A molecular dynamics setup can be scientifically sound and still be frustrating to run: perhaps your lab uses a specific GROMACS installation, you need to reproduce a calculation with a particular version, or a local simulation makes your computer feel unresponsive. These are different problems, but GROMACS Wizard’s local settings can help you address them deliberately.
The important first distinction is where the job will run. The custom executable and performance parameters described here apply to local computations. They are not sent to Cloud jobs. The -maxwarn setting is the exception: it applies to both local and Cloud jobs.
Use the version you intend to use
GROMACS Wizard includes a packaged GROMACS version, but for local computations you can select a GROMACS installation already on your machine. This can be useful when you need a particular version for reproducibility or want to run with the installation maintained on your system.
Open GROMACS Wizard and select Settings. The settings show the version of the packaged GROMACS. To use another installation, enable Use a different GROMACS version and provide both the path to its executable and the path to its force-field directory.
- Choose the executable. Browse to
gmx.exeon Windows orgmxon Linux or macOS. GROMACS Wizard displays the recognized version; if it cannot recognize the executable, it displays “invalid.” - Choose the force-field folder. Point to the directory containing the
forcefield.fffolders. For example, the documentation gives$HOME/gromacs/share/top/for Linux and macOS.
A practical habit is to record the selected GROMACS version and force-field directory alongside the details you keep for a calculation. That makes it easier to check later that you are comparing like with like. Before launching, verify both paths rather than assuming that choosing an executable is sufficient: the force-field directory is a separate setting.
Keep local simulations responsive
GROMACS can automatically detect hardware and make use of it, and its automatic choices are often adequate. GROMACS Wizard also sets the number of threads for local jobs below the absolute maximum by default, helping leave resources available for other work while a job runs.
If the thread count is set to 0, GROMACS guesses the number of threads automatically. If you choose a non-zero count below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement. Settings additionally let you specify performance parameters such as ntmpi, ntomp, pme, and maxh.
Rather than changing several values at once, start with the default behavior and adjust only what you have a reason to control. This makes it easier to understand which setting affected a run. The right choices depend on your hardware and simulation; consult the GROMACS Manual’s guidance on mdrun performance for details on the available options.
Treat -maxwarn with care
The -maxwarn option can let gmx grompp continue despite warnings that would otherwise halt execution. Some warnings may be harmless, but warnings often signal something that needs attention. Read and interpret the output before deciding to bypass one: the documentation cautions that this option is not for normal use and may produce unstable systems.
One documented example is a system using a GROMOS force field that produces a warning; in that case, setting -maxwarn to 1 may bypass it. That example is not a reason to ignore other warnings. Check what the message means for your system first.
When you are ready, return to the calculation in GROMACS Wizard and launch it locally with the selected executable and performance settings. For Cloud jobs, use the Cloud workflow instead of expecting local performance parameters to carry over.
Read the GROMACS Wizard settings documentation for the complete instructions.
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