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

A molecular dynamics job can be scientifically ready to run and still hit a practical snag: the GROMACS version available inside your workflow is not the version you need. Perhaps your system already has a preferred installation, or you want to use a specific version for reproducibility. You may also want to adjust local performance settings without making your whole computer unresponsive.

GROMACS Wizard in SAMSON supports both situations. You can select a locally installed GROMACS version and tune performance parameters for local calculations. The key is to keep track of which settings affect which jobs—and to treat warning overrides with care.

Choose the executable and force-field directory together

Open GROMACS Wizard and click Settings. The panel shows the version included with the Wizard. To use another installation, enable Use a different GROMACS version, then provide two paths:

1. The GROMACS executable: select gmx.exe on Windows, or gmx on Linux or macOS. The panel displays the detected version; if SAMSON cannot recognize the executable, it displays “invalid.”
2. The force-fields folder: choose the directory containing the forcefield.ff folders. For example, on Linux and macOS, this may be $HOME/gromacs/share/top/.

These paths work as a pair: choosing an executable is not the only step. Before starting a calculation, check that the executable is recognized and that the selected force-field directory is the one you intend to use. If you are aiming for reproducibility, settle on the exact GROMACS version and force-field directory before running the job, and record those choices with your simulation notes.

Tune local performance without guessing blindly

GROMACS has automatic mechanisms for detecting hardware and making use of it, and those defaults can work well. GROMACS Wizard also lets you specify additional performance parameters for local jobs, including options such as ntmpi, ntomp, pme, and maxh. These can help you control parallelization, domain decomposition, and PME-related behavior.

Thread count is one setting worth understanding. By default, the Wizard uses fewer than the maximum number of threads for local jobs so your computer can remain responsive while a calculation runs. A value of 0 lets GROMACS estimate the number of threads automatically. If you choose a non-zero value below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement.

A practical approach is to start with the defaults, then change a parameter only when you have a specific reason—such as testing a local configuration or freeing resources for other work. Change settings deliberately and keep a record of them so that comparisons between runs remain meaningful.

Keep local and cloud settings distinct

The custom GROMACS executable and additional performance parameters described here apply to local calculations. They are not sent to Cloud jobs, so adjusting them will not tune a calculation launched in the Cloud.

The -maxwarn option is different: it applies to both local and Cloud jobs. It can let gmx grompp continue despite warnings that would otherwise stop execution. Some warnings may be harmless, but many are not; bypassing them can produce an unstable system. Use this option only after interpreting the messages and understanding why you want to proceed. One example described in the documentation is setting -maxwarn to 1 for a warning encountered with a GROMOS force field. This is not a general-purpose fix for setup problems.

A quick pre-run check

• Is the selected executable the intended version, and is it recognized?
• Does the force-field path contain the appropriate forcefield.ff folders?
• Are the performance settings intended for a local job?
• Have you read any warnings before considering -maxwarn?

For the complete instructions and related guidance, read the GROMACS Wizard settings documentation.

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