GROMACS Wizard – Using custom GROMACS version and performance parameters

This section is a part of the GROMACS Wizard tutorial.

Using a custom GROMACS version

GROMACS Wizard comes with one of the latest versions of GROMACS. But it also provides you with the possibility to use your own version of GROMACS for local computations. This might be useful if you would like to use the GROMACS package installed on your system or use a specific GROMACS version for reproducibility reasons.

To use a locally installed version of GROMACS, press the Settings button at the top of GROMACS Wizard.

There you can see the version of the shipped GROMACS package. If you would like to use another version of GROMACS that is installed on your machine, then check the Use a different GROMACS version option and provide two paths:

  1. A path to the GROMACS executable (gmx.exe on Windows or gmx for Linux and MacOS) by clicking on the button. Note that the version of the chosen GROMACS package will also be displayed (if the executable was not recognized then “invalid” will be displayed instead).
  2. A path to the force fields folder where all the forcefield.ff folders are present (e.g. $HOME/gromacs/share/top/ on Linux and MacOS).

Maximum warnings option

The -maxwarn option can be used to override warnings printed by gmx grompp that otherwise halt output. In some cases, warnings are harmless, but usually they are not. It is advisable to carefully interpret the output messages before attempting to bypass them with this option. Please note that this is not for normal use and may generate unstable systems.

One of the possible uses is when you simulate a system with a GROMOS force field that leads to a warning, so to bypass this warning you can set the -maxwarn option to 1.

Note: this option applies both to local and Cloud jobs.

Additional performance parameters

“The GROMACS build system and the gmx mdrun tool have a lot of built-in and configurable intelligence to detect your hardware and make pretty effective use of it. For a lot of casual and serious use of gmx mdrun, the automatic machinery works well enough.” (source: GROMACS Manual)

Note: these options apply only to the local jobs, they are not transmitted to the Cloud jobs.

By default, GROMACS Wizard sets the number of threads to be used for running local jobs to be lower than the maximum number of threads so that when performing computations it won’t block your OS and other programs. If it is set to 0 then GROMACS will guess the number of threads, i.e. it will use the maximum available number of threads. If set to a non-zero value that is less than the number of (logical) cores then it will also use the “-pin on” parameter to pin threads to cores for better performance.

The Settings provide you with the possibility to specify additional performance parameters that will be used when running GROMACS locally. For example, you can specify the level of parallelization, control parameters of domain decomposition, and PME algorithms.

The possible options include but are not limited to, for example: ntmpi, ntomp, pme, maxh. Please see the following link for more information and more options: GROMACS Manual – Getting good performance from mdrun.

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