When the Packaged GROMACS Setup Isn’t the One You Need

A molecular dynamics run can be technically ready to launch and still be blocked by a practical mismatch: perhaps you need to use a GROMACS installation already on your workstation, keep a particular version for reproducibility, or adjust local resource use so your computer remains responsive. GROMACS Wizard provides settings for these situations—but it helps to know which settings affect which jobs before changing them.

This guide focuses on a simple distinction: the GROMACS executable and performance parameters are local choices, while the -maxwarn option also applies to Cloud jobs. Keeping that difference in mind can save time when comparing runs or troubleshooting a setup.

Choose the GROMACS version deliberately

GROMACS Wizard includes a GROMACS package, but you can select another installation for computations run locally. This is useful when your workflow depends on a version installed on your machine or when you want to use a specific version for reproducibility.

Open GROMACS Wizard and click Settings. If you want to use a local installation, enable Use a different GROMACS version and provide two paths:

  1. The executable: choose gmx.exe on Windows, or gmx on Linux or macOS. The settings display the detected version; if the executable is not recognized, it will be shown as “invalid.”
  2. The force-field directory: point to the folder containing the forcefield.ff folders. For example, the documentation gives $HOME/gromacs/share/top/ as a Linux and macOS location.

Providing both paths matters: selecting an executable alone does not tell the wizard where to find the force fields. Before launching a calculation, check that the selected executable is recognized and that the chosen directory is the one intended for your workflow.

Settings for selecting a custom GROMACS executable and force-field folder

Tune local performance without guessing blindly

It is tempting to set every available resource to its maximum, especially when a simulation is taking longer than expected. But the default behavior has a practical purpose: GROMACS Wizard sets the number of threads for local jobs below the absolute maximum so that the machine can remain responsive while a job runs.

A thread setting of 0 lets GROMACS guess the number of threads automatically. If you specify a non-zero number below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement. The settings can also accept additional performance parameters, including ntmpi, ntomp, pme, and maxh.

A useful approach is to change settings only when you have a reason to do so: for example, when you want to control parallelization or adjust domain-decomposition or PME-related behavior. Record the version and settings you use if you need to compare runs later. The available parameters and their effects depend on GROMACS; consult the GROMACS Manual’s guide to mdrun performance before choosing values.

GROMACS Wizard performance settings

Know when a setting does not apply

Local performance parameters are not transmitted to Cloud jobs. If a Cloud calculation is behaving differently from a local one, changing local thread or performance settings will not tune the Cloud run. The custom local GROMACS selection is also intended for local computations.

The -maxwarn option is different: it can override warnings from gmx grompp that would otherwise stop execution, and it applies to both local and Cloud jobs. This is not a routine fix. Warnings may indicate real problems, and bypassing them can produce an unstable system. Read and interpret the messages first. The documentation notes one possible case: a GROMOS force field may produce a warning that can be bypassed by setting -maxwarn to 1.

A quick pre-run check

  • Are you running locally or in the Cloud?
  • For a local run, is the intended GROMACS executable recognized?
  • Does the selected force-field folder contain the relevant forcefield.ff folders?
  • Are your performance settings intentional, and have you checked what the selected parameters mean?
  • If considering -maxwarn, have you understood the warning rather than simply suppressing it?

For the full instructions, see the GROMACS Wizard settings documentation.

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

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