When the Default Isn’t Right: Choosing Your Local GROMACS Setup

A molecular dynamics run can be held up by a mismatch between the GROMACS version you need and the one a workflow uses by default. Or perhaps you want to make better use of your local machine without leaving it unresponsive. GROMACS Wizard addresses both needs through its local settings—but it helps to know which settings affect local jobs, which also affect cloud jobs, and what to check before changing them.

Start by deciding what needs to match

There are two common reasons to use a custom GROMACS installation: your system already has a version you want to run, or you need a specific version for reproducibility. In either case, decide which version you intend to use before launching the calculation. If reproducibility matters, also identify the force-field directory associated with that installation. A version number alone may not be enough to describe the setup you selected.

Open GROMACS Wizard and select Settings. The panel displays the version of the GROMACS package shipped with the extension. To use a different installation for local computations, enable Use a different GROMACS version and provide both required paths:

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

Providing both paths is important: the executable identifies the GROMACS program, while the force-field directory points to the force fields available to it. If the displayed version is invalid, check that you selected the executable itself rather than its containing folder.

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

Tune local performance without guessing

GROMACS already has mechanisms to detect hardware and use it. GROMACS Wizard sets the number of threads for local jobs below the absolute maximum by default, helping keep the computer responsive while a calculation runs. If the thread count is 0, GROMACS chooses the number automatically. If you set a non-zero count below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement.

The Settings panel also allows additional local performance parameters, including options related to parallelization, domain decomposition, and PME algorithms. Possible parameters include ntmpi, ntomp, pme, and maxh. Rather than changing several values at once, adjust only what you need and keep a record of the settings used. That makes it easier to compare runs and to return to a known configuration. For details on the available parameters and GROMACS performance, consult the GROMACS Manual.

GROMACS Wizard local performance settings

Know which settings apply where

The distinction between local and cloud jobs is easy to miss. A custom GROMACS installation and the additional performance parameters described here are for local computations; those local performance parameters are not transmitted to cloud jobs. The -maxwarn option is different: it applies to both local and cloud jobs.

Use -maxwarn cautiously. It can allow gmx grompp to continue past warnings that would otherwise halt execution, but warnings often indicate something that deserves investigation. Bypassing them can generate unstable systems, so read and interpret the output before overriding anything. The documentation describes one possible case: a GROMOS force field may produce a warning that can be bypassed by setting -maxwarn to 1. That example is not a reason to ignore other warnings.

A practical pre-run check

  1. Confirm whether the calculation will run locally or in the cloud.
  2. For a local run, verify the selected executable and the displayed GROMACS version.
  3. Check that the force-field path contains the expected forcefield.ff folders.
  4. Review thread and performance settings, changing only parameters you have a reason to tune.
  5. Read warnings before deciding whether -maxwarn is appropriate.

This short check can prevent a common source of confusion: expecting local choices to affect a cloud calculation, or assuming that selecting a custom executable alone specifies the entire local setup.

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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