Avoid Slowdowns: How to Fine-Tune GROMACS Performance in SAMSON

Molecular modelers often find themselves bottlenecked by simulation runtimes, especially when running locally. You might be using powerful hardware, but your jobs are still dragging—and it’s not always clear why. If you’ve ever wondered whether GROMACS is making full use of your cores, or if there’s anything more you can do to squeeze out extra performance, this post is for you.

GROMACS Wizard in SAMSON includes a convenient set of performance tuning options that let you control how simulations run locally. These options don’t apply to Cloud jobs, but if you’re working locally—e.g., on your high-performance workstation—this can make a big difference.

Default Behavior: Convenient but Conservative

By default, GROMACS Wizard automatically sets the number of threads to be lower than your system’s maximum. This means your OS and other applications won’t suffer, but your simulations might run slower than necessary. If you need more speed—and your system can handle it—you might want to tweak these settings manually.

Understanding Thread Usage

Let’s break down what’s happening under the hood:

  • The GROMACS build system tries to detect your hardware and optimize thread usage automatically.
  • If the number of threads is set to 0 (default), it uses all available cores.
  • Setting a non-zero value (less than total cores) triggers -pin on, pinning threads to specific cores. This can improve performance through better cache usage and reduced overhead.

Settings

Accessing Performance Options in SAMSON

To access these options:

  1. Open GROMACS Wizard in SAMSON.
  2. Click on Settings at the top.
  3. Scroll to the section where performance tuning options are displayed.

Here you can adjust settings such as:

  • ntmpi: Number of MPI threads
  • ntomp: Number of OpenMP threads
  • pme: Controls particle-mesh Ewald methods, useful for long-range electrostatics
  • maxh: Sets maximum allowed wall-clock time for runs

These parameters allow advanced users to fine-tune how their simulations take advantage of parallelism and system architecture. For most day-to-day work, the default should be fine—but when you’re troubleshooting performance or running large models, these knobs give you more control.

Best Practices

  • Start with small test runs when changing performance settings to validate stability and performance.
  • Avoid setting thread numbers that exceed your system’s logical core count.
  • Make sure all cores remain reasonably busy during the run (use top or performance monitoring tools).
  • Refer to the GROMACS Manual for detailed descriptions of performance flags.

With a bit of tuning, you’ll see noticeable speedups in your local GROMACS jobs—and fewer reasons to rely exclusively on the Cloud for performance-heavy workloads.

To learn more, visit the full documentation page: GROMACS Wizard Settings in SAMSON.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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