACS will also apply the
-pin onoption, which helps performance by pinning each thread to a specific core.
To access these options, click on the Settings button in the GROMACS Wizard interface:
Advanced Parameters for Power Users
The Settings panel also allows specification of additional performance-related parameters. These options give you more control over how GROMACS handles parallelization and computational load:
-ntmpi: Set the number of MPI threads (useful for cluster configurations).-ntomp: Set the number of OpenMP threads for parallel execution.-pme: Choose the method used for Particle Mesh Ewald (e.g., CPU, GPU loads).-maxh: Limit the maximum amount of simulation time in hours, to avoid overrunning.
These settings let you tailor performance profiles to your specific needs—whether you’re running small tests or longer simulations on powerful workstations. However, always test moderate values first to see how your system handles them, especially if you’re working on a laptop or shared desktop.
Important Limitations
Note that these performance configurations only apply to local jobs. If you are submitting to the Cloud jobs through GROMACS Wizard, these local performance settings are ignored.
Conclusion
Knowing how to efficiently manage resources when running simulations locally can greatly improve your workflow. You can avoid system slowdowns and still benefit from faster GROMACS jobs by carefully adjusting thread counts and exploring advanced parameters when needed.
To learn more about performance settings and other configurations in GROMACS Wizard, please visit the full documentation at this link.
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