A molecular dynamics job can be scientifically ready to run and still hit a practical snag: the GROMACS version on your computer is different from the one you need, or the calculation competes with everything else you’re doing on that machine. GROMACS Wizard lets you choose a locally installed GROMACS version and adjust performance parameters for local jobs. Knowing which settings affect which jobs can help you avoid a frustrating round of guesswork.
First, decide where the job will run
The key distinction is local versus Cloud. A custom GROMACS executable and the performance parameters described here apply to local computations. They are not sent to Cloud jobs. The -maxwarn setting is different: it applies to both local and Cloud jobs.
So before changing anything, identify the job you’re preparing. If it will run locally, check the executable, force-field directory, and local performance settings. If it will run in the Cloud, don’t expect local performance choices to carry over.
Choose a specific local GROMACS installation
Open GROMACS Wizard and select Settings. The panel shows the version included with the Wizard. To use another version installed on your computer, enable Use a different GROMACS version and provide both the GROMACS executable and the folder containing the force fields.
For the executable, browse to gmx.exe on Windows or gmx on Linux or macOS. The Wizard displays the detected version; if it cannot recognize the executable, it displays “invalid.” That gives you a useful first check before launching a calculation. You also need to point to the force-fields folder containing the forcefield.ff directories. One example location on Linux and macOS is $HOME/gromacs/share/top/.
This is especially useful when you need to use a system installation or keep a calculation tied to a particular GROMACS version for reproducibility. Before starting, decide which version and force-field directory you intend to use, then check that the Wizard is pointing to those choices.
Keep your computer usable while a job runs
GROMACS can often detect hardware and choose effective settings automatically. GROMACS Wizard also sets the number of threads for local jobs below the machine’s absolute maximum by default, helping leave resources available for other work.
A thread setting of 0 lets GROMACS guess the number of threads automatically. If you choose a non-zero number below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement. The settings can also specify performance parameters such as ntmpi, ntomp, pme, and maxh.
A sensible starting point is to keep the defaults unless you have a reason to change them. If you do tune them, change settings deliberately and record what you used. The available choices can affect parallelization, domain decomposition, and PME algorithms; the GROMACS performance guide explains the options in more detail.
Treat warnings as information, not obstacles
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 unstable systems. One documented example is a GROMOS force-field simulation that generates a warning, where setting -maxwarn to 1 may be used to bypass it. This is not intended as a routine setting.
In short: confirm the job location, verify both custom paths if using a local installation, and adjust performance settings only when needed. For the full instructions, see the GROMACS Wizard settings tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.