A molecular dynamics run can be scientifically well planned and still become frustrating for a practical reason: the GROMACS version available inside your workflow may not be the one you need. Perhaps your lab already has a local installation, or you want to use a particular version for reproducibility. Meanwhile, changing performance settings without knowing whether they affect local or cloud jobs can lead to confusing results.
GROMACS Wizard lets you choose a locally installed GROMACS version and adjust performance parameters for local computations. The key is to treat these as two separate decisions: first select and verify the software and force-field directory, then tune local execution only if you have a reason to do so.
Start by choosing the version deliberately
Open GROMACS Wizard and select Settings. The settings show the version included with the Wizard. To use a different installation, enable Use a different GROMACS version and provide both the executable path and the force-fields folder.
The executable is gmx.exe on Windows and generally gmx on Linux or macOS. The second path should point to the folder containing the force-field directories, such as $HOME/gromacs/share/top/ on Linux or macOS. These are distinct inputs, so having the executable path alone is not enough to complete the configuration.
Check the displayed version after selecting the executable. If it is shown as invalid, the executable was not recognized; revisit the path rather than assuming the intended version will be used. This small verification step can prevent a mismatch between the version you meant to run and the one actually selected.
Make reproducibility a concrete choice
When a result needs to be repeated later, record the exact GROMACS version and force-field directory used for the run. A note such as “used local GROMACS” leaves important details unspecified. Before starting, decide which installation you intend to use, confirm that the Wizard recognizes it, and make sure the force-field folder is the one you planned to use. This turns a settings choice into a reproducible part of your workflow.
Using a custom installation is optional: the Wizard also comes with a GROMACS package. The useful question is not whether custom is always better, but whether the packaged version meets the needs of this particular local calculation.
Tune performance without confusing local and cloud jobs
GROMACS has automatic mechanisms for making use of hardware, and those defaults may be sufficient. GROMACS Wizard sets the number of threads for local jobs below the absolute maximum by default, helping keep the computer responsive while a job runs. If the thread count is 0, GROMACS guesses the number automatically. If a non-zero value below the number of logical cores is used, the Wizard also uses -pin on to improve thread placement.
The Settings allow additional local performance parameters, including options related to parallelization, domain decomposition, and PME algorithms. Examples include ntmpi, ntomp, pme, and maxh. Adjust these only when there is a clear reason to depart from automatic behavior, and change settings deliberately so you can understand what changed between runs.
One important boundary: these performance parameters apply to local jobs. They are not transmitted to cloud jobs. If a calculation is launched in the Cloud, changing local thread or performance settings will not tune that cloud run. The -maxwarn option is different: it applies to both local and cloud jobs.
Use -maxwarn with care
-maxwarn can let gmx grompp continue past warnings that would otherwise halt execution. Some warnings may be harmless in a particular context, but warnings often indicate something that deserves investigation. Read the messages and understand their implications before bypassing them; overriding warnings can produce unstable systems. One documented example is a GROMOS force field that produces a warning, for which setting -maxwarn to 1 can bypass it. This is an exception to assess, not a routine way to silence output.
A practical sequence is: select the intended local executable, verify the recognized version, set the force-field folder, leave performance automation alone unless you need to tune it, and inspect warnings rather than dismissing them automatically. Then launch the calculation with the settings appropriate to the job’s location.
For more details, see the GROMACS Wizard settings documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.