When the packaged GROMACS setup isn’t the one you need

A molecular dynamics workflow can be ready to run—and still be using the wrong local GROMACS installation. Perhaps you need to match a particular version for reproducibility, or your system already has a GROMACS build you want to use. And once the simulation starts, you may want to adjust how local CPU resources are used without making your computer unresponsive.

GROMACS Wizard supports both needs through its settings. The key is to treat the executable, force-field directory, and performance options as parts of one local setup—and to remember that some settings behave differently for cloud jobs.

Choose the installation deliberately

Open GROMACS Wizard and select Settings. The panel shows the version included with the extension. To use a GROMACS installation on your computer instead, enable Use a different GROMACS version and provide two paths.

1. The executable: select gmx.exe on Windows, or gmx on Linux or macOS. GROMACS Wizard displays the detected version; if it cannot recognize the executable, it displays “invalid.”
2. The force-field folder: select the directory containing the forcefield.ff folders. The documentation gives $HOME/gromacs/share/top/ as an example for Linux and macOS.

This two-path requirement is easy to overlook. Selecting a different executable alone does not complete the setup: the force-field directory must also point to the intended installation. If you need reproducible runs, decide which exact version and force-field directory you intend to use before launching the calculation, then confirm the displayed version in Settings.

Tune local performance without guessing

GROMACS has built-in logic for detecting hardware, so manual tuning is not automatically necessary. GROMACS Wizard sets the number of threads for local jobs below the maximum by default, helping keep the machine responsive while a job runs.

The thread setting has a useful distinction: a value of 0 lets GROMACS choose the number of threads automatically. If you specify a non-zero value below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement. Settings can also include options for parallelization, domain decomposition, and PME algorithms, such as ntmpi, ntomp, pme, and maxh.

A practical approach is to start with the defaults, change only the parameter you have a reason to adjust, and keep track of the settings used for a run. These performance parameters apply to local jobs only; they are not sent to Cloud jobs. If you switch from local execution to the Cloud, do not assume the same local tuning options carry over.

Use -maxwarn with care

The -maxwarn option can let gmx grompp continue despite warnings that would otherwise halt execution. Some warnings may be harmless, but many are not. Read and interpret the messages before considering an override: bypassing warnings can produce an unstable system, so this is not a routine troubleshooting shortcut. One documented example is a GROMOS force-field warning that may be bypassed by setting -maxwarn to 1. Unlike the local performance settings, this option applies to both local and cloud jobs.

Before you launch

• Check that the selected executable is the intended GROMACS version.
• Check that the force-field path contains the force-field folders you intend to use.
• Keep local performance settings separate from assumptions about Cloud jobs.
• Read any warnings before deciding whether -maxwarn is appropriate.

When the setup is ready, return to the calculation in GROMACS Wizard and launch it locally with the selected executable and performance settings. For the full instructions, see the GROMACS Wizard settings documentation. For performance options in more depth, consult the GROMACS Manual: Getting good performance from mdrun.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.